ImageJ .
User Guide
The ImageJ User Guide
.
Tiago Ferreira
Wayne Rasband
February ,
Note This document is highly enriched in hypertext links and was thought as a
fullysearchable, selfcontained, annotatable, oine manual cf. Conventions Used in This Guide.
Given ImageJs heavy development this guide will always remain an unnished draft and
should be considered complementary to the remaining ImageJ documentation resources cf.
Getting Help. As such, all ImageJ users and developers are encouraged to contribute to
future editions of this manual see About This Guide. The latest version of this document can
always be obtained from http// imagej.nih.gov/ij/docs/userguide.pdf. A HTML version is also
available online at http//imagej.nih.gov/ij/docs/guide/ or as a downloadable ZIP archive.
Contents
Release Notes For ImageJ . Noteworthy Macro Listings Conventions Used in This Guide viii
ix x xi
I
Getting Started
What is ImageJ Installation Maintaining ImageJ Getting Help
II
Working with ImageJ
Shortcuts and Modier Keys Finding Commands Undo and Redo Image Types and Image
Formats Stacks, Virtual Stacks and Hyperstacks Color Images Selections Settings and
Preferences
III
Extending ImageJ
iii
Macros Scripts Plugins
. . . . . . . . . . . . . . . . . . . . . . Magnifying Glass . . . . . Multipoint Tool . . . Freehand Selection
Tool . . . . . . . . . . . . . . . . . . . . . . . . Elliptical Selection Tool . . Open. . . . . Wand Tool . . Point
Tool . . . . . . Arrow Tool . . . . Polygon Selection Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. File . . . . . . . . . . . . . . . . . . . Text Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . iv . . . . . . . . . . . . . Brush Selection Tool . . . . . . . . . . . . . . . . . . . . . . . .
Rectangular Selection Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Scrolling Tool . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . Oval Selection Tool . . . . . . . . Macro Tools . . . . . . . . . Color Picker .
. . . . . . . . Macro Toolset Switcher . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . Line Selection Tools . . . . . Open Next O Open Samples
Open Recent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tool . . .
..........................................................................
. . . . . . . . . Scripting in Other Languages Running ImageJ From the Command Line ImageJ
Interoperability IV The ImageJ User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
..........................................................................
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Round Rectangular Selection . . . . Angle
Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Contextual Menu The Results Table The
ImageJ Editor V ImageJ Commands New . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . Image . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . Revert r . . . . . Invert I . . . . . . . . . . . Fill f . . . . . . . . . . . . . . . . . . . . Show
Info. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Adjust . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . Options . . . . . . . . . . . . . . . . . . . . . . . Type . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . p . . . . . . . . . . . . . . . . . . . . . . . Quit . . . . . . . . . . . . . . . . . . . . Print. . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Duplicate. . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Paste Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Selection . . . . . . . . . . . . . . . . . . i . . . E . D . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Properties. . . . . . . . . Lookup Tables . . . .
. . . Copy to System Paste v . . . . . . . . . . . . . . . . . . . . Rename. . . . . . . . . . . . . . . . . . . . .
Copy c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Save As . . v . . . . . . . . . . . . . . . . . Cut x . . . . . . . . . . . . . . . . P . . Import . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Scale. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Clear Outside . . . Edit . . . . . . . . . . . . . . . . . . . . Transform . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . Page Setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Close w . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . Smooth S . . . . . . . . . . Clear . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . Color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Undo
z.........................................................................
. . . . . . . . . . . . . . . . . . . . . . . . . . Hyperstacks . Overlay . . . . . . . . . . Save s . . . . . . . . . . . . . .
. . Close All . . . . . . . . . . Stacks . Crop X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Draw d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
..........................................................................
. . . . . . . . . . . . . . . . . . . . . . . . . Zoom . . . . Process . . . . . . . . . . . . . . . . . . . . . . .
..........................................................................
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . Window . . . . . . . . . . Clear Results . . . . . . . . . . . . . . . . .
..........................................................................
. . . . . . . . . . . . . . . . . New . . . . . . Measure. . . . . . . . . . . . Noise . . . . Label . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . Find Maxima. . Surface Plot. . . . . . . . . . . . . . . . Distribution. . . Repeat Command R . . .
. . . . . . Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Put Behind tab . . Tile . . . . . . . .
. . . . . . . . . . Math . . . . vi . . . . . . . . . . . . . . . . . . Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . Summarize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Plugins . . . . . . . . . . . . . . . . . . . Show All . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Histogram h . . . . . . . . . . . . . Binary . .
. . . . . . . . . . . . .. . . . . . . . . . . . . . Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . Cascade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Run. . Compile and . .
Subtract Background. . m . . . . . . . . . . . . . . . . . . Set Scale. . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . Find Edges . .
Enhance Contrast . . . Calibrate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Set
Measurements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Image Calculator. .
..........................................................................
. . . . . . . . . . . . . . . . . . . . Analyze . . . . . . . . . . . . . . . . . . . . . . . . . . . Gels . . . . . . . . . . . . . . . .
. . . . . Sharpen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . FFT . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . Analyze Particles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Plot Prole k . . . . .
. . Shadows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . ImageJ Website. . . . . . Resources. . . . . . . . . . . . . . . . . . . . . . . . . . About
Plugins . ImageJ News. . . . . . . . . . . . . . . . . Macro Functions. . . . About ImageJ. . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Update ImageJ. . . . . . . List Archives. . . . . . . . . . .
. . . . . . . . . . . . . . . Macros. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. Refresh Menus . . . . . . . . . . . . . . . . . . . . . Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . Plugins. . . . . . . . . . . . . . . . . . Search Website. Dev. . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Installation. . . . VI Keyboard Shortcuts Alt Key Modications Shift Key Modications Ctrl Key or
Cmd Key on Macs Modications Space Bar Arrow Keys Keyboard Shortcuts for ImageJ Tools
Credits ImageJ Related Publications List of Abbreviations and Acronyms Index About This
Guide vii . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
....................................................................
Improved histograms displaying scaled LUTs . . . . . . The TIFF reader displays detailed
descriptions when ImageJ is in debug mode . . . . Command line scripts can now run ImageJ
in batch mode . . . . . . . . .. . . . . . . . . Improved Image Stacks Label. . . . . . . . . . . command .
command . . . . . .. Added Undo support to the Image Scale. . . . . . . . . . . . Improved Particle
Analyzer with support for virtual stacks and RGB images . . . . . . . . . . Improved Image Adjust
Color Threshold. . . . . . . . . . . . Detailed release notes for version . . . . . . . . . Image Color
Merge Channels. . . . . . . . . . . This list is not extensive. . . . . Added the Edit Selection Fit
Circle command . . . . . . . viii . . . . Added the Edit Selection Line to Area command . .
Improved FITSWriter . are available on the ImageJ News web site http//imagej. . . . . . . . . . . .
. . . . . . . . . . Added support for measurement of reex angles . . . . . . . . Image Stacks D
Project. . . and Image Scale. . . . . . . . . Improved and redesigned Results table . Added
hyperstacks support to the Image Duplicate. . . . . . . . . . . . . . Added the Edit Selection To
Bounding Box command . . . . . . . . . . . . . . . . . ummarized S Release Notes For ImageJ . . . .
. . . . . . . Added the Image Stacks Tools Make Substack. . . . command . . . . . . . . adds the
BioFormats plugin to the Java compilers classpath . . . . . . . . . . . . . . . . . . command . . . . .. . .
. . Added the Elliptical Selection Tool . . . . . . . . . . .html. . . . . . . . . . . . . . . . . Overlays are
preserved when saving in JPEG or PNG format . Added conjunction and exclusive
disjunction operations to the ROI Manager . . . . . . . . . . . . D command . . . . . . . . . . . . .. . .
Compile and Run. now works with hyperstacks and /bit images . . Image Stacks Z Project. . .
E . . . . . . . . . . . . . . .nih. . . . . . . . . . . . . ImageJs CurveFitter now resolves parameter
userdened equations . . now preserves LUTs and display ranges . . . . . Improved handling of
DICOM images . . . . . . . . . . . . . Added the Image Stacks Tools Grouped Z Project. . . . .. .
File Revert now works with stacks and hyperstacks . . . . . . . .. . . . . . Improved downsizing
when using Image Adjust Size. . . .gov/ij/notes. . . . . no longer caps the frame rate at fps . . . .
. . . . . . . . . . . . . Improved Image Stacks Orthogonal Views H command . . . . . . . . . . . . . . . . .
. . . . . . . E command . . . . . . File Save As AVI. . . . . . . . . . . now works with RGB
hyperstacks .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Reducing Memory
Requirements When Importing Images . . . . . . . . XVI Working With HEX Colors . . . . . . . . . .
..........................................................................
. . . . . . . . . . . . . . . . . Opening Virtual Stacks by Drag amp Drop . G XIX Selecting Multiple
ROIs in the ROI Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . Applying Auto
Brightness/Contrast to Entire Stacks . . . . . . . . . . . . . . . XIII Display Range of DICOM
Images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . VII Warning on JPEG compression .
. . . . VIII Drawing Lines Wider Than OnePixel . . . . . . . . Image Types Lossy Compression
and Metadata . . . . . . . . XV Scrolling Zoomed Images . . IX X XI Transferring Selections
Between Images . . . . . XVII Creating Binary Masks . . . . . . . . . . . . . . . . . . . . . . . . . Opening
les File Open. . . . . . . .Noteworthy I II III IV V VI Frontmost Window and Windows Activation .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . XIV Embedding Color Annotations in
Grayscale Images . . . . Toggling Calibrated Units . File Import and Drag amp Drop . . . . . . . .
. . . . . . . . XII Brightness/Contrast of High BitDepth Images . . . . . . . . . . . . XVIII lobal
Calibrations . Converting Composite Selections . . ix . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . Assigning Keyboard Shortcuts to ImageJ Tools . . . . . . Ensuring specic settings at
launch. . . . . . . . . Setting File Open Samples for oline usage. . . . . . . . . .Macro Listings
Creating MGB images . . . . . . . . x . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Creating MGB
images with the Image Calculator. . . . . Obtaining Histogram Lists . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . command. . . . Customizing the Image Popup
Menu. . . . . . Cycling Through ImageJ Tools Using Keyboard Shortcuts . . . . . . . . . . . . . . .
The full list of these informational notes is available on page ix.. or a task that has been
extended to more image types. Creating MGB images on page are typeset with the same
syntax markup provided by the The Fiji Script Editor for syntax highlighting in ImageJ. D
means pressing Shift D .g. a command with better usability. Filenames.. Image
Duplicate..nih. D. Selected highlights of version .. e. A new feature implemented in ImageJ ..
The ImageJ User Interface. Macro functions and code snippets are typed in monospaced
font. . Useful tips and reminders are placed in Noteworthy boxes numbered by upper case
roman numerals e.e.Conventions Used in This Guide If you are reading this guide on a
computer screen you will notice that internal document links are displayed in gray e. . such
as the ImageJ website. are displayed in dark blue.g. Typically.gov/ij/. These should be
interpreted as New in IJ . e.g.. the /Applications/ImageJ/macros/ folder. .g. ImageJ
commands are typed in sans serif typeface with respective shortcut keys anked by square
brackets e. are listed on page ix and agged with colored marginal notes. A routine that has
been improved since previous versions. is unchecked. see Jrme Mutterers IJED plugin. a
faster or more precise algorithm. . resetMinAndMax. I on page . le extensions and directory
names are indicated in italic. As explained in Shortcuts and Modier Keys this notation implies
shiftmodiers i. Part IV. http//imagej. .g. Scripts and macros e.g... A preexisting command that
has been renamed or moved to a dierent menu location in ImageJ . Improved in IJ . Changed
in IJ . The full list of macro listings is available on page x. while links to external URLs. d only
the D key and assumes that Require control key for shortcuts in Edit Options Misc.
html. Custom acquisition.Part I Getting Started What is ImageJ ImageJ is a public domain
Java image processing and analysis program inspired by NIH Image for the Macintosh.
Installation Detailed information for Linux. It can measure distances and angles. It can read
many image formats including TIFF. bit and bit images. or later virtual machine.nih. either as
an online applet or as a downloadable application. GIF. JPEG. rotation and ips. Mac OS X. It
can calculate area and pixel value statistics of userdened selections.gov. Userwritten plugins
make it possible to solve almost any image processing or analysis problem. Mac OS and
Windows installation of ImageJ is available at http//imagej. edge detection and median
ltering. The program supports any number of windows images simultaneously. It can display.
analysis and processing plugins can be developed using ImageJs built in editor and Java
compiler. edit. is a Special Volunteer at the National Institute of Mental Health. so
timeconsuming operations such as image le reading can be performed in parallel with other
operations. ImageJ is being developed on Mac OS X using its built in editor and Java
compiler. DICOM. sharpening. All analysis and processing functions are available at any
magnication factor. It runs. Density or gray scale calibration is also available. plus the BBEdit
editor and the Ant build tool. ImageJ was designed with an open architecture that provides
extensibility via Java plugins.gov/ij/docs/install/index. The author. It is multithreaded. save
and print bit. It supports standard image processing functions such as contrast manipulation.
process. Image can be zoomed up to and down to . Mac OS X and Linux. The source code is
freely available. FITS and raw. Specially useful are the . Bethesda. Maryland. analyze. It
supports stacks and hyperstacks. Downloadable distributions are available for Windows. It
does geometric transformations such as scaling. smoothing. Wayne Rasband wsrnih. a
series of images that share a single window. It can create density histograms and line prole
plots. BMP. USA. Spatial calibration is available to provide real world dimensional
measurements in units such as millimeters. on any computer with a Java . limited only by
available memory.
. v. . segmentation. Fiji has these benets it comes with the complete source. . Release
updates are announced frequently and are labeled alphabetically e. Python. Maintaining
ImageJ Once installed. Typically. command. feature extraction and D visualization. bundles a
set of plugins in a coherent menu structure. For developers. Manager works with
microscopes from all four major manufacturers. . . Fiji targets image registration. For
users.jar le. are labeled . including release updates and daily builds.app on Mac OS X.
described in detail on the top of ImageJ News page. it bundles many useful libraries and it
has a comprehensive build system. . Jython. Fiji is easy to install and update. Daily builds.
most scienticgrade cameras and many peripherals used in microscope imaging.m. Other
software packages based on ImageJ Fiji Fiji Fiji Is Just ImageJ was presented publicly for the
rst time on the ImageJ User and Developer Conference in November . command can be
used to upgrade or downgrade the ij. This web page can also be opened using the Help
Installation.g. Note that the installation packages may not contain the latest bug xes so
straight after a rst installation it is recommended to upgrade the ij. It is particularly adapted to
professional astronomy images. these releases contain several new features and bug xes.
and combinations thereof. Clojure. on the other hand. zstacks. updating ImageJ consists only
of downloading the latest ij. it is properly version controlled. It also supports many scripting
languages BeanScript.. Ruby. among others. stitching. the Help Update ImageJ.jar le to
other versions. It lets you execute common microscope image acquisition strategies such as
timelapses. Bio is an integrated development environment for ecological modeling with a
main focus on individual based modeling and spatially explicit models. multichannel
imaging.jar le.The ImageJ User Guide Maintaining ImageJ platformspecic Troubleshooting
and Known Problems sections. SalsaJ Bio SalsaJ is a software dedicated to image handling
and analysis in the classroom. This le is installed in the ImageJ folder on Linux and Windows
or inside the ImageJ. Manager Manager is a software package for control of automated
microscopes. and has a lot of comprehensive documentation. The easiest to perform this
task is to use the built in command Help Update ImageJ. bundles a Java runtime and JavaD.
. Releases and Updates As mentioned.
. Macros and Tools Updater.nih. . . a macro toolset that performs liveupdating of macros
listed on the ImageJ web site http//imagej.q. You can obtain and know more about plugins on
ImageJs plugins page Help Plugins. In addition. will not update any of the plugins you may
have installed . This bundle features a vast collection of plugins related to microscopy and is
described in an extensively illustrated online manual. . Running Help Update ImageJ. .
assemble your own ImageJ bundle by gathering the plugins that best serve your needs
probably. provide selfupdating mechanisms e. ended with . toolsets. MBF ImageJ The MBF
ImageJ bundle also known as ImageJ for Microscopy is maintained by Tony Collins at
MacBiophotonics. an installation package is created. . tools. Plugins..html. .g. release notes
for daily builds can be found at http //imagej. Note that you can use multiple distributions
simultaneously.The ImageJ User Guide Maintaining ImageJ with numeric subindexes e.n
and are often released without documentation.gov/ij/download. When a release cycle ends
v.. Typically. however.g. . McMaster University. The freely available plugins the ocial
distribution of ImageJ contains only a subset from independent contributors around the world
plays a pivotal role in ImageJs success . See also Luts. two ImageJ distributions can also be
obtained with a preorganized collection of plugins. downloadable from http//imagej. and in all
the sites listed on the bottom of ImageJs plugins page http//imagej. Plugins are addons that
extend ImageJs functionality beyond its basic core cf. Nevertheless.gov/ij/macros/ Certain
plugins. this package bundles a selected list of addons macros.gov/ij/source/releasenotes.
with . Fiji ships with a built in convenient updater that knows whether your les are uptodate.
v. if available. ImageJ Information and Documentation Portal.u.gov/ij/plugins/more. ImageJ
Distributions Fiji As mentioned earlier.nih. Fiji is distributed with several plugins and libraries
that greatly simplify the use of ImageJ. obsolete or locally modied.nih.nih. someone else at
your institute/university already started one or create symbolic links to share plugins between
dierent ImageJs. . . v. Furthermore. ObjectJ and the LOCI BioFormats library. etc.html.
scripts and plugins. however.
The membership base includes experienced programmers. Specially useful are the RSS
feeds and the frames and threads view provided by Gmane. plugin
development.nih.de/wiki/index.mpicbg.gov/ij/list.php/MainPage . .com/group/jidevel Fiji
developer discussion.phpidvideostartampsvideo http//www. Mailing lists a ImageJ
http//imagej. The ImageJ for Microscopy manual http//www.fr/wws/info/imagejmacro The
ImageJ macro support group connects a network of ImageJ users who are specically
interested in improving their skills in writing macros and plugins for ImageJ. . Can be
accessed via the Help List Archives. Specic documentation on advanced uses of ImageJ
macro programming.html . e ImageJX http//groups.html General user and developer
discussion about ImageJ.tudor.php . The Fiji webpage http//pacic. command.google.
.com/user/jichannel . is discussed in Extending ImageJ. and new users who are interested in
learning to write their very rst macros.inra.nih. command.org/mailman/listinfo/imagejdevel For
communication and coordination of the ImageJDev project. f ImageJDev http//imagejdev. c IJ
Macro Support Group http//listes. . most of them listed at http//imagej.com/group/imagejx
Highly technical developer discussion about ImageJ future directions. .google. Several online
documents. Video tutorials on the ImageJ Documentation Portal and the Fiji YouTube
channel http//imagejdocu. .gov/ij/links.lu/doku. etc. b Fiji users http//groups.tudor.youtube.
You may nd it easier to search and browse the list archives on these mirrors.ca/imagej/ . The
ImageJ online documentation Can be accessed via the Help
Documentation.google.com/group/jiusers General Fiji user discussion. d Fiji developers
http//groups. The ImageJ Information and Documentation Portal ImageJ wiki
http//imagejdocu. This list is also mirrored at Nabble and Gmane.The ImageJ User Guide
Getting Help Getting Help Below is a list of the ImageJ help resources.
.lu/doku.macbiophotonics.
. Because there will always be a natural lag between the implementation of key features and
their documentation it may be wise to check briey the ImageJ news website Help ImageJ
News. If you think you are facing a bug try to upgrade to the latest version of ImageJ Help
Update ImageJ. .g. . Read the documentation les described earlier in this section before
posting.. . . a le hosting service instead.gov/ij/docs/faqs. . The ImageJ mailing list is an
unmoderated forum subscribed by a knowledgeable worldwide user community with
advanced users and developers. you should always follow basic netiquette. Detailed
instructions on how to submit a bug report are found at http//imagej. quote only as much as
absolutely necessary and relevant. b Stay on topic Do not post otopic messages. e. You
should also check if you are running the latest version of the Java Virtual Machine for your
operating system. htmlbug. . . To have your questions promptly answered you should
consider the following . . Use. Look up the mailing list archives Help List Archives.The
ImageJ User Guide Getting Help Using Mailinglists If you are having problems with ImageJ. .
. . Most of your questions may already been answered.e. As with any other mailing list.
Remember that in most cases you can nd answers within your own ImageJ installation
without even connecting to the internet since the heuristics for nding commands or writing
macros have been signicantly improved in later versions see Finding Commands and
Extending ImageJ. c Be careful when sending attachments Refrain from attaching large
les.nih. namely a Use descriptive subject lines Re Problem with ImagegtSet Scale command
is much more eective than a general Re Problem. i. unrelated to the message thread. . you
should inquiry about them in the appropriated list. . d Edit replies You should include only the
minimum content that is necessary to provide a logical ow from the question to the answer..
g. i. if the BampC window is already opened. have a look at The ImageJ User Interface and
ImageJ Commands. In addition. Denoted by Alt or Alt in this document. Denoted by Shift or
Shift in this document. Shift Alt Youll learn more and more shortcut keys as you use ImageJ.
e.. I Frontmost Window and Windows Activation In ImageJ. all operations are performed on
the active frontmost image which has its title bar highlighted. . in this guide each command
has its shortcut key listed on its name anked by square brackets. on a Macintosh computer
running ImageJ the Command key Cmd replaces the functionality of the control key of other
operating systems. shiftmodiers are not explicitly mentioned a capital A means ShiftA and
assumes that Require control key for shortcuts in Edit Options Misc. Similarly. . command.
Although a control key is typically present on Apple keyboards. because almost all shortcuts
are listed throughout ImageJ menus. pressing Enter on any image will bring the ImageJ
window to the foreground. If a window is already open it will activate when its opening
command is rerun.e. For example. except when using The ImageJ Editor. the command Edit
Invert I can be evoked by Shift I or Ctrl Shift I if Require control key for shortcuts is checked. .
Ctrl will always refer to both throughout this guide.Part II Working with ImageJ For a detailed
description of all ImageJ menus and toolbar buttons most are selfexplanatory. pressing its
keyboard shortcut Shift C will activate it. For sake of simplication.e.. . is unchecked i. This is
also the Option or Meta key on many keyboards. you wont have to hold down the Control key
to use menu shortcuts. Shortcuts and Modier Keys There are three modier keys in ImageJ
Control Command Key on Apple keyboards Denoted by Ctrl or Ctrl in this document. The full
list of ImageJ shortcuts see Keyboard Shortcuts can be retrieved at any time using the
Plugins Utilities List Shortcuts. Please note that the notation for these keybindings is case
sensitive. ..
If Show full information is checked the Command Finder will display in which menu or .
Doubleclicking on a command will run that command. . . Alternatively pressing the up or
down keys will move keyboard focus to the list and the selected command can be run by
pressing Enter . . . . . the list will only show commands that match that substring. Command
Finder The quickest way to nd a command without having to navigate through all the menus
is using the builtin Command Finder Plugins Utilities Find Commands. Evoke the prompt by
pressing L as in command Launcher. .The ImageJ User Guide Finding Commands Finding
Commands There are two expedite ways of nding your way through the extensive list of
ImageJ commands. Locator or List. Pressing Backspace switches focus back to the prompt.
Pressing Esc closes the window. If you type part of a command name. . l and Plugins Utilities
Search. l command.jar le the listed command is located. l Plugins Utilities Search. macros
and plugins Plugins Utilities Find Commands. If multiple commands match. . . click with the
mouse to select a command to run. Plugins Utilities Find Commands. If only a single
command matches then that command can be run by pressing Enter . .
the line number where the string was found is displayed. There is an option to search the
macros folder and also an option to search the ImageJ source code if it has been
downloaded from imagej. commands. . . See also Control Panel. . . For selections.java les
contain circumstanced information as commented code. a macro that searches for a menu
entry and tries to retrieve the java source le of the respective plugin Undo and Redo
Probably the rst thing you will notice is that ImageJ does not have a undo/redo buer. . .
double click on a le path to open that le in an editor window. . If the Search Contents option
is checked.nih.jar. This command runs the macro Search in ij. scripts . See also Plugins
Utilities Reset. . ImageJ source les contain detailed annotations useful to both developers
and regular users that want to know more about ImageJ routines and algorithms. If you
cannot recover from a mistake. Since most macros . you can always use File Revert r to
reset the image lo its last saved state. Keyboard Shortcuts and SourceCodeRetriever. The
results are displayed in the Log window.js and plugins source . In the Log window. you can
use this utility to retrieve les not only related to a image processing routine e.g. Undo Edit
Undo z is currently limited to the most recent image editing / ltering operation. searches
recursively for a particular string case sensitive or not contained in the le names or le
contents in a chosen folder or in ImageJ/macros folder if Search Macros Folder is checked.
With time you will appreciate that this is necessary to minimize memory overhead. Multi
Undo plugin Image Types and Image Formats Digital Images are twodimensional grids of
pixel intensities values with the width and height of the image being dened by the number of
pixels in x rows and y columns . . cell or histology. that reruns the previous used command
skipping Edit Undo z and File Open. . background or colocalization but also topics related to
a certain scientic context such as radiogram.The ImageJ User Guide Image Types and
Image Formats Search Command Plugins Utilities Search.. In ImageJ the equivalent to Redo
is the Process Repeat Command R. Edit Selection Restore Selection E can be used to
recover any misdealt selection.gov/ij/download/src/ and extracted into the ImageJ folder. U.
Indeed.txt.ijm.
The ImageJ User Guide Image Types and Image Formats direction. see Settings and
Preferences. PGM and FITS. These are bit images. gray levels. In computing. The
characteristics of this range. . oset to rst images. BMP. A bit image has tones ranging from to
. transparency. ImageJ opens LZW and PackBits compressed TIFF les.e. e.e. Indeed. i. A bit
image has tones black. . etc. the most frequent types of images that ImageJ deals with are
bit bit bit Images that can display gray levels. GIF. . gap between images are printed to the
log window when ImageJ is running in Debug Mode Edit Options Misc. and unsigned if it can
only represent positive numbers. gray levels. oating point describes a system for
representing numbers that would be too large or too small to be represented as integers.
Images can be bit. In addition.g. File Save s. Images that can display . pixels picture
elements are the smallest single components of images. . In terms of bits per pixel bpp. bits
unsigned . See also Color Images Native Formats Natively i. DICOM. Ti tags and information
needed to import the le number of images. TIFF Tagged Image File Format is the default
format of ImageJ cf. without the need of thirdparty plugins ImageJ opens the following
formats TIFF. Many more formats are supported with the aid of plugins. Thus. bits. Green
and Blue channel.. JPEG. These are discussed in Nonnative Formats. gray. gray. . These
are oating point grayscale images. the number of unique intensity brightness values that can
exist in the image is dened as the bitdepth of the image and species the level of precision in
which intensities are coded. . i. holding numeric values pixel intensities that range between
black and white. bit real or RGB color.. in bit images a pixel can have any intensity value
including NaN Not a Number. Images that can display . and white. RGB color images can
also be bit color images bit color images with additional eight bits coding alpha blending
values. Improved in IJ . TIFF les with multiple images of the same type and size open as a
stack. TIFF les can be opened and saved as ZIP archives. RGB Color Images that can
display values in the Red. PNG.e. II. A numeric variable is signed if it can represent both
positive and negative numbers.
PBM Portable BitMap and PPM Portable PixMap are simple image formats that use an
ASCII header. i to display the FITS header. Because both these plugins are under active
development. an error message is displayed. Portable GrayMap. FITS Flexible Image
Transport System image is the format adopted by the astronomical community for data
interchange and archival storage. ImageJ supports custom DICOM dictionaries. ImageJ only
supports uncompressed AVIs. Audio Video Interleave is a container format which can
contain data encoded in many dierent ways. More information here. . A DICOM sequence
can be opened using File Import Image Sequence. ImageJ rst checks whether it can natively
handle the format. VII Nonnative Formats When opening a le. a plugin bundled with ImageJ.
PGM AVI See also Nonnative Formats. If ImageJ does not recognize the type of le it calls for
the appropriate reader plugin using HandleExtraFileTypes. . the ImageJ web site lists more
than fty plugins that recognize more exotic le formats. If that fails. . More information can be
found here. Note that most MJPG motionJPEG formats are not read correctly. Input/Output
plugins . File Import .txt. II. VII. such as the one at http//imagej. See also Native Formats.
Support in ImageJ is limited to uncompressed DICOM les. Use Image Show Info. . i to
display the DICOM header information. If nevertheless the le cannot be opened. various YUV
compressed formats. Use Image Show Info. DICOM les containing multiple images open as
a stack. or by dragging and dropping the folder on the ImageJ window.The ImageJ User
Guide Image Types and Image Formats DICOM Digital Imaging and Communications in
Medicine is a standard popular in the medical imaging
community.gov/ij/download/docs/DICOMDictionary. it is important that you keep them
updated. Acquisition plugins. a remarkable plugin that supports around eighty of the most
common le formats used in microscopy. it tries to open the le using the LOCI BioFormats
library if present. More information here. Attempts to open AVIs in other formats will fail. In
addition and as of this writing. and PNG or JPEGencoded individual frames. . II. Imported
sequences are sorted by image number instead of lename and the tags are preserved when
DICOM images are saved in TIFF format. . The ImageJ Documentation Portal maintains a
list of le formats that are supported by ImageJ.nih.
command opens other multiimage. To create a new stack.g. The Image Stacks submenu
contains commands for common stack operations. The images that make up a stack are
called slices. The File Import Raw.. These image sets are called stacks. In stacks.
introducing artifacts see VII. .e. . Most ImageJ lters will. e. . . n and set the Slices eld to a
value greater than one. Native Formats. and later. metadata associated with the image.
Virtual Stacks and Hyperstacks Stacks ImageJ can display multiple spatially or temporally
related images in a single window. and saves stacks as multiimage TIFFs.. There are several
things to keep in mind when working with virtual stacks . . A folder of images can be opened
as a stack either by dragging and dropping the folder onto the ImageJ window or or by
choosing File Import Image Sequence. Virtual Stacks Virtual stacks are disk resident as
opposed to RAM resident and are the only way to load image sequences that do not t in
RAM. simply choose File New Image. None of the above is saved in other formats cf. an
intensity value on a regular grid in a three dimensional space. the slider is preceded by a
play/pause icon that can be used to start/stop stack animation. Alt / dialog box. Stacks. . . in
ImageJ . In addition.The ImageJ User Guide Stacks. Virtual Stacks and Hyperstacks II Image
Types Lossy Compression and Metadata Two critical aspects to keep in mind when
converting images Lossy compression Transcoding an image into a format that uses lossy
compression will alter the original data. i. these types of data are intended for human
interpretation only and are not suitable for quantitative analyses Metadata In ImageJ.
selections and overlays are also saved in the TIFF header cf. ImageJ opens multiimage TIFF
les as a stack. a pixel which represents D image data in a bitmap image becomes a voxel
volumetric pixel. Rightclicking on this icon runs the Animation Options. This is the case. As
such. such as scale. for JPEG formats with the exception of some JPEG images that use
lossless compression. A scrollbar provides the ability to move through the slices and.
process all the slices in a stack.. as an option. gray value calibration and user comments is
only supported in ti and zip compressed ti images. . All the slices in a stack must be the
same size and bit depth. uncompressed les. File Save s. with IJ .
You can easily run out of memory using commands like Image Crop X because any stack
generated from commands that do not generate virtual stacks will be RAM resident. Process
Virtual Stack or the Process Batch Virtual Stack. TIFF stacks with a . since ImageJ . The V
on the window titles denotes a virtual image see Virtual Stacks.. Raw. . . . . . so changes
made to the pixel data are not saved when you switch to dierent slice. . namely TIFF Virtual
Stack.. .. Virtual Stack Opener.The ImageJ User Guide Stacks. Hyperstacks dimensionality
can be reduced using the Image Hyperstacks Reduce Dimensionality. cf. See also ImageD.
In addition. .tif extension open as virtual stacks when dragged and dropped on the toolbar
icon cf. Virtual Stacks and Hyperstacks Stacks and Hyperstacks in ImageJ File Open
Samples Mitosis MB. Z commands. D stack. . You can work around this by using macros e. .
TIFF virtual stacks can usually be accessed faster than JPEG virtual stacks. LOCI
BioFormats and RegisterVirtualStackSlices plugins. Virtual stacks are readonly. to save in
TIFF format ImageJ appends a V to the window title of virtual stacks and hyperstacks see
Hyperstacks. . . . A JPEG sequence can be converted to TIFF by opening the JPEG images
as a virtual stack and using File Save As Image Sequence. . . Stack From List. Several
builtin ImageJ commands in the File Import submenu have the ability to open virtual stacks. .
. AVI. . . command implemented in ImageJ . . . . . Image Stacks Z Project. .g. or Image
Hyperstacks Channels. . III. Process Virtual Stack and VirtualStackFromList macros . Image
Sequence.
c channels or wavelengths and t time frames. See also Image Hyperstacks submenu Color
Images ImageJ deals with color mainly in three ways pseudocolor images. the image
displays a pixel with a dened amount of each color.bit that has color assigned to it via a
lookup table or LUT. RGB images. RGB/ HSB stacks.macbiophotonics.htm. green and blue
values. This is literally a table of gray values with matching red. See also Image Lookup
Tables submenu This section is partially extracted from the MBF ImageJ online manual at
http//www. Dierences in color in the pseudocolored image reect dierences in intensity of the
object rather than dierences in color of the specimen that has been imaged.
ca/imagej/colourimageprocessi. Pseudocolor images A pseudocolor or indexed color image
is a single channel gray image .The ImageJ User Guide Color Images III Opening Virtual
Stacks by Drag amp Drop In ImageJ .tif extension open as virtual stacks when dragged and
dropped on the toolbar icon. So instead of displaying a shadow of gray. y height. and
composite images. Similarly to the scrollbar in Stacks. z slices. .. Hyperstacks Hyperstacks
are multidimensional images. the frame slider t has a play/pause icon. extending image
stacks to four D or ve D dimensions x width. Hyperstacks are displayed in a window with
three labeled scrollbars see Stacks and Hyperstacks. and later TIFF stacks with a .
CIE Lab and YUV color spaces. There can be signicant advantages in processing colors
stored in other formats. how much white is added to the pure color. ISBN ... The frequency of
colorblindness is See Wootton R. accessed .iam. But certain ranges of colors are hard to
distinguish. M. such as HSB Hue. .. using the HSB system over the traditional RGB system
may be advantageous. . Image Analysis in Histology Conventional and Confocal
Microscopy.. In addition. Brightness also know as Value HSV system or Lightness HSL
systems describes the overall brightness of the color. R. conversions between image types
are performed using the Image Type submenu.. specially those that do not follow the basic
principles of Color Universal Design. Color images are typically produced by color CCD
cameras. the Color Threshold. Conveying Color Information People see color with signicant
variations.. June This section is partially extracted from Masataka Okabe and Kei Ito.
command implemented in version . RGB is the most commonlyused color space.g. true color
images such as RGB images reect genuine colors.e. Color Universal Design CUD How to
make gures and presentations that are friendly to Colorblind people. Saturation.. Citing
Masataka Okabe and Kei Ito from the Color Universal Design Organization in Japan
Colorblind people can recognize a wide ranges of colors. .The ImageJ User Guide Color
Images True color images As described in Image Types and Image Formats. Brightness .
Cambridge University Press. performs segmentation on the HSB. Hue describes the attribute
of pure color. Indeed. E. processing only the brightness channel in routines that require
grayscale images is a signicant computational gain. You can read more about the HSB color
model here. the green in an RGB image reects green color in the specimen. Springall D.
Polak J. http//jy.e.jp/color/. However. In the HSB color space. i. In ImageJ. the popular
phrase One picture is worth ten thousand words may not apply to certain color images. i.
processing color information stored in the form of RGB images may not be the most ecient
method. Several other plugins related to color processing can be obtained from the ImageJ
website. in which color lter arrays Bayer mask are placed over the image sensor.
RGB.utokyo. In terms of digital imaging processing. since the Brightness component of an
HSB image corresponds to the grayscale version of that image. Saturation characterizes the
shade of color. ac. and therefore distinguishes between colors. Color Spaces and Color
Separation Color spaces describe the gamut of colors that imagehandling devices deal with.
. Magenta is the equal mixture of red and blue. Z tool to recolor the red channel. In ImageJ.
one in Asian . the probability that at least one of them is colorblind is whopping Redgreen
images and partial color blindness. There should be more than ten colorblind in a room with
people assuming male and female. Substituting red with magenta bottom row is the simplest
way to compensate for color vision deciencies.The ImageJ User Guide Color Images fairly
high. There are always colorblind people among the audience and readers. which is easily
distinguishable for colorblind. In ImageJ. in Fiji. . and one in African males are socalled
redgreen colorblind. One possibility of such a macro would make use of the Image Color
Channels. protanopia third panel are the most common types of partial color blindness red /
green confusion. . Colorblind people that have diculties recognizing the red component can
easily recognize the blue hue. RGB images can be easily converted to MGB with a simple
macro cf. or. There is a good chance that the paper you submit may go to colorblind
reviewers. Extending ImageJ. Deuteranopia second panel. Supposing that your paper will be
reviewed by three white males which is not unlikely considering the current population in
science. you can simulate color blindness on your images using the Vischeck plugin. . .
fourth panel is quite rare. One in Caucasian . using the Image Color Simulate Color
Blindness command. One practical point dened by the Color Universal Design is the use of
magenta in red green overlays. Tritanopia blue / orange confusion. The region of double
positive becomes white. .
r . / This macro replaces Red with Magenta in RGB images using the Edit gt Color gt
Channels .. More than channels can be merged or kept separate Selections Although
ImageJ can display simultaneously several selections or regions of interest ROIs. rename
title quot MGB quot .. command / i f bitDepth exit quot This macro requires an RGB image
quot . Color Composites In a composite image colors are handled through channels. // Enter
Batch mode title getTitle . . Each channel is kept separate from the others and can be turned
on and o using the Channels tool Image Color Channels. This feature allows.e . command. b
title quot blue quot .. Z. g title quot green quot . // Restore GUI mode Alternatively. Selections
can be measured Analyze .g. . . setBatchMode true . setActiveChannels quot quot . Red run
quot Magenta quot . // Run Image gt Type gt RGB Color rename title quot MGB quot . . //
Retrieve the image title run quot Make Composite quot . // Run Image gt Lookup Tables gt
Magenta run quot RGB Color quot . The advantages with this type of image over plain RGB
images are . only one selection can be active at a time. quot red amp r green amp g blue
amp b quot .The ImageJ User Guide Selections Listing Creating MGB images with the
Channels. r title quot red quot . . ... Process Image Calculator. tool / i f bitDepth // Ignore non
. setBatchMode true . run quot Split Channels quot . i . // Rename the image setBatchMode f
a l s e . / This macro replaces Red with Magenta in RGB images using the Process gt Image
Calculator . // Select first channel . quot . . run quot Merge Channels . title getTitle . Z tool. to
perform measurements on a specic channel while visualizing multiple. or bit and can be
displayed with any lookup table . b . e.. . // Run Image gt Color gt Make Composite Stack . .
imageCalculator quot Add quot . can be used to mirror the red channel on the top of the blue
channel by adding the red component to the blue Listing Creating MGB images with the
Image Calculator. setBatchMode f a l s e . Channels can be .RGB images exit quot This
macro requires an RGB image quot ..
The status bar displays the coordinates of the upper left corner of the selection or the
bounding rectangle for nonrectangular selections as it is being moved. . To move the
contents of a selection. or by double clicking on the Point Tool. Black and White. . Notice the
cursor changes to an arrow when it is within the selection. Selection Color can be changed in
Edit Options Colors. In addition. lled Edit Fill f or ltered Process Filters submenu. in the case
of area selections. . . . Edit Paste v. In addition. Orange. Use Edit Selection Restore
Selection E to restore a selection back after having deleted it. Once created. It is highlighted
in the center of the Point/Multipoint Tool cf. Notice also the lled handler in the polygon
selection and the absence of point handlers in Composite Selections. it is also possible to
create nondestructive image overlays Image Overlay submenu. . Most of commands that can
be useful in dening or drawing selections are available in the Edit Selection submenu. to a
hand when over a selection handler. deleted or added Three types of area selections In
ImageJ. Edit Copy c. since ImageJ . and then click within the selection and drag. m. Yellow.
Listed below are the most frequent manipulations involving selections Deleting Choose any
of the selection tools and click outside the selection. Selections can be moved by clicking
and dragging as long as the cursor is within the selection and has changed to an . Blue.
selections can be contoured or painted with any other color cf. Green. or use Edit Selection
Select None A.The ImageJ User Guide Selections Measure. drawn Edit Draw d. Selections
can be nudged one pixel at a time in any direction using the arrow keys A selection can be
transferred from one image window to another by activating the destination window and
using Edit Selection Restore Selection Moving Adjusting Nudging Managing . Edit Selection
Properties. vertexes of polygon selections can be adjusted by Alt/Shiftclicking cf. to a
crosshair when outside the selection. Rectangular Polygon Composite Cursor outside
selection Selection can be moved Selection can be resized Edge can be moved. The ImageJ
window. y. rather than the selection itself. Cyan. Polygon Selection Tool. Selections can be
initially outlined in one of the nine ImageJ default colors Red. Magenta. Area selections can
be adjusted with the Brush Selection Tool.
Drawing inside current selection while pressing Alt creates a hole removing content from
ROI. For example. Thus. and restored using File Open. . it may be useful to convert a
composite ROI into a polygon using the Edit Selection Enlarge. . Calling this function from
the AutoRun macro in the StartupMacros. The setOption macro function can be used to set
this and several other ImageJ options cf. Selections can be saved to disk using File Save As
Selection. If the IJprefs.The ImageJ User Guide Settings and Preferences E. This le is stored
in the /Library/Preferences/ folder on Mac OS X.txt is erased.g. Composite Selections
Composite selections are noncontiguous ROIs containing more than one cluster of pixels
and/or containing internal holes. e. See also ROIPolylineROI macro Settings and
Preferences ImageJ preferences are automatically saved in a preferences le. . see X. the
Shift key must be released after adding the selection. . ImageJ creates a new one the next
time it is opened resetting all parameters to their default values. . . to work with multiple
selections. Composite ROIs are typically originated with the Brush Selection Tool but they
can be dened with any other selection tool using key modiers. Builtin Macro Functions
setOption. the IJprefs. . to make sure that . In these cases. Sometimes.txt le ensures
preferences are set each time ImageJ starts. it may be wise to check the status of this
parameter before each analysis. The following modier keys can be use to create composite
selections Shift Drawing outside current selection while pressing Shift creates new content.
command.. the Limit to threshold option Analyze Set Measurements. .txt text le. will aect
most measurements performed on thresholded images. . in the /. Several macros and
plugins also write parameters to this le. . Alt Note that some operations may not be
performed properly on complex ROIs. To add a nonsquare rectangle or ellipse. it may be
useful to override or restore certain settings that may have been changed during a working
session. So. specially when working on multiple computers.imagej/ folder on Linux and in the
ImageJ folder on Windows. Use the ROI Manager Analyze Tools ROI Manager.
f a l s e . Background color is black and foreground color is white Edit Options Colors. . true .
are set properly at startup. setOption quot Display Label quot . Bicubic interpolation is
preferred over bilinear e. . . . setOption quot Bicubic quot .quot . true . . . . quot foreground
white background black quot . se tF oregroundColor . true . . . . . . See also FAQs on the
ImageJ Documentation Wiki . se tB ackgroundColor .. . macro quot AutoRun quot setOption
quot DebugMode quot . setOption quot BlackBackground quot .txt le Listing Ensuring specic
settings at launch. .. Edit Selection Straighten. . the following AutoRun macro could be
appended to the StartupMacros. . Measurements are not restricted to thresholded pixels
Limit to Threshold in Analyze Set Measurements.g. true . setOption quot Limit to Threshold
quot . TIFF tag values are displayed by ImageJ Debug Mode in Edit Options Misc. . Binary
images are processed assuming white objects on a black background Black background in
Process Binary Options.. The name of the measured image name is recorded in the rst
column of the results table Display Label in Analyze Set Measurements. .The ImageJ User
Guide Settings and Preferences . . . // run quot Colors . .
any macro le placed in the ImageJ/plugins folder with an . ImageJ uses the Mozilla Rhino
interpreter to run JavaScripts. copy it to the clipboard Ctrl A Ctrl C . only les with an
underscore in the name would be listed. . Most of the example macros are also available in
the macros folder. The ImageJ macro language a Javalike language contains a set of control
structures.ijm extension and once installed executed by selecting the macro name in the
Plugins Macros submenu.class les. Much more powerful. by clicking on an icon in the
ImageJ toolbar. Plugins are written in the Java programming language . exible and faster
than macros most of ImageJs builtin menu commands are actually plugins but harder to write
and debug. On the other hand. To try one. by pressing a key or. scripts lack the simplicity of
macro language and feel less integrated in ImageJ. open it in a browser window and drag it
directly to the ImageJ Window or. inside the ImageJ folder. scripts or plugins. The ImageJ
Editor.Part III Extending ImageJ ImageJ capabilities can be extended by loadable code
modules in the form of macros. operators and builtin functions and can be used to call builtin
commands and other macros.txt and .ijm extensions.java source les and compiled to . Run it
using the editors Macros Run Macro command Ctrl R . The easiest way to create a macro is
to record a sequence of commands using the command recorder Plugins Macros Record. in
the case of Macro tools.txt or . There are more than example macros.ijm extension will be
installed in the Plugins menu like any other plugin before version . A macro is saved as a text
le . pasting the macro into a new editor window cf. Plugins Scripts Macros A macro is a
simple program that automates a series of ImageJ commands. scripts have full access to all
ImageJ and Java APIs but do not need to be compiled scripts and macros run interpretively.
Macro code is stored in text les . Below is a short description of these three type of ImageJ
addons Macros The easiest way to execute a series of ImageJ commands. plugins and
scripts are available through the ImageJ web site. on the ImageJ Web site. Similarly to
plugins. switch to ImageJ. . . . and run File New System Clipboard V Ctrl Shift V . macros. In
addition.
It is thoroughly documented and constantly updated http//imagej. It provides an up to date
printable manual for the ImageJ macro language http//imagej. Example JavaScript programs
are available at rsb.info.gov/ij/developer/macro/functions. JavaScript Programming
Resources on ImageJ JavaScript scripting include .mpicbg.gov/ij/docs/macroreferenceguide.
. Mac users.js can be run using the Macros Run Macro command otherwise Macros Evaluate
JavaScript Ctrl J must be used.jar into the plugins folder.html . The Builtin Macro Functions
webpage Help Macro Functions. Tutorials on the Fiji webpage http//pacic. .nih.nih. added
support for JavaScript scripting. Scripts can be opened in the editor as any other macro
cf.php/IntroductionintoMacroProgramming . It is also included with the Mac version of ImageJ
. These resources are indispensable guides to the ImageJ macro language . . . for Linux and
Windows to run JavaScript. This booklet compiles most of the documentation dispersed
throughout the web related to ImageJs macro programming. and users of earlier versions of
Java. The ImageJ Macro Language Programmers Reference Guide by Jrme Mutterer and
Wayne Rasband.jar. Plugins Scripts ImageJ . This JAR le is available at rsb. Macros.info. .
Since ImageJ . ImageJ uses the Mozilla Rhino interpreter built into Java . must download
JavaScript.nih. the indispensable guide to the builtin functions that can be called from the
ImageJ macro language.gov/ij/macros/js/. and later. thread safe JavaScript code can be
generated using the Recorder Plugins Macros Record. Scripts with the extension .pdf .tudor.
.The ImageJ User Guide Scripts Macro Programming The ImageJ community has created
excellent tutorials on macro programming.nih.de/wiki/index. Howtos and tutorials on the
ImageJ Documentation Portal http//imagejdocu.lu/ See also
Scripts.gov/ij/download/tools/JavaScript. in the ImageJ/plugins/tools folder.
mpicbg. The ImageJ web site. Tutorials on the Fiji webpage http//pacic. especially starting up
No equivalent of macro sets Cannot use most of ImageJs built in macro functions Requires
knowledge of complex ImageJ and Java APIs No support for batch mode Cannot create
tools and toolbar menus Not compatible with Function Finder and CodeBar No debugger
CodeBar is a convenient ActionBar that retrieves snippets and common tasks frequently
used in macro writing.php/JavascriptScripting Advantages and disadvantages of JavaScript
in ImageJ.de/wiki/index. break. ActionBars provide one or many easy to use button bars that
extend ImageJs graphical user interface.The ImageJ User Guide Plugins . operator. with
growing documentation http//imagej. access the full ImageJ API and use all standard and
thirdparty Java APIs in a plugin.gov/ij/developer/javascript.nih. continue. A thorough
comparison between dierent scripting languages is available on the Fiji webpage. This opens
a wide range of possibilities of what can be done in a plugin. Plugins Plugins are a much
more powerful concept than macros and scripts and most of ImageJs builtin menu
commands are in fact implemented as plugins. which means that you can use all features of
the Java language.html . The most common uses of plugins are lters performing some
analysis or processing on an image or image stack and I/O plugins for reading/writing .
Extensive documentation Standardized JavaScript Disadvantages Slower. JavaScript
Advantages Full access to ImageJ and Java APIs Richer language objects. You can read
more about the ActionBar plugin at the ImageJ Documentaion Portal. Quoting Werner Bailer
Plugins are implemented as Java classes. etc.
The ImageJ User Guide Scripting in Other Languages not natively supported formats from/to
le or other devices. Note that. Resources.mpicbg. syntax highlighting. bookmarks and
several other tools that simplify scripting workows in ImageJ. there are many other things you
can do with plugins. The editor features full undo support. Changed in IJ
.php/IntroductionintoDevelopingPlugins .mpicbg. For more information see the Fiji website at
http//pacic.php/ScriptEditor. tabs.gov/ij/developer/index.nih.uzh.jar les in the plugins folder
with at least one underscore in their name will be installed. http//imagej. including the ImageJ
macro language. Fiji adds extra support for BeanShell. .ch/acardona/jitutorial/ .mpicbg.
Plugins in the plugins folder are listed at the bottom of the Plugins menu. But as you can see
when looking at the plugins listed on the ImageJ plugins page. plugins in JAR le directories
that start with a lower case letter.de/wiki/index. Dedicated tutorials on the Fiji webpage
http//pacic. such as rendering graphics or creating extensions of the ImageJ graphical user
interface. Developing ImageJ Plugins More information on how to develop ImageJ plugins
can be obtained on the following documents . Clojure. The following documents will introduce
you to the advanced scripting capabilities of Fiji . Dedicated tutorials on Fijis webpage
http//pacic.d an later.de/wiki/index. .class and .php/Scriptingcomparisons The Fiji Script
Editor Fiji features a powerful script editor that is an invaluable help when writing scripts in
any of Fijis supported languages. . with IJ .ini. The extensive tutorial on scripting Fiji with
Jython by Albert Cardona http//www. Developer Resources Page on the ImageJ website
Help Dev. at startup.tudor.lu/ Scripting in Other Languages Support for other languages is
possible in ImageJ using Fiji and its powerful editor.html . Only .de/wiki/index. ImageJ no
longer automatically installs. Python and Ruby. Dedicated tutorials on the ImageJ
Documentation Portal http//imagejdocu.
Running ImageJ From the Command Line Improved in IJ . ImageJ recognizes the following
command line options quotfilenamequot Opens a le. Examples macro analyze.tif
/Users/wayne/images/blobs.tif Species the path to the directory containing the plugins
directory. Example ijpath /Applications/ImageJ Species the port ImageJ uses to determine if
another instance is running. which can be retrieved using getArgument.tif e.m.The ImageJ
User Guide Running ImageJ From the Command Line The Fiji Script Editor ImageJA .
Examples blobs. Examples port use default port address port use default port address port
do not check for another instance Runs a macro or script. passing it an optional argument.ijm
macro analyze /Users/wayne/images/stack ijpath path port macro path arg .
The ImageJ User Guide
ImageJ Interoperability
batch path arg
Runs a macro or script in batch no GUI mode, passing it an optional argument. ImageJ exits
when the macro nishes. Evaluates macro code. Examples eval quotprintHello, worldquot
eval quotreturn getVersionquot Runs an ImageJ menu command. Example run quotAbout
ImageJ...quot Runs ImageJ in debug mode
eval quotmacro codequot
run command
debug
See also ImageJ Documentation Portal Command line, Running ImageJ in headless
mode, Linux installation
ImageJ Interoperability
Several packages exist that allow ImageJ to interact with other applications/environments
MIJ A Java package to exchange images from MATLAB to ImageJ This package, written by
Daniel Sage and Dimiter Prodanov, oers static methods to exchange images between
imageJ and MATLAB. MIJ also allows MATLAB to access all builtin functions of ImageJ as
well as thirdparty ImageJ plugins. More information is available on the MIJ website
http//bigwww.ep.ch/sage/soft/mij/. RImageJ R bindings for ImageJ Bindings between R GNU
S The free software environment for statistical computing and graphics and ImageJ. The
documentation for RImageJ, developed by Romain Francois, Philippe Grosjean and Paul
Murrell, is available at http//cran.rproject.org/web/packages/RImageJ/RImageJ. pdf.
CellProler CellProler http//www.cellproler.org/ contains an ImageJ module that allows ImageJ
plugins to be run in a CellProler pipeline RunImageJ.
Part IV
The ImageJ User Interface
ImageJ Window
Unlike most image processing programs ImageJ does not have a main work area. ImageJs
main window is actually quite parsimonious containing only a menu bar at the top of the
screen on the Mac, a Toolbar, a Status bar and a Progress bar. Images, histograms, proles,
widgets, etc. are displayed in additional windows. Measurement results are displayed in The
Results Table. Most windows can be dragged around the screen and resized.
The ImageJ window version .l. A B C D E F G H
Status bar Rectangular Selection Tool and Round Rectangular Selection Tool Oval Selection
Tool, Elliptical Selection Tool and Brush Selection Tool Polygon Selection Tool Freehand
Selection Tool Straight Line Selection Tool, Segmented Line Selection Tool, Freehand
Selection Tool and Arrow Tool Angle Tool
Progress bar Point Tool and Multipoint Tool Wand Tool Text Tool Magnifying Glass Scrolling
Tool Color Picker
AH Custom Macro Tools loaded from StartupMacros.txt, /macros/tools/ or /macros/toolsets/
Macro Toolset Switcher
Toolbar
The ImageJ toolbar contains tools for making selections, drawings, zooming and scrolling,
etc. In addition, the rightside of the toolbar contains seven slots that can host any of the tools
and tool sets available on the ImageJ website cf. Macro Tools. All ImageJ tools share
common features
The on the bottom right corner of some icons in the toolbar depicts a contextual menu that
can be accessed by rightclicking on the tool icon.
The ImageJ User Guide
If an Options dialog is available for a particular tool, it can be accessed by double clicking on
the tool icon e.g., Wand Tool.
Status bar
When the cursor is over an image, pixel intensities and coordinates are displayed in the
status bar. After running a lter, elapsed time and processing rate in pixels / second is also
displayed. When clicking on the status bar the ImageJ version, the Java version, memory in
use, memory available and percent memory used will be displayed. As selections are
created or resized, selection properties e.g., location, width, etc. are displayed on the status
bar. In addition, clicking on ImageJs status bar, forces the Java garbage collector to run,
which may help to reclaim unused memory cf. Edit Options Memory amp Threads. . . .
See also Plugins Utilities ImageJ Properties. . . , Help About ImageJ. . .
IV
Toggling Calibrated Units
If a spatial scale has been dened cf. Image Properties. . . P, or Analyze Set Scale. . . ,
selection properties are displayed in the Status bar in calibrated units. Resizing or moving
while holding down Alt forces this information to be displayed in pixels.
Progress bar
The progress bar, located to the right of the status bar, shows the progress of timeconsuming
operations. It will not appear if the operation requires less then approximately one second.
IV. . Tools Rectangular Selection Tool Location. XIV . Specify. height. . Oval Selection Tool
Location. Round Rectangular Selection Tool This tool shares the same toolbar slot and the
same modier keys with the Rectangular Selection Tool. XIV . Because its an annotation tool
the round rectangle is displayed in foreground color instead of selection color see Point Tool.
. width. . . IV. and aspect ratio are displayed in the status bar during drawing. K.The ImageJ
User Guide Area Selection Tools . . See also Rectangular Selection Tool. Specify. Corner
arc size can be adjusted by double clicking on its icon. . The following modier keys apply to
the Oval Tool Shift Alt Ctrl Ctrl Alt Selection becomes circular Width / height are changed
with arrow keys one pixel at a time Selection is resized around the center Current aspect
ratio is maintained while resizing See also Elliptical Selection Tool. and aspect ratio are
displayed in the status bar during drawing. . The following modier keys apply to the
Rectangular Tool Shift Alt Ctrl Ctrl Alt Selection is constrained to a square Width / height are
changed with arrow keys one pixel at a time Selection is resized around the center Current
aspect ratio is maintained while resizing See also Round Rectangular Selection Tool. Color
Picker. height. width. XIV .
Polygon Selection Tool Creates irregularly shaped selections dened by a series of line
segments. Brush diameter can be adjusted by double clicking on the tool icon. When nished.
Polygon Selection Tool. . . To adjust eccentricity. XIV . The following modier keys apply to
the Brush Tool Shift Alt Brush is always added to the selection Brush is always subtracted
from selection See also Composite Selections. IV . drag the handlers on its minor axis
conjugate diameter. drag the handlers on its major axis transverse diameter. Elliptical
Selection Tool New in IJ . height. Location. . Enlarge. Freehand Selection Tool As with the
polygon selection tool. click repeatedly with the mouse to create line segments. See also
Oval Selection Tool. To create a polygon selection. Brush Selection Tool Adjusts the shape
of any area selection using a circular brush . Enlarge. To rotate or resize. ImageJ
automatically draws the last segment. . and ImageJ automatically draws the last segment.
Ellipse properties are adjusted by dragging the four handlers on its antipodal points .
Location and intensity of starting pixel are displayed in the status bar during drawing. IV.
Clicking outside the area selection and dragging along its boundary will shrink the boundary
inwards. XIV . The following modier keys apply to the Polygon Tool Shift Alt Clicking on a
point with with the Shift key pressed adds a new point Clicking on a point with with the Alt
key pressed removes it See also Segmented Line Selection Tool. width. See also Freehand
Line Selection Tool. . click in the small box at the starting point or double click. . XIV . and
aspect ratio are displayed in the status bar during drawing. IV.The ImageJ User Guide Area
Selection Tools . The vertex points that dene a polygon selection can be moved and modier
keys can be used to delete or add new vertexes to the polygon. Clicking inside the area
selection and dragging along its boundary will expand the boundary outwards.
g.g. Tolerance The wand takes the pixel value where you click as an initial value. /connected
particles can be traced within an intensity range. . T. To visualize what happens. Note that
the wand tool may not reliably trace some objects. either click inside near the right edge.
especially one pixel wide lines.. at the WandAutoMeasureTool macro. . it follows it until it
returns to the starting point. . the wand does not follow a onepixel wide diagonal line because
the pixels of that line are not fourconnected. opens the conguration dialog box in which three
modes connected. Double clicking on the wand tool icon or running Edit Options Wand Tool.
Wand Tool Creates a selection by tracing objects of uniform color or thresholded objects. . if
you have an area of constant value dissected by a onepixel wide diagonal line. It then selects
a contiguous area under the condition that all pixel values in that area must be in the range
initial value tolerance to initial value tolerance. e. imagine a turtle that starts moving to the
right from where you click looking for an edge. Once it nds the edge. the connected wand will
jump over the line and include the other part of that area. . This is the default mode of the
Wand Tool in ImageJ . connected or Legacy plus a tolerance value can be set . connected
Only the four neighbors of a pixel are considered neighbors. E. and earlier. On the other
hand. So the wand follows a diagonal line if you click onto it. connected Each pixel is
considered to have eight neighbors.The ImageJ User Guide Area Selection Tools . To
automatically outline and measure objects have a look. unless they are thresholded
highlighted in red using Image Adjust Threshold. Legacy In this mode no neighbor is checked
and no tolerance is used. The Wand Tool. or outside to the left of the object. To trace an
object..
IV. . XIV . The three line selection tools share the same toolbar slot. Line Selection Tools
Use these tools to create line selections. or click in the small box at the starting point. .
widget. . IV. Segmented Line Selection Tool Works exactly as described for the Polygon
Selection Tool Create a segmented line selection by repeatedly clicking with the mouse. ..
Arrow Tool . . Set Scale. Double click on any line tool to specify the line width by opening the
Image Adjust Line Width. The following modier keys apply to the Segmented Line Tool Shift
Alt Clicking on an existing point with the Shift key down adds a point Clicking on an existing
point with the Alt key down deletes it See also Polygon Selection Tool. . To switch to a
dierent tool. right click on the current line tool and select the desired tool from the dropdown
menu. . Straight Line Selection Tool The following modier keys apply to the Straight Line
Tool Shift Alt Forces the line to be horizontal or vertical Keeps the line length xed while
moving either end of the line Forces the two points that dene the line to have integer
coordinate values when creating a line on a zoomed image While moving either end of the
line rotates/resizes it about its center Ctrl See also Calibration Bar. The points that dene a
segmented line selection can be moved or deleted. Freehand Selection Tool.The ImageJ
User Guide Line Selection Tools . See also Freehand Selection Tool. Double click when
nished. .. Each click will dene a new line segment. and new points can be added. Length and
to do are displayed in the status bar. XIV . Freehand Line Selection Tool Select this tool and
drag with the mouse to create a freehand line selection. IV. XIV . ..
K. . . add arrows to a nondestructive overlay using Image Overlay Add Selection. . Filled
Notched Open Single headed Double headed As with other tools. . changing Color will
change foreground color and not selection color see Point Tool. . Width and Size in pixels
can be adjusted by dragging the respective sliders or by direct input. Angle Tool This tool
allows you to measure an angle dened by three points. Note that marks modify the image it
may be wise to work with a copy and color marks are only available with RGB images see
XIV. . Point count is displayed on the Status bar Altclicking on a point will delete it. Color
Picker. . Apart from the six arrow styles listed here. b or Edit Draw d to permanently draw an
arrow see XIV.. to count objects or to record pixel coordinates. Alt . Because it is an
annotation tool. Double click on the angle tool icon to enable the measurement of reex
angles. Mark Width If greater than zero. Point Tool Use this tool to create a point selection. a
mark of the specied diameter will be permanently drawn in the current foreground color cf. .
Altclicking and dragging with the rectangular or oval selection tool will delete multiple points
Double clicking on the point tool icon or running Edit Options Point Tool. . The angle is
displayed in the status bar while the selection is being created or adjusted. . a Headless
option is also available. Press M Analyze Measure. holding down Shift will force the arrow to
be horizontal or vertical.The ImageJ User Guide Tools Double clicking on the tool icon opens
the Options prompt depicted on the left. Improved in IJ . K. displays its conguration dialog
box. Straight Line Selection Tool key modiers can be used when creating an arrow. e. m to
record the angle in the The Results Table. The following modier keys apply to the Point Tool
Shift Shiftclicking will add more points. Color Picker. .g. .
b to add the text nondestructively to the overlay. . Black and White. ImageJ will automatically
advance to the next stack slice. each point selection will be displayed with an accompanying
numeric label. Magenta. . Selections. or double click on the text tool. Note that this feature
will only allow one point per slice. See also Point Tool. . Note that if Mark Width is not zero.
Green. See also Multipoint Tool. clicking on the image records the pixel location and
intensity. . Cyan. . Use Image Overlay Add Selection. Selection Color Species the selection
color. chosen from one of the nine ImageJ default colors Red. Label Points If checked. every
time a point selection is measured a mark will be painted cf. If unchecked. Use Edit Options
Fonts. Cell Counter plugin . Cell Counter plugin . to specify the typeface. Text Tool Use this
tool to add text to images. size and style. Similarly. Label Points is checked and
AutoMeasure and AutoNext Slice are deselected. It creates a rectangular selection
containing one or more lines of text. Orange. Double clicking on the tool icon runs the Image
Overlay Add Selection. Multipoint Tool The Multipoint Tool selects multiple points behaving
as the Point Tool when Shift is pressed. See also TextDemo macro . m. Note that the
selection color is highlighted in the center of the Point/MultiPoint Tool cf. Yellow. Alt can also
be used to remove points. Blue. Edit Draw d can be used to paint the mark Mark Width
diameter at the location of each point. . . Use the keyboard to add characters to the text and
the backspace key to delete characters. . Measure. Add to ROI Manager If checked. .The
ImageJ User Guide Tools AutoMeasure If checked. . Use Edit Draw d to permanently draw
the text on the image. b command. AutoNext Slice If checked. when using Edit Draw d marks
are painted with the diameter of Mark Width. points will be automatically added to the ROI
Manager. . As described for the Point Tool.
. and percent. Double click on the magnifying glass icon to revert to the images original
magnication. The current magnication is shown in the images title bar. Colors can also be
picked up from the Color Picker CP window Image Colors Color Picker. . . .. . .. K window
using any tool. . . Scrolling Tool Allows you to scroll through an image that is larger than its
window. Clear Outside and Cut x use the background color. XV . .. ... Magnifying Glass Click
on the image with this tool to zoom in.The ImageJ User Guide Tools . Edit Draw d and Edit
Fill f use the foreground color.. The following modier key applies to the Color Picker Tool Alt
Altclicking with the Color Picker Tool on an image will change the background color See also
Image Types and Image Formats. the eye dropper is drawn in the current foreground color
while the frame around it is drawn in the current background color. In the icon. The following
modier keys apply to the Magnifying Glass Tool Shift Alt When zooming in will prevent the
window from being enlarged. . When using other tools except the text tool. . . Rightclick or
Altclick to zoom out. XIV . . . you can temporarily switch to this tool by holding down the
space bar see XV. Will zoom out rightclick behavior See also Zoom . Double clicking on the
tool icon will display the Color Picker window. . . There are possible magnication levels . Edit
Clear. Color Picker Sets the foreground drawing color by picking up colors from any open
image. . . .. .
Macro toolsets can be obtained at http//imagej.txt le ImageJ/macros folder. Macro Tools The
tools on the right side of the toolbar all slots between Color Picker and Macro Toolset
Switcher are dened by macros in the StartupMacros.nih. . or replaced entirely using the
Macro Toolset Switcher menu.txt toolset . Macro Toolset Switcher Use this dropdown menu
to switch to alternative macro tool sets located in the ImageJ/ macros/toolsets folder.. The
following modier key applies to the Macro Toolset Switcher Shift Shiftclicking on the Toolset
Switcher will open the selected toolset le on the dropdown menu . . Luts Macros and Tools
Updater macro Macro Toolsets distributed with ImageJ . .gov/ij/macros/toolsets/ or created.
macros and scripts. While the StartupMacros. e. command. Note that you can use Toolset
Creator to create Menu Tools for running plugins. which can be opened using the Plugins
Macros Startup Macros.The ImageJ User Guide Contextual Menu . or to revert to the default
ImageJ/macros/StartupMacros. .htmltools has more information about macro tools.txt le.
using Toolset Creator. all other toolsets must be located in the ImageJ/ macros/toolsets
subfolder.txt le is located in the ImageJ/macros/ directory.nih. These tools can be customized
by editing the StartupMacros. See also Macro Toolset Switcher.txt are automatically installed
in the Plugins Macros submenu and in the toolbar when ImageJ starts
up.gov/ij/developer/macro/macros. The macro language documentation at http//imagej.
Contextual Menu As mentioned earlier macros and macro tools in the StartupMacros.g.
.. quot . quot Original Scale quot .txt le also installs the contextual popup menu displayed
when rightclicking on an image.. quot . according to what item was chosen. i f cmd quot Help
. the StartupMacros. .g. quot .. Note that denes menu separators .. Listing Customizing the
Image Popup Menu. e. quot showMessage quot About Popup Menu quot . This menu
passes the chosen item as a simple string to the quotPopup Menuquot macro.The ImageJ
User Guide Contextual Menu In addition. command from the contextual menu one can
simply add that command to the list of items dening the PopUp Menu. quot .. Any menu has
a name and a list of menu items. quot . edit the line that starts with n quot quot quot var
pmCmds quot in ImageJ / macros / StartupMacros . quot .g... quot . quot quot . quot Rename
. txt and several other macro toolsets Duplicate . quot Search . items macro function allows
the creation of a new menu. The newMenuname. reinstalling the StartupMacros using the
Macro Toolset Switcher will revert the contextual menu to its default. newArray quot Help ..
quot .. From this point you can decide what to do. quot Startup Macros . Magic Montage may
also replace the default menu with specialized ones. macro quot Popup Menu quot cmd
getArgument ... quot Record . quot Find Maxima . quot Capture Screen quot . / The quot
Popup Menu quot macro defines the menu that is displayed when right / var pmCmds
newMenu quot Popup Menu quot . The ImageJ Macro Language Programmers Reference
Guide explains how this menu can be customized The menu that is displayed when a user
rightclicks or ctrlclicks on an image window can be customized through installation of the
quotPopup Menuquot macro. .. In this case. quot Paste Control . quot To customize this
menu ... quot quot . quot clicking or ctrl . e l s e run cmd ... txt . quot . Other macros and
toolsets e. quot Monitor Memory .... to add the ability to run the Process Subtract
Background.clicking on an image .. quot . It is part of the startup macros StartupMacros . So..
Font and Results . quot Startup Macros . Alias for the Analyze Set Measurements. quot .
The arrow keys can be used to vertically scroll the window. A contextual menu listing the
majority of these commands can be accessed by rightclicking anywhere in the Results
window. Font This menu contains commands to adjust font size. Results Summarize Alias for
the Analyze Summarize command. . Note that ImageJ will not output measurements to
duplicated tables. Because ImageJ outputs measurements exclusively New in IJ . quot . quot
Paste Control . quot . Results Set Measurements. quot Capture Screen quot . renaming the
table will freeze its contents. . Results Distribution.. The Results Table Improved in IJ .. The
ImageJ Results table version . newArray quot Help . ... quot Monitor Memory . quot Rename
... quot . Renames the table. . . . . .. Columns width can be adjusted by clicking on and
dragging the vertical lines that separate the column headings. .. quot . quot . quot Original
Scale quot . Selected lines can be deleted by pressing the backspace key. . ...The ImageJ
User Guide The Results Table var pmCmds newMenu quot Popup Menu quot . quot .. Table
commands are organized in four menus File . quot Find Maxima . quot . File Rename. quot
Duplicate . quot quot . File Save As. Exports the measurements as a tabdelimited or
commadelimited text le as dened in Results Options. to the Results table. quot . .
command.... Edit . Alias for the Analyze Distribution.. .. Most of ImageJ analyses are printed
to the Results table. .k. quot Record . . Creates a new table containing a copy of the data. .
quot Search . Results Clear Results. quot Subtract Background . File Duplicate... quot quot ..
Alias for the Analyze Clear Results command. . . quot quot . . command. quot ..
Custom extensions e. l. Print. Edit . command.ods allow ImageJ tables to be imported
seamlessly by spreadsheet applications.The ImageJ User Guide The ImageJ Editor Results
Options. . . Macros and Debug .csv. Font This menu contains commands to adjust font size
and type. Evaluate Line y. Opens the Edit Options Input/Output. . . The editor commands are
organized in ve menus File . Similarly to any other text editor this menu contains commands
related to text handling as well as commands for locating text. . or any nonASCII characters.
. nonprinting characters that sometimes appear when cutting and pasting from other sources.
. install or evaluate macro code Run Macro r. Specially useful are Go to Line. . Scripts and
Plugins can be opened and executed in the ImageJ editor. .g. i command. This dialog box
enables you to quickly go to a specied Zap Gremlins This command nds and deletes the
extraneous nonvisible. it allows to specify the le extension to be used when saving data..
Font . etc. Abort Macro Exits the macro Install Macros i. File Edit Basic le operations Open. .
See also Plugins New Table. . . Analyze Analyze Particles. Macros This menu contains
commands that allow you to run. ImageJ tables are saved in CSV format if File extension for
tables is .csv. Note that the copied text will substitute any other information present in the le
header and will only be available in images saved as TIFF see II. Ctrl L line of code. Ctrl R
Runs the macro or the selected lines of code. Save. Ctrl I Adds the macros contained in the
editor to Plugins Macros submenu Plugins Macros Install. . . cf. dialog in which is possi ble to
specify if column headers and row numbers should be saved or copied from ImageJ tables
including the Summarize table. . In addition. . being available through the Image Show Info. .
such as email messages that may contain extraneous control characters. .xls or . The
ImageJ Editor Macros . are listed in this menu. Copy to Image Info This command will copy
the selected text or the entire contents of the editor if no selection is present to the image
header. Ctrl Y Runs the line of code that contains the insertion point.
. .html le stored in the macros folder a local copy of http//imagej. forcing Function Finder to
download a fresh copy the next time it is launched.The ImageJ User Guide The ImageJ
Editor Menu Commands Debug Window Main Window Edit Go to Line Edit Find Macros
Function Finder The ImageJ editor version . You start a debugging session initiating Debug
Macro. . You can debug a macro using the commands in the Debug menu. The variable
names and values in the Debug window are updated. Ctrl J Runs JavaScript code in the
editor window. which is highlighted. F. Debug Macro d. and the active images title. .
Functions are read from the functions. Evaluate JavaScript j. Use one of the following
commands to continue execution. Step e. Note that Run Macro runs JavaScript code if the
title of the le ends with . This le is deleted by Help Update ImageJ. You can then single step
through the macro code by repeatedly running Step. not a daily build . which initially displays
the memory usage. Ctrl E Executes the highlighted statement and advances to the next. . .js.
Ctrl Shift F Retrieves macro functions in the same way Command Finder retrieves
commands. The macro stops running at the rst executable line of code. command every time
ImageJ is updated to a release version i. Debug This menu contains seven commands
related to the macro debugging. Ctrl D Starts running the macro in debug mode and opens
the Debug window.n.e.nih. gov/ij/developer/macro/functions. Function Finder.html. number of
open images.
Run to Insertion Point. . Ctrl Shift E Runs the macro to a statement that was previously
dened by clicking the mouse on an executable line of code. Fast Trace T. Ctrl Shift T Same
as above. Abort Exits debug mode. Run Runs the macro to completion at normal speed
similarly to Macros Run Macro.The ImageJ User Guide The ImageJ Editor Trace t. Ctrl T
Runs the macro. displaying variable names and values in the Debug window as they are
encountered. but faster.
See also Hyperstack.. Hyperstack. . bit grayscale unsigned. A dialog box allows you to
specify the image title. Width and Height specify the image dimensions in pixels. . . . . . . . .
Fill With White.txt.Part V ImageJ Commands File As in any other image processing software.
. See also Plugins New . type. command. Image Types and Image Formats .. stacks. . n
Creates a new image window or stack. . basic le operations are listed in this menu. See also
Plugins New Text Window. Name is the title that will be used for the Window. bit oat
grayscale or RGB color. Most are selfexplanatory. hyperstacks or text windows. . . Table. Set
Slices to a value greater than one to create a stack. . Text Window N Creates a new text
window with the title Untitled. Black or Ramp species how the image is initialized. Image.
Type is the image type bit grayscale. Alias for the Image Hyperstacks New Hyperstack.
Macro.. . New Contains commands for creating new images. . dimensions and initial content.
..txt. GIF. Cut x. . See also File Import . System Clipboard V Opens the contents of the
operating system clipboard. See also Edit Copy c. . Also opens ImageJ and NIH Image
lookup tables .xls or . .ijm. or in a format supported by a reader plugin.java extensions .
JPEG. Paste Control. Internal Clipboard Opens the contents of the internal ImageJ clipboard.
Opens an image and displays it in a separate window. Results tables in tabdelimited text
format .lut extension. Image les must be in TIFF. BMP. Open Next O Closes the current
image and opens the next image if any in its directory. V .. Paste Control. . .csv extension
Selections . . Image Types and Image Formats. . See also Edit Copy to System.zip extension
Text les . DICOM. Holding Alt opens the previous image if any in its directory.roi or . . Virtual
Stacks.The ImageJ User Guide File . PGM or FITS format. .js and . .. . Open. Cut x.
path replace fldr . gov / ij / images / to a local subfolder of ImageJ s directory named quot
samples quot. setImageURL method to change the default / macro quot AutoRun quot fldr
getDirectory quot imagej quot quot samples quot . reading raw les.. in bulk.The ImageJ User
Guide File V Opening files File Open. Note that almost every format known to ImageJ can be
opened by dragging and dropping the le into the ImageJ Window.gov/ij/images/ or. The
AutoRun macro in the StartupMacros. These sample images are useful for creating. from
http//imagej. path of Sample Images http // imagej . .zip. nih . quot file // quot path quot / quot
.nih. command opens formats natively supported by ImageJ images and nonimages les.txt le
can be used to change the default path of sample images.g.g. probably the most used is
blobs. Sample images can be downloaded from http//imagej. allowing a complete oline
usage of the File Open Samples submenu Listing Setting File Open Samples for oline usage.
Open Recent The submenu shows a list of the recently opened les. Click on a lename to
open it.gif Open Samples Blobs K B. . . Among all. File Import and Drag amp Drop While the
File Open. . Most of ImageJs Input/Output plugins are installed on this submenu. quot quot .
Open Samples Opens example images hosted on the ImageJ Web site. call quot ij . Prefs
.gov/ij/download/sampleimages.. images in ASCII format or loading images over the network.
. E. testing and debugging macros since routines can be applied to the same image.
setImagesURL quot . regardless of where the macro is run. the File Import submenu
provides access to plugins for additional le types e. / This macro calls the Prefs . quot quot
.nih. Note that Fiji provides this feature by default . in the illustration below a remote macro le
is opened by dragging its URL directly from a Web browser.
to convert to a dierent type. Images must all be the same size and type.The ImageJ User
Guide File . DICOM. There are two dialog boxes one to select the folder and one to specify
options. Input/Output plugins. . In the rst dialog. JPEG. Use the second depicted on the left to
specify which images to open. Image Sequence. GIF. Virtual StackFromList macro. select
any of the images in the folder and click Open. select any of the images in the folder and
click Open. V . or to open the images as a virtual diskresident stack. Import This submenu
lists the installed image reader plugins. import will start with the n th image in the folder. They
can be in TIFF. Starting Image If set to n. In the rst dialog. Opens a series of images in a
folder as a stack. or in a format supported by the HandleExtraFileTypes plugin. FITS or PGM
format. There are two dialog boxes one to select the folder and one to specify options. Use
the second depicted on the left to specify which images to open. The parameters are
Number of Images Species how many images to open. . Starting Image If set to n. Images
must all be the same size and type. or to open the images as a virtual diskresident stack.
JPEG. . If set to to every third image will be opened. They can be in TIFF. or in a format
supported by the HandleExtraFileTypes plugin.. Increment If set to every other image will be
opened. Changed in IJ . The parameters are Number of Images Species how many images
to open. BMP. to reduce the image size. to convert to a dierent type. GIF. BMP. to reduce
the image size. See also Nonnative Formats. File Name Contains Enter a string into this eld
and ImageJ will only open les whose name contains that string. import will start with the n th
image in the folder. Acquisition plugins. etc. Opens a series of images in a folder as a stack.
DICOM. FITS or PGM format.
oracle.gov/ij/docs/menus/le.g.tif. name.tif. lists the values of the image number and image
series tags. entering reduces the amount of memory needed to open a stack by . E. Regex
Syntax Character Classes . ampamp azAZ Meaning Either lower or upper case A Any digit
from through A digit plus any other character Any character sequence An optional digit At
least a digit Any character that is not a digit A digit that is not A digit or lower or upper case
letter .nih. the stack will be opened in numeric le name order e.The ImageJ User Guide File
Enter Pattern Regular expressions regex can be typed here for advanced ltering cf. Virtual
Stacks. ampamp Delimit the set of characters to match Character ranges Any character Zero
or more of the preceding item Zero or one of the preceding item One or more of the
preceding item Negation AND Intersection OR Alternation Example aA .tif. Use Virtual Stack
When checked. See also OpenSeriesUsingFilter macro Regularexpressions basic syntax
summary. Help Opens http//imagej.g.tif instead of alphanumeric order e. For more
information on regex ltering see http//download. name. Basic syntax of regularexpressions
Scale Images Setting a value less than will reduce memory requirements. Information
widthheightdepth size of the stack that will be created is displayed at the bottom on the
dialog box. name.tif. name. Sort Names Numerically When checked. are always sorted by
the image number tag . but access time is slower and changes are lost when switching to a
dierent image in the stack cf. .. images are opened as a readonly virtual diskresident stack
using a version of the Virtual Stack Opener plugin.. This allows image sequences too big to t
in RAM to be opened. and is updated dynamically.g.tif.. DICOM les in the same series tag .
name.. part of the ListDicomTags macro set.
name.com/javase/tutorial/essential/regex/.htmlseq. Convert to RGB Allows a mixture of RGB
and grayscale images to be opened. The List Stack Tags macro.
the File Import Image Sequence. bit signed integer images are converted to unsigned by
adding . command no longer features the Convert to bit grayscale checkbox. Image Type
There are fourteen choices depicted above. Interleaved RGB images have pixels stored
contiguously rgbrgbrgb. You will need to know certain information about the layout of the
image le. Image Width The number of pixel in each row of image data. .d. green and blue
image data stored in separate bit sample planes. and the oset to the beginning of the image
data..The ImageJ User Guide File VI Reducing Memory Requirements When Importing
Images Since ImageJ . ImageJ saves RGB images both TIFF and raw in interleaved format.
Raw. . Image Height The number of rows in the image. use the Use virtual stack option and
then convert to bit using File Type bit. . in a single image plane. As a replacement. . .
including the size of the image. . . Gap Between Images The number of bytes from the end of
one image to the beginning of the next. Planar RGB images have the red. Oset to First
Image The number of bytes in the le before the rst byte of image data. If this value is greater
than the actual number of images the resulting stack will get truncated to the actual size.
Number of Images The number of images stored in the le. Set this value to
widthheightbytesperpixeln to skip n images for each image read. an option that could reduce
memory requirements by for bit images and by for bit and RGB images.. Use this command
to import images that are not in a le format directly supported by ImageJ. bit Bitmap images
are converted to bit. .
blues and greens. Save As Text Image. . . . . disable Scale When Converting in Edit Options
Conversions.gov/ij/docs/menus/le. LittleEndian Byte Order Probably needs to be checked
when importing bit or bit grayscale images from littleendian machines such as Intel based
PCs. LUT. . . . . . The images must all be the same size and type. Note that lookup tables
with le names ending in . . Opens a text le. . ImageJ will import all the images in the folder as
a stack. See also Image Types and Image Formats .The ImageJ User Guide File White is
Zero Should be checked if black pixels are represented using numbers that are less than the
numbers used for white pixels. . Opens a tabdelimited text le as a bit real image see Text
Images.. Opens an ImageJ or NIH Image lookup table. or drag and drop. changing this eld
should x the problem. . Use Virtual Stack Images are imported as virtual stacks. Note that
text les can also be opened using File Open.htmlraw. or drag and drop. If your images look
like photographic negatives. Open All Files in Folder If checked.nih.. The raw LUT le must be
bytes long and contain reds. to prevent the image from being scaled to . Text File. a ramp
image is created to display the LUT. For text les with integer values no larger than . . Before
converting. If no image is open.lut can also be opened using File Open. The images width
and height are determined by scanning the le and counting the number of words and lines. or
a raw lookup table. . . use Image Type bit to convert to bits. Help Opens http//imagej. Text
Image.. . See also OpenTextImagesAsStack macro.
URL.xls . .tif le///Dimagesneuron. . Improved in IJ . Opens an ImageJ Results table.. . using
a URL.csv and . or virtual stack.. . Stack From List. . Other URLs ending with / or . from a text
le containing a list of image le paths. or uncompressed as a stack or virtual stack one slice
per video frame.g and later.html are opened in the users default browser. The images can be
in dierent folders but they must all be the same size and type.. ... With IJ . . The Input URL is
saved in the ImageJ preferences le and retrieved across IJ restarts. . . AVI. . The Virtual
Stack From List macro demonstrates how to generate a list of images and then use that list
to open the images as a virtual stack. . TIFF Virtual Stack. Uses a built in version of the AVI
reader plugin to open an AVI le JPEG or PNG compressed.nih.tif http//imagej. . that contain
multiple DICOM images. les can also be opened by drag and drop.dcm le///Macintosh
HD/images/Nanoprobes. or drag and drop but macros must use this command to gain
access to the dialog box options. .The ImageJ User Guide File . Opens a TIFF le as a virtual
stack. . .gov/ij/ opens the ImageJ website Results.nih. or any tab or commadelimited text
le.gov/ij/images/ct. it is possible to open zip archives. AVI les can also be opened using File
Open. Opens a stack. Downloads and displays known formats to ImageJ specied by a URL.
Some example URLs are http//imagej. . .
b an improved version of the plugin retrieves animation speed from image frame rate. an
option to open the movie as a virtual stack. selections. Can also be used to save
measurement results. bit and bit images are saved using bigendian byte order. JPEG. with IJ
. and later. By default. . . . adds support for YUV formats. create a rectangular selection and
use the Image Duplicate. Save s Saves the active image in TIFF format. bit. . II. Saves the
active image or stack in TIFF format in redundancy with File Save s. . plugin source code. an
option to convert to bit grayscale. lookup tables. To save only a selected area. . . ImageJ
only supports a restricted number of AVI formats cf. along with many bug xes. Note that
Save s and File Save As Ti. . Check Save TIFF and Raw in Intel Byte Order in the Edit
Options Input/Output. An alert is displayed if there are unsaved changes. Nevertheless. Ti. II.
. VII . In addition. . Save As Use this submenu to save the active image in TIFF. selections
and overlays are also saved in the TIFF header. TIFF is the only format other than raw that
supports all ImageJ data types bit.. . the default format of ImageJ cf. dialog box to save using
littleendian byte order. bit oat and RGB and the only format that saves spatial and density
calibration. and selection XY coordinates.The ImageJ User Guide File Since version . Close
w Closes the active image. the ability to specify the starting and ending frame. See also
Native Formats. Close All Closes all open images. . D command. GIF. or raw format. are
redundant commands. .
determines the number of digits to the right of the decimal point.. Since IJ . reducing the
likelihood of color artifacts. Saves the active image as a spreadsheet compatible tabdelimited
text le. . . setting Distance in Pixels to .. Text Image.. . Edit JPEG Quality Edit Options
Input/Output. .g. By default. See also II. . Saves the active image in JPEG format. For a
higher value. RGB images must rst be converted to bit color using using Image Type bit
Color. VII VII Warning on JPEG compression The JPEG format uses lossy compression that
can result in artifacts.. . E. . . each pixel is converted to grayscale using the formula gray
redgreenblue/ or the formula gray . Known Distance to and Unit of Length to inch will set the
DPI to . Stacks are saved as animated GIFs. Jpeg.The ImageJ User Guide File . and later. .
Saves the active image in GIF format. . . dialog box. . For RGB images. You should never
used this format on images to be segmented or measured. the Decimal Places eld in
Analyze Set Measurements. . use a unit of inch in the Analyze Set Scale. dialog. Gif. . Lower
values produce smaller les but poorer quality. This value is shown on the title of the save
dialog prompt. . Flatten F. The value to be used as the transparent index can be set in the
Edit Options Input/Output. . . . Color subsampling is disabled when the value is set to . .
dialog box to specify the JPEG compression level . Larger values produce larger les but
better quality. . . . For calibrated images and oatingpoint images. blue if Weighted RGB to
Grayscale Conversion is checked in Edit Options Conversions. the DPI in the JPEG header
is set to . Alt / or rightclick on the on the play/pause icon that precedes the stack slider to set
the frame rate. Use Image Stacks Tools Animation Options. red . green . . overlays are
embedded when saving in Jpeg format cf. See also Import Text Image.
bit images are saved as unsigned bytes. Raw Data. bit images are saved as oats and RGB
images are saved in three bytes per pixel bits interleaved format. . . bit DICOM are saved as
signed shorts.. . dialog box. unsigned bit images are saved as unsigned shorts and signed bit
images e. .The ImageJ User Guide File Text Images File Import Text Image.g.. . . Saves the
active image or stack as a TIFF le inside a compressed ZIP archive. . . . bit and bit oat
images are saved using bigendian byte order unless Export Raw in Intel Byte Order is
checked in the Edit Options Input/Output. . . . and File Save As Text Image. Saves the active
image or stack as raw pixel data without a header. .. File Open Samples CT K. Zip.
In IJ . FITS. PNG or Uncompressed. so e. Raw. t. Improved in IJ . The default compression
is JPEG. . PGM. Filenames are padded with leading zeroes.. With IJ . images are saved
using Namet d z d c d in which d is the incremental number of specied Digits. Saves a Stack
or a hyperstack as an image sequence. Image Sequence.tif. AVI. Use slice labels as
lenames Stacks only If checked. . Improved in IJ . Image Types and Image Formats. Text
Image. . JPEG. . overlays are embedded when saving in JPEG or PNG format. z. Exports a
stack or hyperstack as an AVI le . Frame Species the frame frequency. Digits The number
digits of the incremental sequence. . the frame.. Compression JPEG. . . . Name Species the
leading string that will be common to all numeric lenames. Alt / and Image Properties.. . the
slice and c. With hyperstacks. GIF. The proposed value is read from Image Stacks Tools
Animation Options. and later. . Format Species the output format that can be set to either
BMP.g. P. Start At Stacks only Species the starting number of the sequence. or Zip cf. TIFF.
. PNG. as long as the unit of Frame Interval is sec. the channel. See also File Import AVI.
overlays are embedded when saving in JPEG or PNG format. and later.The ImageJ User
Guide File . each slice will be saved with its own label and no numeric sequence will be
used. for the depicted snapshot the rst image would be saved as mitosistzc. .
the value to be used as the transparent index . . reverting it to its last saved state. except
RGB. With IJ . . . . . Saves the current area selection boundary to a le. overlays are
embedded when saving in PNG format. . Changed in IJ . LUT. bit images are saved as bit
PNGs. ... . . . . to restore the selection. dialog box. With bit images. Saves the active image in
FITS Flexible Image Transport System format . . . . oval and straight line selections cannot
be exported. . are saved as bit PNGs. . .. stack or hyperstack from disk. Use the Path Writer
plugin to save coordinates at evenly spaced one pixel intervals.The ImageJ User Guide File .
All image types. . XY Coordinates. Since IJ . active selections are saved in the TIFF header
by default cf. . The byte le consists of red values. It is actually a shortcut for closing the
window without saving. Revert r Improved in IJ . . PNG. Coordinates of rectangular.
Improved in IJ . Exports the XY coordinates of the line selection or area selection boundary
as a two column. and then reopening it. Prior to ImageJ . . Results. See also Undo and Redo
. tabdelimited text le. and later.. Saves the active images lookup table to a le. Saves the
active image in PNG Portable Network Graphics format. Selection. . Improved in IJ . FITS. . .
. . . Exports the contents of the Results window as a tabdelimited or commadelimited . green
values and blue values.. Reloads the active image. File Save As Ti. for none can be set in
the Edit Options Input/Output.b this command used to be named Measurements. .csv text le.
Use File Open..
The ImageJ User Guide File . . and later. . . p Improved in IJ . . Quit Prompts you to save all
unsaved images and then exits. Draw border If checked. . . Print title If checked. . overlays
are embedded when printing. For a higher value. current selection will be printed instead of
the entire image. Jpeg. . You can also exit ImageJ by clicking on the close button in its
windows title bar. The Page Setup dialog allows you to control the size of printed output.. the
image will be printed in the center of the page instead of in the upper left corner. dialog to
increase of decrease the size of printed images. Prints the active image. Known Distance to
and Unit of Length to inch will set the DPI to . . setting Distance in Pixels to . use a unit of
inch in the Analyze Set Scale. Print. Center on page If checked.g. Use the Page Setup. . . . .
cf. . Print actual size Considers the DPI information in the image header typically . ImageJ
will print a one pixel wide black border around the image. about the unzoomed screen size of
the image. Selection only If checked. With IJ . The size of the printed image is determined by
the Scale value and the width and height of the image in pixels. Page Setup. plus other
printing options Scale Values less than reduce the size of printed images and values greater
than increase the size. The size of the printed image will normally be slightly less its size on
the screen unzoomed. dialog. E. Rotate If checked. corresponds to pixels per inch ppi. the
image will be rotated to the left before being printed. Images larger than the page are scaled
to t. Spatial calibration is ignored. the title of the image will be printed at the top of the page.
Edit Undo z Described in Undo and Redo. allowing it to be dragged with the mouse.The
ImageJ User Guide Edit . . . The pasted image is automatically selected. Paste Control. See
also Edit Copy to System. Paste Control. See also Paste Control. Cut x Copies the contents
of the current image selection to the internal clipboard and lls it with the current background
color. . Click outside the selection to terminate the paste. copies the entire active image.
Copy to System Copies the contents of the current image selection to the system clipboard. .
. The amount of image data copied is shown in the status bar. Paste Control. If there is no
selection. . Copy c. . Copy c Copies the contents of the current image selection to the
internal clipboard. Paste v Inserts the contents of the internal clipboard or from the system
clipboard if the internal clipboard is empty into the active image. . See also File New System
Clipboard V. . . . . . See also File Internal Clipboard. Select Edit Undo z to abort the paste
operation.
. . a dialog is displayed oering the option to ll the selection in all stack images. . After
pasting. Fill the selection by pressing F to avoid this dialog. . Color Picker . See also Image
Overlay Add Image. white/black pixels are transparent and all other pixels are copied
unchanged. See also Clear. Draw d. Color Picker . Fill f Fills the current selection with the
current foreground color. See also Clear Outside. . . . With stacks. Fill f. Fill f. Color Picker .
Clear Outside Erases the area outside the current image selection to the background color. .
the Paste Control transfer modes are the same as those listed in the description of Process
Image Calculator. The Blend mode is the same as the Image Calculator Average mode. See
also Clear. a dialog is displayed oering the option to clear the selection in all stack images.
use the Paste Control popup menu to control how the image currently being pasted is
transferred to the destination image. With stacks. Paste Control. Clear Erases the contents of
the selection to the current background color. Clear by pressing Backspace to avoid this
dialog. Except for Blend and Transparent.The ImageJ User Guide Edit . In Transparent
mode. Backspace and Del keys are shortcuts to this command.
Draw the selection by pressing D to avoid this dialog. a dialog is displayed oering the option
to draw the selection in all stack images. . If the line width is odd . Rectangular selections but
not polygonal selections or traced selections that happen to be rectangular are an exception
to this rule For rectangular selections. . the center of the line drawn is displaced from the
selection edge by / pixel to the bottom right. With stacks. .. . Selection Select All a Creates a
rectangular selection that is the same size as the image. command. . to change the line
width. See also Image Lookup Tables Invert LUT . of the entire image or selection. Thus the
line center the line in case of line width is inside the selection at the top and left borders. .
XIV. The foreground and background colors can also be set using the Edit Options Colors.
but outside at the bottom and right borders. similar to a photographic negative. VIII VIII
Drawing Lines Wider Than OnePixel If the line width is an even number. command. . Use the
Edit Options Line Width. the selection boundary is at the center of the line. Invert I Creates a
reversed image. Color Picker. onepixel wide outlines are always drawn inside the rectangle.
Thicker lines are drawn as for the other selection types. Draw d Outlines the current selection
using the current foreground color and line width. .The ImageJ User Guide Edit . . Select
None A Deactivates the selection in the active image. . or double click on the line tool.. . .
See also Analyze Label. .
The ImageJ User Guide Edit Original Fit Spline Fit Circle Fit Ellipse Convex Hull Make
Inverse Create Mask To Bounding Box ROI manipulations using the Edit Selection submenu
commands. . . IX Transferring Selections Between Images You can transfer a selection from
one image to another by activating the image with the selection. the command creates a
circle with the same area and centroid of the selection. . With open shapes lines and points.
then pressing Shift E the keyboard shortcut for Edit Selection Restore Selection E. .
Composite selections are not supported. pp is used. . activating the destination image. Vol. .
. Fit Circle New in IJ . A selection is saved when you Delete the selection by clicking outside
of it Draw a new selection Deactivate the image containing the selection Close the image
containing the selection Use a command that deletes or modies the selection See also
Analyze Tools ROI Manager. Fit Spline Fits a cubic spline curve to a polygon or polyline
selection. With closed shapes. Direct leastsquares tting of algebraic surfaces. the tting
algorithm Newtonbased Pratt t described in Pratt V.. Computer Graphics. Restore Selection
E Restores the previous selection to its original position... Fits a circle to a multipoint with at
leas points or area selection .
Make Inverse Creates an inverse selection. The same tting algorithm is used to measure the
major and minor axis lengths and angle when Fit Ellipse is selected in Analyze Set
Measurements. so black is and white is unless Black Background in Process Binary Options.
. orientation and centroid as the original selection. Note that selections can be either lled or
contoured. See also DrawEllipse macro .. . and vice versa. magenta.. ConvexitySolidarity
macro. which can be thought of as a rubber band wrapped tightly around the points that dene
the selection. Properties.The ImageJ User Guide Edit . The ellipse will have the same area. .
cyan. See also Fit Ellipse. The nine default selection colors black. XVII . ConvexHullPlus
plugin . red.. yellow can be typed as text. blue. y Opens a dialog box that allows user to
assign a contour color Stroke Color and a contour width Width to the active selection or a
lling color. green. Create Mask Creates a new bit image called Mask whose pixels have a
value of inside the selection and outside. Fit Ellipse Replaces an area selection with the best
t ellipse. white. See also Process Binary Convert to Mask. . orange. . Convex Hull Replaces
a polygon of freehand selection with its convex hull. . Any other color must be typed in hex
notation see Working With HEX Colors. ... this image has an inverting LUT. . By default.
Create Selection Creates a selection from a thresholded image or a binary mask . but not
both. is checked.. What is inside the selection will be outside. .
X Converting Composite Selections Enter zero in the Edit Selection Enlarge. . however. . the
band is made by growing out the original selection. See also FlipSelection macro . Make
Band. Grows an area selection by a specied number of pixels. dialog box to convert a
composite selection into a polygon selection. selections can also be named using this
command.jar. This command runs the RotateSelection macro in ij. Enlarge.. XVI .. . then the
original selection corresponds to the hole i. This command runs the MakeSelectionBand
macro in ij.jar. Takes an area selection and creates a band with a thickness of the specied
number of pixels. . See also Selections. Enter a negative value to shrink the selection. . b. .
Image Overlay Add Selection. . If you imagine the band as a doughnut shape. Note.jar. . .
ShrinkSelection is a variation of this macro that does not shrink from the image edges.The
ImageJ User Guide Edit Similarly to the Analyze Tools ROI Manager. that the conversion
may fail if the composite ROI is composed of more than one piece and/or contains internal
holes. . . .. . Rotates the selection by the specied number of degrees negative number
indicate counterclockwise rotation.e. This command runs the EnlargeSelection macro in ij.
Rotate. . .
to adjust the width of the line selection. Shiftclick on a point to duplicate it. . Check Oval to
create an elliptical selection.. Use the Image Adjust Line Width. . Altclick on a point to delete
it. Width and Height are the dimensions of the selection. Specify. . In this case. Drag the
points along the line selection to reposition them. This command straightens a curved object
in an image. . Check Spline Fit in the Line Width widget to t a cubic spline curve to the points
that dene the line. it is not necessary to check the status of the Spline Fit checkbox since Edit
Selection Straighten. . Improved in IJ .The ImageJ User Guide Edit . Edit Selection
Straighten. the selection is positioned so X Coordinate and Y Coordinate dene the center of
the selection. opened by double clicking on the line tool icon. If Centered is checked. also
works with straight line selections. .k and later. . . Press Shift E Edit Selection Restore
Selection E to restore accidentally deleted lines. Opens a dialog that allows your to dene a
rectangular or elliptical selection. will assess if the line has already been prepared for
straightening by a runquotFit Splinequot. . otherwise they dene the upper left corner. widget.
With IJ . Straighten. . X Coordinate and Y Coordinate dene the position of the selection. .
Straighten. quotstraightenquot call. the object dened by the line selection is rotated to be
horizontal. The curved object must rst be outlined using the segmented line tool. . .. .
. . Options Use commands in this submenu to change various ImageJ user preference
settings. . . Requesting a higher degree of compression a lower value will result in smaller
les. . . Use for none. . .The ImageJ User Guide Edit . GIF and PNG transparent index
Species the transparent color used for images saved in GIF and PNG formats. Displays a
dialog box that allows the width of lines generated by the Edit Draw d command to be
changed. Line Width. see II. If there is no selection the ROI Manager is open. . Add to
Manager t Adds the current selection to the ROI Manager Analyze Tools ROI Manager.
widget. but poorer image quality. . Converts a line selection to an area traced ROI. This
legacy command has been superseded by the Image Adjust Line Width. . Line to Area New
in IJ . Straight lines must be wider than one pixel. . Converts a nonrectangular selection to
the smallest rectangle that completely contains it... .... Input/Output. To Bounding Box New in
IJ . . Note that lossy JPEG compression creates serious artifacts. JPEG quality Species the
compression level used by File Save As Jpeg. . Note that PNG and GIF transparency only
works with bit images. . .
. Check this option to export images using the order used by Intel based processors
littleendian. Use JFileChooser to open/save Enables versions of File Open and File Save As
that use the Java JFileChooser instead of the native OS le open and save dialogs. . .txt and .
it is slower. . . Use this dialog to control how plots generated by ImageJ are displayed Image
Stacks Plot Zaxis Prole. .. etc. uses more memory. . Improved in IJ . Fonts. .xls extensions
are saved in tabdelimited format and les with . . . Files with . size.. Analyze Plot Prole k. This
Wikipedia article has more information. .The ImageJ User Guide Edit File extension for
tables Sets the default extension to be used when saving tables see The Results Table.
Save TIFF and raw in intel byte order Species the byte order used when saving bit and bit
images using File Save As Raw Data. . . . . . and does not behave like the le open and save
dialogs used in other applications.. when Raw is chosen as the format. .csv extensions are
saved in commadelimited format. Opens a small window with three popup menus for
specifying the type face. or File Save As Image Sequence. The main advantage of
JFileChooser is the ability to open multiple les by shiftclicking to select multiple contiguous
les and controlclicking to select more than one individual le. style and antialiasing Smooth
checkbox of the font used by the Text Tool. Results Table Options Species if column
headers and row numbers should be saved or copied from ImageJ tables such as the
Results and Summarize windows see The Results Table. . On the other hand. Analyze
Calibrate. Analyze Tools Curve Fitting. . . . Prole Plot Options.
The ImageJ User Guide
Edit
Plot Width and Plot Height Specify the length in pixels of the Xaxis Plot Width and Yaxis Plot
Height. Fixed yaxis Scale If checked, the Yaxis range is xed and the specied Minimum Y and
Maximum Y values are used, otherwise, plots are scaled based on the minimum and
maximum gray values. Do not Save xvalues If checked, List, Save. . . and Copy. . . buttons
will appear in prole plot windows. Autoclose If checked, prole plot windows will be
automatically closed when List, Save and Copy are clicked on. Vertical Prole If checked, row
average plots of rectangular areas or line selections wider than pixel will be generated
instead of the default column average plots. Note that evoking Plot Prole k with Alt B will
generate vertical proles. List values If checked, the list of values will be automatically
opened. If Autoclose is also checked, the plot is closed and only the list of values remains
open. Interpolate line proles If checked, prole values will be interpolated along the line
selection Draw grid lines If checked, gray grid lines will be drawn in the plot. Help Opens
http//imagej.nih.gov/ij/docs/menus/edit.htmlplotoptions. .. Arrow Tool. . .
See Arrow Tool. .. Point Tool. . .
See Point Tool. .. Wand Tool. . .
See Wand Tool.
The ImageJ User Guide
Edit
..
Colors. . . Displays a dialog box that allows you to set Foreground Color, Background Color
and Selection Color.
See also Color Picker, Image Color Color Picker. . . K,
Point Tool
..
Appearance. . . This dialog contains options that control how images are displayed, an option
to display better looking toolbar icons, and an option to set the menu font size. Interpolate
zoomed images Uses interpolation instead of pixel replication when displaying zoomed
images. Open Images at Newly open images are displayed using magnication image pixel
screen pixel.
Black Canvas Causes the image canvas white by default to be rendered in black. This is
useful when looking at Xray images in order to avoid high contrasting intensities at the image
edges. No image border Displays images without the default one pixel wide black border.
Use inverting lookup table Causes newly opened bit images to have inverted pixel values,
where white and black . This is done by both inverting the pixel values and inverting the LUT.
Use the Image Lookup Tables Invert LUT command to invert an image without changing the
pixel values. Double Buer Selections Reduces icker when working with complex selections
but it also increases memory usage and slows screen updates. It is not needed on Mac OS
X, which has built in double buering. Antialiased tool icons Smooths and darken the tool
icons in the ImageJ window. This option is enabled by default on all operating systems. On
Windows XP, enable Clear Type subpixel antialiasing to improve the quality of text in menus.
Menu font size Species the size of the ImageJ window menu font. Use a size of zero to use
Javas default menu font size. Changing the font size requires the restarting of ImageJ. This
option is ignored on Mac OS X. Help Opens
http//imagej.nih.gov/ij/docs/menus/edit.htmlappearance.
The ImageJ User Guide
Edit
..
Conversions. . . Use this dialog to set options that control how images are converted from
one type to another.
Scale When Converting ImageJ will scale from minmax to when converting from bit or bit to
bit or to scale from minmax to when converting from bit to bit. Note that Scale When
Converting is always checked after ImageJ is restarted. Weighted RGB Conversions ., ., .
When checked, the formula gray .red.green.blue is used to convert RGB images to
grayscale. If it is not checked, the formula gray red green blue/ is used. The default weighting
factors ., ., ., which are based on human perception, are the ones used to convert from RGB
to YUV, the color encoding system used for analog television. The weighting factors can be
modied using the setRGBWeights macro function. .. Memory amp Threads. . . Use this
dialog to specify the maximum amount of memory available to ImageJ and the number of
threads used by lters when processing stacks. Java applications such as ImageJ will only
use the memory allocated to them typically MB but this dialog allows the user to allocate
more than the default. Note that specifying more than of real RAM could result in virtual RAM
being used, which may cause ImageJ to become slow and unstable. Also note that this
dialog cannot be used to set the memory allocation if ImageJ is run from the command line
or by double clicking on ij.jar. Maximum Memory bit OS and a bit version of Java are required
to use more than MB of memory. Windows users must be running a bit version of Windows
and must install a bit version of Java. Mac users must be running OS X . or later and may
need to use the Java Preferences utility in /Applications/Utilities/Java to select a bit version of
Java. They may also need to switch to the ImageJ application. Linux users need to be
running bit versions of Linux and Java. The title of the Memory amp Threads dialog box
changes to Memory bit when ImageJ is running on a properly congured bit system.
Improved in IJ .
A Target of . Status bar. that otherwise. Target Species the Java version of the class les
created by Plugins Compile and Run. Use this dialog to modify the proxy settings of the Java
Virtual Machine. Displays a dialog box with options for the Plugins Compile and Run. Help
Opens http//imagej. .txt .g. should be used to create plugins capable of running on all ImageJ
versions. .htmlmemory. . .The ImageJ User Guide Edit Parallel Threads for Stacks Defaults
to the number of available processors determines the number of parallel threads used by
commands in the Process Filters and the Process Math submenus when processing stacks.
forces the Java garbage collector to run every time the user clicks on the ImageJ status bar.
Generate Debugging Info javac g If checked. Help Opens http//imagej.. Target cannot be set
higher than the version of Java ImageJ is currently running on. Plugins compiled with a
Target of . See also FAQs on the ImageJ Documentation Wiki New in IJ . . . Compiler. A
Target of . Run garbage collector on status bar click If checked. command. .nih. wouldnt be
able to open the example images File Open Samples submenu. .. will not run on earlier
version Java. Target Species the Java version of the class les. will not run on earlier versions
of Java. .nih. Plugins compiled with a Target of . information needed by Java debuggers will
be included in the class les. should be used to create plugins capable of running on all
versions ImageJ. which may help to reclaim unused memory cf. e. . Proxy
Settings.gov/ij/docs/menus/edit. This may be required for ImageJ to connect to the internet in
certain machines running behind HTTP proxies. Settings are saved in the ImageJ
preferences le IJPrefs. Target cannot be set higher than the version of Java ImageJ is
currently running on..htmlcompiler. .gov/ij/docs/menus/edit.
detects a divide by zero while dividing one bit real image by another. max largest positive
value and NaN NotaNumber can be entered as the Divide by zero value. Use pointer cursor
If checked. plugins that attempt install themselves in a submenu with only one command are
instead installed in the Plugins Miscellaneous submenu. Displays a dialog box containing
miscellaneous options. if ImageJ should open DICOM images as bit oat. This option can also
be used to work around a bug on Windows where the text cursor is sometimes used in place
of the crosshair. See also Image Types and Image Formats Improved in IJ . Divide by zero
value Species the value used when Process Image Calculator. Require control / command
key for shortcuts If checked. . menu This option can reduce the size of the Plugins menu. this
avoids the problem where . which normally creates a Plugins TurboReg submenu that
contains only one command. . preventing it from running o the bottom of the screen. . .. .
ImageJ will suppress the dialog that asks Process all xx slices only the current slice will be
processed. The default is innity. DICOM. In addition to numeric values. This dialog sets
options related to the handling of DICOM images. On Windows. When this option is enabled.
Run single instance listener If checked. . if voxel depth should be calculated based on the
distance between the rst and last slices and if coronal/transverse sections should be mirrored
when using the Image Stacks Orthogonal Views H command. .The ImageJ User Guide Edit .
An example of such a plugin is TurboReg. ImageJ will use an arrow cursor instead of the
default crosshair that is sometimes dicult to see on grayscale images in areas of medium
brightness. innity positive or negative innity. requires the Control key Command key on Macs
to be pressed when using keyboard shortcuts for menu commands. Namely. Misc. ImageJ
will use sockets to prevent multiple instances from being launched.. Move isolated plugins to
Misc. Hide quotProcess Stackquot dialog If checked.
Note that you may get a security alert the rst time ImageJ starts with this option
enabled.htmlmisc.gov/ij/docs/menus/edit. ImageJ does not require external socket access so
it is okay to deny it access in the security alert.nih. Help Opens http//imagej. Debug mode If
checked. It also prevents multiple instances when running ImageJ from the command line. .
causes ImageJ to display debugging messages in the Log window. Close the Log window to
disable display of debugging messages.The ImageJ User Guide Edit another copy of ImageJ
starts each time an image is dragged and dropped on the ImageJ icon.
. I. Supported conversions in ImageJ Image Type bit bit bit bit bit color RGB color RGB stack
HSB stack I Single images only. .. . I. i displays these two values as Display range. S bit I. S
bit color RGB color I. S . red . . ImageJ converts bit and bit images and stacks to bits by
linearly scaling from minmax to ... green . where min and max are the two values displayed in
the Image Adjust Brightness/Contrast. green. S I. . S I .. RGB Stack Converts to a slice red. I.
S I. Note that this scaling is not done if Scale When Converting is not checked in Edit
Options Conversions. S . S I. blue if Weighted RGB Conversions is checked in Edit Options
Conversions. S . The active image must be RGB color. Image Show Info. . bit Converts to bit
grayscale.The ImageJ User Guide Image .. S I. bit Color Converts to bit indexed color using
Heckberts mediancut color quantization algorithm. bit Converts to signed bit oatingpoint
grayscale. .. S I. bit Converts to unsigned bit grayscale.. . RGB images are converted to
grayscale using the formula gray red green blue/ or gray . The active image must be RGB
color. . RGB stack HSB stack .. S I. . S Stacks bit I. I I I.. A dialog box allows the number of
colors to be specied. blue stack. An attempt to perform an unsupported conversion causes a
dialog box to be displayed that lists the possible conversions. S submenu. . ... C. RGB Color
Converts to bit RGB color. S I. Image Type Use this submenu to determine the type of the
active image or to convert it to another type...
Please note that windowing does not aect image data cf. C. threshold levels and image size.
which typically can show only display shades of gray. .The ImageJ User Guide Image HSB
Stack Converts to a slice hue. With bit and bit images. The active image must be RGB color.
the display is updated by changing the mapping from pixel values to bit display values.. .
How these intensities are interpreted is specied by the image type. . while values above the
window are white. the data are mapped to bit by windowing. the HDRexplorerTool. It may
happen that the initial windowing performed by ImageJ on these high bitdepth or HDR
images is suboptimal. XII Brightness/Contrast of High BitDepth Images When displayed. The
window is dened by minimum and maximum values that can be modied using Image Adjust
Brightness/Contrast. Therefore. saturation and brightness stack. according to either the
optimal for each individual slice if Use Stack Histogram is unchecked or the overall stack if
Use Stack Histogram is checked. The default behavior of the BampC tool Image Adjust
Brightness/Contrast. From the ImageJ website bit and bit grayscale images are not directly
displayable on computer monitors. . . Use this tool to interactively alter the brightness and
contrast of the active image. The window denes the range of gray values that are displayed
values below the window are made black. . Adjust This submenu contains commands that
adjust brightness/contrast. . C is to use the overall stack histogram. C Improved in IJ .
Brightness/Contrast. so pixel . the intensity of each pixel that is written in the image le is
converted into the grayness of that pixel on the screen. so pixel values are unchanged. XI
Applying Auto Brightness/Contrast to Entire Stacks The Process Enhance Contrast
command can be used to adjust the brightness and contrast of each slice in a stack.
brightness and contrast are changed by updating the images lookup table LUT. With bit
images. .
A runquotEnhance Contrastquot. quotsaturated. e. bit RGB. Auto ImageJ will automatically
optimize brightness and contrast based on an analysis of the images histogram. A
setMinAndMax macro call is generated if the command recorder is running. Create a
selection. Holding down Shift restores original settings in all channels of a composite image.
Holding down Shift will simultaneously adjust all channels of a composite image. . the
relevant image information is contained only within a narrow range of the grayscale. Reset
Restores the original brightness and contrast settings. Histogram The line graph at the top of
the window. which is superimposed on the images histogram. A bit image consists of
possible gray levels.. Most of times. Minimum and Maximum sliders Control the lower and
upper limits of the display range. The narrower the display range. File Open Samples HeLa
Cells . The optimization is done by allowing a small percentage of pixels in the image to
become saturated displayed as black or white. The display range is set to the full pixel value
range of the image. Each additional click on Auto increases the number of saturated pixels
and thus the amount of optimization. shows how pixel values are mapped to bit display
values. Holding down Shift will simultaneously adjust all channels of a composite image e.
the higher the contrast. Check Propagate to all open images to apply these values to the rest
of the images currently open. A resetMinAndMax macro call is generated if the command
recorder is running. or window. Contrast slider Increases or decreases contrast by varying
the width of the display range.quot macro call is generated if the command recorder is
running. ImageJ displays images by linearly mapping pixel values in the display range to
display values in the range . These two values dene the display range. and the entire image
will be optimized based on an analysis of the selection.g. however. The two numbers under
the plot are the minimum and maximum displayed pixel values. in which signal is restricted to
the Improved in IJ .g. Set Allows to enter the minimum and maximum display range values in
a dialog box. This is the case.. M.The ImageJ User Guide Image pixel values are also
unchanged. Holding down Shift will simultaneously adjust all channels of a composite image.
Brightness and contrast of RGB images are changed by modifying the pixel values. Pixels
with a value less than the minimum are displayed as black and those with a value greater
than the maximum are displayed as white. in low light microscopy. Brightness slider
Increases or decreases image brightness by moving the display range.
This option currently only works with bit images and stacks and with RGB stacks. . . . If there
is a selection. C tool. This command interactively adjusts the Window range of minimum and
maximum Contrast and Level position of that range in the grayscale intensity space
Brightness of the active image in a manner closer to that implemented on medical image
terminals. if the B ampC window is opened. . The Set Display Range dialog allows you to
choose how to scale the range of gray levels of bit images. Enhance Contrast. it will be
closed and the W ampL window will be opened at the same location. . bit Gray level range of
. See also Window/Level. bit Gray level range of . . Window/Level. . bit Gray level range of .
This is the only BampC option that alters the pixel data of nonRGB images. XIII . . XI.
Automatic Automatically selects the best range given the intensity values of the image based
on the percentage of the total number of pixel values from the lowest to highest pixel value.
Apply Applies the current display range mapping function to the pixel data. Being redundant
with the Brightness/Contrast.. bit Gray level range of . only pixels within the selection are
modied.The ImageJ User Guide Image lower end of the grayscale. bit Gray level range of .
Also. it will be closed and the Color window will be opened at the same location. . . Image
Show Info. . bit DICOM image has a Window Center of and Window Width of . . Color
submenu . Click Reset and the display range is set to to . . Color Balance.e. . the File Open
Samples CT K. . . . Press R File Revert r to See also Brightness/Contrast. Auto. . i.
Brightness/Contrast. or BampC Image Adjust Brightness/Contrast. tool. To display the
DICOM tags. i. Set and Apply work as described for Image Adjust Brightness/Contrast. if the
B ampC window is opened. Click Reset on the WampL Image Adjust Window/Level. Press H
Analyze Histogram h and you will see that the minimum pixel value in the image is and the
maximum is . C. . Similarly to the Window/Level. the changes made to one color will be lost
unless Apply is clicked before. . This panel makes adjustments to the brightness and contrast
of a single color of a standard RGB image bit per color channel. note that for bit color images
that load as a stack. C works on single stack slices. For multichannels stacks and
hyperstacks it adjusts each of the color channels independently. so the display range is set
to to centerwidth/ to centerwidth/. C window and the display range will be set to the minimum
and maximum pixel values. press I revert to the initial display range. Maximum and Minimum
sliders. . C.. . Use the dropdown menu to specify which color / channel will be adjusted the
histogram is drawn for the selected color. tags. and the color settings of the Color panel are
ignored. See also Brightness/Contrast. C . NB When switching from one color to another.
ImageJ sets the initial display range based on the Window Center . colors. .The ImageJ User
Guide Image XIII Display Range of DICOM Images With DICOM images.. As an example.
and Window Width . . . .
. checked to measure the aggregate of the selected features. . Hold Shift while adjusting the
minimum to move a xedwidth thresholding window across the range of gray values.The
ImageJ User Guide Image . Method Allows any of the dierent automatic thresholding
methods to be selected . . Upper slider Adjusts the minimum threshold value. . Use this tool
to automatically or interactively set lower and upper threshold values. Display Selects one of
three display modes Red Displays the thresholded values in red. BampW Features are
displayed in black and background in white. . .m. T ImageJ . The Default method is the
modied IsoData method used by ImageJ . to measure features individually. segmenting
grayscale images into features of interest and background. . . These methods are described
on Fijis Auto Threshold website http//pacic. m with Limit to Threshold in Analyze Set
Measurements. . T Improved in IJ . . .php/AutoThreshold.de/wiki/index. and earlier. mpicbg..
Use the Wand Tool to outline a single feature. . Use Analyze Measure. . Threshold. Use
Analyze Analyze Particles. Thresholding methods Highlighted range Holding Shift moves a
xedwidth thresholding window Min/Max values Display mode Manual input Are objects in the
image lighter than the background Image Adjust Threshold. This mode respects the Black
background ag set in Process Binary Options. Lower slider Adjusts the maximum threshold
value.
Note that the nal thresholded image type is RGB. Auto Uses the currently selected
thresholding method to automatically set the threshold levels based on an analysis of the
histogram of the current image or selection. . and pixels above the upper threshold value in
green. Thresholds bit RGB images based on Hue Saturation and Brightness HSB. CIE Lab
or YUV components.l. See also XVII .i and later. New in IJ . For bit oat images Apply will also
run Process Math NaN Background. Dark background To be checked when features are
lighter than the background. . Improved in IJ . not bit gray. the state of the checkbox is
remembered across restarts. . Color Threshold. implemented in version .setOverColor and
setUnderColor methods example. Reset Disables thresholding and updates the histogram.
Set New threshold levels can be entered into this dialog box. thresholded pixels in grayscale.
This command.The ImageJ User Guide Image Over/Under Displays pixels below the lower
threshold value in blue. With IJ . is a builtin version of the Threshold Colour plugin . These
colors can be changed from a macro by calling the ImageProcessor. Apply Sets thresholded
pixels to black and all other pixels to white.. Red Green and Blue RGB. Ranges of the lters
can be set manually or based on the pixel value components of a userdened ROI
experimental.
Dark background To be checked when features are lighter than the background. otherwise.
Black. . Original Restores the original image and updates the buer when switching to another
image. Sample Experimental Sets the ranges of the lters based on the pixel value
components in a userdened ROI. New in IJ . Filtered Shows the ltered image. Color space
Selects the color space HSB. . T. Stack Processes the rest of the slices in a stack if any
using the current settings. . CIE Lab or YUV. values within range are thresholded and
displayed bandpass lter. Thresholding Method Allows any of the dierent automatic
thresholding methods to be selected cf. . . Pass If checked. . With IJ . Threshold.i and later. .
Select Creates a ROI selection based on the current settings. . .The ImageJ User Guide
Image Segmentation of DAPI stained nuclei using Image Adjust Color Threshold. White or
Black amp White cf. Threshold Color Selects the threshold color either Red. values outside
the selected range are thresholded bandreject lter. Threshold. RGB. T. New in IJ . The
selection is made according to the settings dened in the Process Binary Options. the state of
the checkbox is remembered across restarts. dialog.
. K. . . . . Color Picker. Help Opens Color Threshold. See also D Color Inspector/Color
Histogram . if open. . Check Constrain aspect ratio and ImageJ will adjust either the Height
or the Width to maintain the original aspect ratio. the border is lled with the current
background color. . Width and Height may be either expanded or contracted. XIV . The
implementation of the bicubic method CatmullRom interpolation is derived from Burger and
Burge. E . or... See also Image Scale. . . Improved in IJ . See also Size.The ImageJ User
Guide Image Macro Creates a macro based on the current settings which is sent to the
Macro Recorder window Plugins Macros Record. . Two resampling methods are possible
Bilinear and Bicubic interpolation. the border is lled with pixels that have a value of zero. . .
Check the Average when downsizing checkbox for better results when scaling down images .
If the canvas size is increased. . The position of the old image within the new canvas may
also be specied. if Zero Fill is checked. When applicable. . . Changes the canvas size of an
image or stack without scaling the actual image. . Scales the active image or selection to a
specied Width and Height in pixels. other dimensions can also be resized Depth images in
stacks. Canvas Size. Depth slices and Time frames in hyperstacks. . Size. s builtin help.
. . . cm. micron. . Line Width. Width. Pixel Width. See also Image Properties. With tseries
stacks..The ImageJ User Guide Image . . Alt / as long as the unit used is sec. mm. Slices z
and Frames t in the image can be changed as long as the product of c. the Frame Interval in
seconds reciprocal of the frame rate can be viewed and set. also displays le header
information. The Unit of Length a string describing the measuring unit. . This widget is used
to adjust the width of line selections. . . . . . For DICOM and FITS images. and t is equal to
the number of images in the stack. z. Show Info. m. . See also Edit Options Line Width. . P
Improved in IJ .. The number of Channels c. Edit Selection Fit Spline . Height and Depth are
automatically converted if Unit of Length is changed from one known unit nm. . Since IJ .
setting the Frame Interval sets the frame rate used by Animation Options. Checking Spline
Fit ts a cubic spline curve to the points that dene the line. i Opens a text window containing
information about the active image including the pixel or voxel size. Pixel Height and Voxel
Depth all in the Unit of Length unit can be set. It is opened more easily by double clicking on
the Line Selection Tools icon. since IJ . Use the popup menu rightclick in the Info window to
save the information to a text le or copy it to the system clipboard. km or inch to another.k.
Properties. P Use this command to display and set various properties of the current image or
stack. meter. um. .
The stack must be bit or bit grayscale. Z Improved in IJ . of the image coordinate system see
also Analyze Set Measurements. assuming that the slices are in R. Stack to RGB Converts a
two or three slice stack into an RGB image. See also Merge Channels. Split Channels Splits
an RGB image or stack into three bit grayscale images containing the red. Image Scale. Z
Alias for Image Hyperstacks Channels. . E... . cf. . .The ImageJ User Guide Image Origin
always in pixels is the reference point . .g. green and blue.g. With IJ . .M. . . The window
names have an appended red. . Also converts composite images e. File Open Samples
Organ of Corti .. Select None to keep a channel empty lled with . . . D stack this command
splits the stack into separate channels. apply to all images opened during the current
session. G. With composite images and / or hyperstacks e. XVIII. . . i. Z. . . Check Create
Composite to convert grayscale images or stacks into a composite image or hyperstack see
Color Composites. .n and later. B order. Analyze Set Scale.. . . See also Channels. . .
Merges grayscale images or stacks into an RGB image or stack. Check Global to make the
current settings global i.M.. . Merge Channels. . bit RGB into RGB. LUTs and display ranges
are preserved if Create Composite is chosen. Color This submenu contains commands that
deal with color images. File Open Samples HeLa Cells .. green and blue components of the
original. . . . See also Image Show Info.e. Channels Tool.. Check Keep Source Images if you
wish to keep the originals.
K.. describes the color that is displayed for each of the possible pixel values. A lookup table
in ImageJ has up to entries. . Note that RGB color images do not use a lookup table. . It has
two modes Foreground and Background. a image stack or a channel hyperstack into a
composite color image. . Show LUT Displays a plot of the active images lookup table LUT . .
Color Picker. . green and blue values for that entry using a Color Selector window cf. C Shift
C to adjust the brightness and contrast of the current channel. Opens the ImageJ LUT
Lookup Table Editor. Use the Channels. Z tool Shift Z to enable and disable the channels of
a composite image. . radio button to export the LUT as a CSV le. or color table. The entry
index. . Use the List... . A bar under the plot displays the color representation of the pixel
values. and the three values red. are displayed in the ImageJ status bar as you move the
cursor over the LUT Editor window. which aect Edit Fill f. . Click on an entry to edit the red.
The lookup table. See also Show LUT . See also Edit LUT. For and bit images. the range of
displayed pixel values is mapped to . Use Brightness/Contrast.The ImageJ User Guide
Image . green and blue associated with it. click on the . . . Color Picker. Improved in IJ . K
The Color Picker tool enables the user to select foreground and background colors. . Make
Composite Converts in place an RGB image. Edit Draw d and other color drawing
commands.. Edit LUT. . To change modes. . It displays current foreground and background
colors in the selection boxes at the bottom of the window. . .
Clear. . At the center of the color ramp are enlarged red. Holding Alt inserts a blank slice
before the current slice. magenta. Clicking on the Foreground /Background Switcher button
sets the current foreground to the background and vice versa. . The title of the Color Selector
window Foreground Color or Background Color indicates the current selection mode.
manually change the values in the text boxes. blue. The left half of the palette varies only in
brightness while the right half varies only in saturation. Saturation and Brightness color
model. Draw d. The Black /White Reset button sets the foreground to black and the
background to white. Add Slice Inserts a blank slice after the currently displayed slice. . .
Clear Outside. The color palette is based on HSB Hue. Image Types and Image Formats ..
To get precise colors. shown on the right in the illustration. Hue increases as you go down
the palette while saturation and brightness values are split horizontally. cyan. and yellow
colors for quick selection. K tool. Stacks This submenu contains commands that work with
stacks.The ImageJ User Guide Image desired selection box. Color Ramp Algorithm H B S
Red Yellow Green Color Selectors Black White Ramp Cyan Blue Magenta Foreground Color
Background Color Foreground/Background Switcher Black/White Reset The Color Picker.
See also XIV. Fill f. Use the sliders to specify the RGB values of the foreground or
background color. green. To the left of the color palette is a grayscale ramp that goes from
pure black to pure white. Double clicking on a color brings up one of the Color Selectors.
. . Improved in IJ . In a bit image. For nonRGB images. if the foreground color is red RGB .
Previous Slice lt Displays the slice that precedes the currently displayed slice. intensity of
drawn selections will be / . . Holding Alt lt will skip nine slices backward. e.The ImageJ User
Guide Image XIV Embedding Color Annotations in Grayscale Images Color marks are only
available with color images or grayscale images that have been converted to RGB. Set Slice.
the easiest way to embed true color selections in grayscale images is to use the Image
Overlay Add Selection. Images To Stack Creates a new stack from images currently
displayed in separate windows. Although this issue can be overcome by converting the
image into RGB Image Type submenu. . . See also Arrow Keys will skip . The user must
enter a slice number greater than or equal to one and less than or equal to the number of
slices in the stack.. b command followed by Image Overlay Flatten F. background /
foreground color will be painted in equivalent gray levels.. Delete Slice Deletes the currently
displayed slice. Displays a specied slice. .. Holding Alt nine slices forward. . See also Arrow
Keys .g. ... . Next Slice gt gt Displays the slice that follows the currently displayed slice.
. image titles without extension will be used as stack labels. Use Title as Labels If checked. .
and to select the layout of the resulting grid. a dropdown menu allows to choose a
conversion method Copy center / topleft Stack will have the width of the widest open image
and the height of the highest open image.. bicubic interpolation cf. This can be useful for
visual comparisons of a series of images stored in a stack and to create panel gures. Keep
Source Images If checked. Other images are scaled to the new slice dimensions. instructions
are displayed that explain how to create c. . Scale smallest / largest Stack will have the
dimensions of the smallest / largest open image. Bicubic interpolation is used if Bicubic
interpolation is checked cf. . z or t montages. Smaller images will then be copied either to the
center or to the upper left corner of the slice. . Bicubic Interpolation If checked. Image Size.
Stack To Images Converts the slices in the current stack to separate image windows.. .
original images are kept. Name Species the title of the stack to be created.The ImageJ User
Guide Image Method If images dier in size. E. A dialog box allows you to specify the
magnication level at which the images are copied. Title Contains Enter a string into this eld
and ImageJ will only convert to stack images whose name contains that string. Borders are
lled with pixels that have a value of zero. Adjust Size. will be used if any of the Scale
methods was previously chosen. Make Montage Produces a single image which contains the
images from a stack displayed in a grid format. . . With hyperstacks that are not directly
supported . . and Image Scale.
/ Reconstructs one or more orthogonal slices through the image volume represented by the
current stack or hyperstack . .The ImageJ User Guide Image Label Slices If checked. .
command. Increase Output spacing to reduce the size of the output stack. . . If no slice
metadata exists the setMetadataquotLabelquot. RC Montage plugin. string macro function
can be used to customize slice labels images are labeled with slice numbers. . Note that the
Label. A dialog allows you to specify the spacing of the reconstructed slices. See also Stacks
Tools Montage to Stack.. Reslice. Magic Montage a macro toolset to reorder and manipulate
images in the montage a video tutorial can be found here . Output spacing Determines the
number of orthogonal slices that will be reconstructed. Increasing Output spacing reduces
the size of the output stack. . . Use Foreground Color If checked. The estimated size of the
output stack and the amount of available memory are displayed at the bottom of the dialog.
borders and labels are drawn in the foreground color and blank areas of the panel are lled
with the background color. images are be labeled in the panel. command can also be used to
draw labels in stack slices.
XY and XZ coordinates are displayed in the title of the projection panels. no interpolation will
be done. Flip vertically If checked. Help Opens http//imagej.gov/ij/docs/menus/image. Avoid
interpolation If checked. . . E. and D Viewer . the size of the output stack in determined by
Slice count.The ImageJ User Guide Image Start at Determines the image edge top. The
intersection point of the three views follows the location of the mouse click and can be
controlled by clicking and dragging in either the XY. a stack is created by shifting by Output
spacing the line down and to the left to generate additional slices for the output stack. XZ or
YZ view. Stack Slicer DisplayTP plugins.. the command shortcut. Improved in IJ . In this
case. if a stack displays sagittal sections. . coronal YZ projection image and transverse XZ
projection image will be displayed through the dataset. . Rotate degrees If checked. The
mouse wheel changes the screen plane in all three views.g. Orthogonal Views H Provides an
orthogonal view display of the current stack or hyperstack . left. See also D Project. See also
Dynamic Reslice and Radial Reslice plugins .htmlreslice. The two extra planar views are
displayed in sticky panels next to original image and can be toggled using Shift H . Volume
Viewer. . Start at is replaced by Slice count if there is a line selection. each slice in the output
stack will be ipped vertically. Edit Options DICOM. each slice in the output stack will be
rotated ..nih. . P. . With lines selections. . Voxel dimensions can be adjusted in Image
Properties. bottom or right from which reconstruction starts.
See also Grouped Z Project. Z Project. . . D Project. . Average Intensity projection outputs
an image wherein each pixel stores average intensity over all images in stack at
corresponding pixel location. .. Median projection outputs an image wherein each pixel stores
median intensity over all images in stack at corresponding pixel location. Maximum Intensity
projection MIP creates an output image each of whose pixels contains the maximum value
over all images in the stack at the particular pixel location. .The ImageJ User Guide Image . .
. . Average Intensity projection outputs an image wherein each pixel stores average intensity
over all images in stack at corresponding pixel location. Improved in IJ . With ImageJ . . Plot
Zaxis Prole. . . Sum Slices projection creates a real image that is the sum of the slices in the
stack. Projects an image stack along the axis perpendicular to image plane the socalled z
axis . Five dierent projection types are supported.l and later. Standard Deviation projection
creates a real image containing the standard deviation of the slices. the preferred projection
method is stored in the preferences le.
The ImageJ User Guide Image . sums the values of all transparent points along each ray and
projects their mean value. Brightest Point projection examines points along the rays. Slice
Spacing The interval. a modication of brightestpoint projection. in pixels. or z. It produces
images with softer edges and lower contrast. brightestpoint. Projection Method Select
Nearest Point projection to produce an image of the surfaces visible from the current viewing
angle. Each frame in the animation sequence is the result of projecting from a dierent
viewing angle. This command creates a sequence of projections of a rotating volume stack
or hyperstack onto a plane using nearestpoint surface. imagine a eld of parallel rays passing
through a volume containing one or more solid objects and striking a screen oriented normal
to the directions of the rays. or meanvalue projection or a weighted combination of nearest
point projection with either of the other two methods partial opacity . make portions of the
volume transparent using thresholding. The choice of projection method and the settings of
various visualization parameters determine how both surface and interior structures will
appear. . or projection plane. projecting the brightest point encountered along each ray.
based on the values of points along its path. The user may choose to rotate the volume
about any of the three orthogonal axes x. At each point in the projection plane. To visualize
this. y. Three methods are available for calculating the projections onto this plane
nearestpoint. a skull.. Each ray projects a value onto the screen. This will display the
brightest objects. but can be useful when attempting to visualize objects contained within a
structure of greater brightness e. and meanvalue. or add a greater degree of visual realism
by employing depth cues. Projection calculations disregard points having values less than
the . . ImageJ projects the volume onto the viewing plane at each Rotation Angle Increment.
D Project. The value of the nearest non transparent point which the ray encounters is stored
in the projection image. such as bone in a CT computed tomographic study. Improved in IJ .
a ray passes normal to the plane through the volume. between the slices that make up the
volume. Lower / Upper Transparency Bound Determine the transparency of structures in the
volume.g. Mean Value projection. beginning with the volume rotated by Initial Angle and
ending once the volume has been rotated by Total Rotation. brightestpoint.
Note that you can also use Image Adjust Threshold. pixels. and D Viewer . Volume Viewer
plugins .e. Interpolate Check Interpolate to generate a temporary zscaled stack that is used
to generate the projections. For both kinds. T to set the transparency bounds. Interior
DepthCueing works only on brightestpoint projections. This checkbox is ignored if the slice
spacing is less than or equal to . See also Orthogonal Views H. specially on overlapping
objects of dierent colors and dimensions. set Opacity to a value greater than zero and select
either Mean Value or Brightest Point projection. while points further away are dimmed
linearly with distance. . To enable this feature. . Surface / Interior DepthCueing Depth cues
can contribute to the threedimensional quality of projection images by giving perspective to
projected structures. . Opacity Can be used to reveal hidden spatial relationships. Surface
DepthCueing works only on nearestpoint projections and the nearestpoint component of
other projections with opacity turned on. Z Project. Setting these thresholds permits making
background points those not belonging to any structure invisible. n of intensity in back to
intensity in front. of intensity in back to of intensity in front and is on when set at ltn i.
Grouped Z Project. you can strip away layers having reasonably uniform and unique intensity
values and highlight or make invisible inner structures. Zscaling eliminates the gaps seen in
projections of volumes with slice spacing greater than . Having independent depthcueing for
surface nearestpoint and interior brightestpoint allows for more visualization possibilities.
Two kinds of depthcueing are available Surface DepthCueing and Interior DepthCueing. The
surface Opacity parameter permits the display of weighted combinations of nearestpoint
projection with either of the other two methods. . . . depthcueing is turned o when set to zero
i. . often giving the observer the ability to view inner structures through translucent outer
surfaces.The ImageJ User Guide Image lower threshold or greater than the upper threshold.
This option is equivalent to using the Scale plugin from the TransformJ package to scale the
stack in the zdimension by the slice spacing in pixels. The depthcueing parameters
determine whether projected points originating near the viewer appear brighter.e. pixels. By
setting appropriate thresholds. The tradeo for this increased realism is that data points
shown in a depthcued image no longer possess accurate densitometric values.
New in IJ .. Help Opens http//imagej. .gov/ij/docs/menus/image. Improved in IJ . e. Text The
string to be drawn after each number when the Format chosen is either or Text label without
numeric sequence. .. Label. Adds a sequence of numbers e. Coordinates of the upper left
corner of the selection or the bounding rectangle for nonrectangular selections are displayed
in the graph title. Plot Zaxis Prole. Plot Pro le k . Requires a point or area selection. .nih.
Note that previously added overlays will be removed. an Interval of will create hour
increments. . labels will be created as nondestructive image overlays. K. Unpadded
sequence. Text Stamps only the contents of the Text eld. timestamps and/or a label to a
stack or hyperstack. Use overlay If checked. Format Species the structure of the label.
Numbers and label are drawn in the current foreground color cf. Converts the label into a
minutes seconds timestamp.g. Stacks Tools Insert. .. .htmllabel. . and Font size of the label
are based on the existing rectangular selection. Image Colors Color Picker. Plots the ROI
selection mean gray value versus slice number.The ImageJ User Guide Image .g. The initial
X. . . Slices outside the Range are not aected. . . See also Prole Plot Options. Pads each
number with leading zeros. Starting value and Interval Specify the rst value and the numeric
steps to be applied. if any. See also Make Montage. metric time values must be used. .Y
location. Note that with timestamps.. Converts the label into a hours minutes seconds
timestamp.
E. For a slices stack and a Reduction Factor of . . Reduces the size of stacks and
hyperstacks by the specied Reduction Factor. .H maxD . .g.. Color Picker. Virtual
stacks/hyperstacks are supported With Hyperstacks. K.. . . . .. See also Concatenate. . . ... If
Combine vertically is enabled. . . Combines two stacks WidthHeightDepth W H D and W H D
to create a new W W maxH .. . Reverse Alias for the Image Transform Flip Z command. the
default reduction is performed in the TDimension. . . height and data type. Unused areas in
the combined stack are lled with background color cf.. Concatenates two images or stacks
that have the same width. . Reduce. . . Tools Combine.D stack. a and a stack would be
combined to create one stack. See also Combine. . E. See also Hyperstacks Reduce
Dimensionality. the reduced stack will be be composed of slices with every second slice
being removed.The ImageJ User Guide Image .g.. but a choice is available to Reduce in
ZDimension instead. creates a new maxW W H H maxD ... Concatenate..D stack.
. taking into account a Border width. A range of images with increment e.. .g. Montage to
Stack. . Note that Group size must divide evenly into the stack size. . Grouped Z Project.
Improved in IJ . Inserts an image or stack into a stack at the specied X and Y Location. . it
does not work with hyperstacks. . . Make Substack. ... . New in IJ . .. See also Image
Duplicate. New in IJ . .. Converts a montage image to an image stack based on the specied
number of rows and columns. This is the opposite of what the Image Stacks Make Montage
command does. The Source Image or Stack must be of the same type as the Destination
Stack. . .g. D . It takes one of three types of input A range of images e. . . . Extracts selected
images from the active stack copying them to a new stack in the order of listing or ranging ..
.... . See also Image Stacks Z Project. Creates a substack of Stack size/Group size slices
with each slice being the result of a Z Projection performed over the range of Group size.g.
See also Demontager plugin . Insert. . . or a list of images e.The ImageJ User Guide Image .
See also Image Stacks Label. . Currently.
Open the Animation Options. Animation Options.. . images that have four D or ve D
dimensions see Stacks. Note that more than one stack can be animated at a time. and later.
See also File Save As Gif. . .The ImageJ User Guide Image . . .. . Stop Animation
Terminates animation of the active stack see Start Animation . . . . P sets the animation
speed as long as the unit used is sec. Selecting Start Animation animates the stack as soon
as the dialog is dismissed. Alt / Use this dialog to set the animation speed in frames per
second. the starting and ending frame. AVI. . Start Animation Animates the active stack by
repeatedly displaying its slices frames in sequence. . . Alt / dialog box to specify the
animation speed pressing Alt or rightclicking on the on the slider play/pause icon opens the
Animation Options. . stacks animation can be toggled using . Hyperstacks This submenu
contains commands that work with hyperstacks. . It is run more easily by clicking on the play
icon preceding stack sliders see Stacks. or to enable oscillating animations. To stop the
animation... As such.. dialog. . evoked by the same shortcut. . The frame rate is displayed in
the status bar. . setting the Frame Interval in Image Properties. click on the slider pause icon.
Note that with IJ . click on the image or use Stop Animation . This dialog can also be
accessed by rightclicking on the play/pause icon that precedes stack sliders and hyperstack
slice sliders see Stacks..
Slices z dimension and time Frames t dimension. Hyperstack to Stack Converts a
hyperstack into a stack in czt order. Checking Label Images will draw the channel number. ..
See also Hyperstacks . Converts a stack into a hyperstack. slices z and frames t within the
stack. slice number and frame number on each image in the hyperstack. Stacks not in czt
order will be shued to be in czt order.. Stack to Hyperstack. . . . RGB stacks are converted
into channel hyperstacks. Hyperstacks have Width. New Hyperstack. . . ImageJ hyperstacks
are always in czt order.. . File New Hyperstack. . Creates a new hyperstack. Image Type see
Image Type and Display Mode see Channels. . Channels c dimension.The ImageJ User
Guide Image . . Channels. See also Hyperstack to Stack . Order is the order of the channels
c. See also Stack to Hyperstack. Z. Color or Grayscale cf. . is an alias of this command.
Height. . Z can be specied. . The channel Display Mode can be Composite.
. Slices n to delete all but the current z slice and Frames n to delete all but the current time
point. Crop X Crops the image or stack based on the current rectangular selection. Shift Z is
the keyboard shortcut for this command. subtractive cyan. In addition. This command
reduces the dimensionality of an hyperstack by creating a new hyperstack with. Channels.
See also Hyperstack to Stack . Composite images are discussed with more detail in Color
Composites. . . for example. The same dropdown menu also provides a convenient list of
primary colors additive red. . . green and blue. Reduce Dimensionality.The ImageJ User
Guide Image . . .. Check Keep Source and the original stack will not be deleted. all the
channels and time points at a given z position or all the z slices for the current channel and
time point. Uncheck Channels n to delete all but the current channel. Z Opens the Channels
window. or brings it to the front if it is already open. several commands hosted in the Image
Color submenu can easily be accessed through the More dropdown menu. magenta. The
expected dimensions and size of the reduced stack are displayed in the dialog. This tool
allows to select the Display mode of composite images. yellow that can be used to
pseudocolor composite channels.
Scaled image/selection are copied to a new image named Title if Create new window is
checked. For stacks and hyperstacks it is possible to specify the range of Channels c.
Renames the active image. As with Image Size. particularly with graphics and text. D New in
IJ . . and check Average when downsizing with scale factors less than . Rename. . etc. hold
Alt to skip the dialog box. use integer scale factors . . . two resampling methods are possible
Bilinear and Bicubic interpolation. . With single images. Duplicate. Improved in IJ . Scale. E
Resizes the image or current area selection by scale factors entered into a dialog box. . . . If
scaling a selection that will not be copied to a new image check Fill with Background Color to
ll with the background color instead of zero. Creates a new window containing a copy of the
active image or rectangular selection.The ImageJ User Guide Image . . Also. . For the best
looking results. . . . . Entire stacks or hyperstacks in the Z Dimension will be scaled if Process
entire stack is checked. when downsizing. . Slices z and Frames t to be duplicated.
smoothing the source image prior to scaling may produce better looking results.
. . K. . see Use this dialog to rotate the active image or selection clockwise the specied
number of degrees. Set Grid Lines to a value greater than zero to superimpose a grid on the
image in Preview mode.. check Fill with Background Color to ll with the background color
instead of zero cf. Color Picker. . Transform This submenu contains commands that perform
geometrical image transformation on the active image or stack.The ImageJ User Guide
Image . . Rotate Degrees Right Rotates the entire image or stack clockwise . With bit and
RGB images.. Flip Z Reverses the order of the slices in a stack zmirror. Rotate. . .. . Flip
Vertically Turns the image or selection upside down ymirror. . Two resampling methods are
possible Bilinear and Bicubic interpolation cf. .. . Rotate Degrees Left Rotates the entire
image or stack counterclockwise . . . Image Size. Flip Horizontally Replaces the image or
selection with a xmirror image of the original.. Check Enlarge to Fit Result and the image will
be enlarged as needed to avoid clipping.. .
. and . you can translate either the current image or all the images in the stack. Translate. .
Check Preview to see how the translation will aect the image. In Improved in IJ . . .. .. Two
resampling methods are possible Bilinear and Bicubic interpolation cf. . shrinks the window.
Zooms in to next higher magnication level and. zooming with the arrow keys requires holding
down either Shift or Ctrl . When a selection exists.. Zooms out to next lower magnication
level and. . There are possible levels shown in the title bar . if needed. With stacks. . The and
or and keys are the preferred way to use the In and Out commands.... Out Improved in IJ .
As a shortcut. . . . See also AlignSlice and AlignRGBplanes plugins . . Image Size. . . . . if
possible. . ... .. Original Scale Displays the image at the magnication used when the image
was rst opened. . XV Scrolling Zoomed Images Hold down the space bar and drag to scroll a
zoomed image.The ImageJ User Guide Image . double click on the magnifying glass tool..
Translates moves the image in the x and y directions by a specied number of pixels. The
background at the edges of the image will be set to . enlarges the window. . . . .. Zoom This
submenu contains commands that control how the current image is displayed. . . .
. macros that exemplify the usage of most Image Overlay submenu commands. dialog to
have images automatically opened at magnication. Press Shift F Flatten F to create an RGB
image with the overlay embedded in it. MakeOverlay and ROI Color Coder. . . .
Nondestructive image overlays. To Selection Zooms in based on the current selection.
points. shapes and text. . Overlay This submenu contains commands for creating and
working with nondestructive image overlays. View Displays the image using magnication
image pixel screen pixel. . b to add the current selection to the overlay.g.. e. .. Set. Sets an
exact zoom to any open image beyond predened zoom levels. An overlay consists of one or
more selections arrows. Outputs from GridOverlay. .. Enable Open Images at in the Edit
Options Appearance. .The ImageJ User Guide Image . this command zooms the image to a
Fit to Screen level. II. . Press B Add Selection. Note that in the absence of a selection. . The
overlay is preserved when an image is saved in TIFF format cf. lines. .
. Stroke Color. The following table exemplies some decimal / hexadecimal equivalents Dec .
white and yellow or using hex notation. . . .. RGB colors that typically range from to can be
succinctly represented as two hexadecimal digits ranging from through FF. . FF .The ImageJ
User Guide Image . the stroke line color and width are ignored if a ll color is specied. . For
example. Hex A B C D E F . blue. E C A . . . RR the intensity of red. ROI Color Coder and
RG BtoHEX macros XVI Working With HEX Colors Hexadecimal notation hex is frequently
used in computing because it can summarize binary code in a humanfriendly manner. . Hold
Alt to skip the Add to Overlay dialog. . Add Selection. . ImageJs builtin macro function toHex
returns hexadecimal representations of decimal numbers and can be used to convert RGB
color values into hex color notation see RGBtoHEX macro. . See also Selection Properties.
Except for text selections. GG the intensity of green and BB the intensity of blue. or a digit
number in the form AARRGGBB where AA species the alpha blending value. . Previously
added overlays are removed if New Overlay is checked. The table below provides the
conversion of some RGB color triplets into hex notation. Colors are specied using the name
of one of the eight default colors black. Improved in IJ . displaying the dialog box depicted on
the left. red. . green. . . . XVI. . Hex color codes must be given as either a digit hexadecimal
number in the form RRGGBB opaque colors. . magenta. . Stroke Width and Fill Color to be
set. cyan. b Adds the current selection to the overlay. ROI Manager. y. . .
FFFF BFFFFF FFFFF FFFFF Red Orange . Image selections behave only partially as
regular selections e. Opacity values are thus obtained using /. .... .. A blending alpha value
can be specied in the Opacity eld. if any. . FFFF BFFFFF FFFFF FFFFF . Opacity of image
selections can be adjusted using Edit Selection Properties. . . Blue .Y location are based on
the existing rectangular selection. .. ROI Manager. . . . .The ImageJ User Guide Image
Hexadecimal notation of RGB colors. The initial X. . Alpha values can be omitted for fully
opaque colors. . Select Create image selection to create overlay images that can be moved
around the image. . From ROI Manager Creates an overlay from the selections on the ROI
Manager list see ROI Manager. . Opacity FF BFFF FFF FFF Cyan . Hide Overlay Causes
ImageJ to stop displaying the overlay displayed by Show Overlay. Add Image. . G. .g. can be
added to the ROI Manager list but cannot be resized or rotated. Show Overlay Displays an
overlay that was hidden by Hide Overlay. . . . FFC BFFFC FFFC FFFC Yellow . See also
Paste Control. As with RGB triplets. image selections are not saved in the TIFF header. . . .
In addition. FF BFFF FFF FFF List generated by the RGBtoHEX macro using the default
selection colors of ImageJ . . Adds an image to the overlay. B Magenta . FFFF BFFFFF
FFFFF FFFFF Green FF BFFF FFF FFF RGB Color R. Note that previously added overlays
will be removed. y. alpha values range from fully transparent to solid color. .
This command is equivalent to clicking on Apply in Image Adjust Brightness/Contrast. pixels
with a value of zero are white and pixels with a value are black. For bit images.The ImageJ
User Guide Image . .nih.gov/ij/ download/luts/luts. it is equivalent to clicking on Apply in
Image Adjust Threshold. at http//imagej. .. pixels values are not altered. Note that previous
items in the ROI Manager list will be deleted. . . Apply LUT Applies the current lookup table
function to each pixel in the image or selection and restores the default identity function.nih.
This modies the gray values so that when the image is viewed using the default grayscale
lookup table it will look the same as it did before. To ROI Manager Copies the selections and
images in the current overlay to the ROI Manager. .zip. For thresholded images. If no image
is open. Lookup Tables This submenu contains a selection of color lookup tables that can be
applied to grayscale images to produce falsecolor images.. . resized or recolored see ROI
Manager. unlike Plugins Utilities Capture Image. as a ZIP archive. which creates a
WYSIWYG What You See Is What You Get image that is the same size as its window.
Remove Overlay Permanently clears the overlay so that it cannot be restored using Show
Overlay. . .. a ramp image is created to display the color table.gov/ij/download/luts/ or. where
they can be edited moved. only the way the image is displayed on the screen. Flatten F
Creates a new RGB image that has the overlay rendered as pixel data. T. Unlike the Edit
Invert I command. the value v of each entry in the table is replaced by v. More than additional
lookup tables are available at imagej. .. With inverted LUTs. .. . The RGB image is the same
size as the active image. . Invert LUT Inverts the current lookup table. C. See also Macro
Toolset Switcher .
Find Edges Uses a Sobel edge detector to highlight sharp changes in intensity in the active
image or selection. lters. Process submenu Smooth S. including point operations. Smooth S
Improved in IJ . This lter replaces each pixel with the average of its neighborhood. and
arithmetic operations between multiple images . Increases contrast and accentuates detail in
the image or selection. The File Open Samples Blobs K B image will be used in most of the
illustrations of this section. The nal image is produced by combining the two derivatives using
the square root of the sum of the squares. Sharpen Improved in IJ . . Blurs the active image
or selection. Sharpen. . This lter uses the following weighting factors to replace each pixel
with a weighted average of the neighborhood . but may also accentuate noise.The ImageJ
User Guide Process Process This menu lists all commands related to image processing.
Two convolution kernels shown below are used to generate vertical and horizontal
derivatives. Find Edges and Enhance Contrast .
. Determines the local maxima in an image and creates a binary masklike image of the same
size with the maxima. . For RGB images. . Noise Tolerance Maxima are ignored if they do
not stand out from the surroundings by more than this value calibrated units for calibrated
images. Analysis is performed on the existing rectangular selection or on the entire image if
no selection is present. or one segmented particle per maximum. In other words. List
Displays the XY coordinates of each maximum in the Results window.The ImageJ User
Guide Process . which uses the Euclidian distance map. . . For accepting a maximum.
maxima of luminance are selected. Only one maximum within this area is accepted. . Count
Displays the number of maxima in the Results window. Maxima Within Tolerance All points
within the Noise Tolerance for each maximum. Exclude Edge Maxima Excludes maxima if
the area within the noise tolerance surrounding a maximum touches the edge of the image
edge of the selection does not matter. this area must not contain any point with a value
higher at than the maximum. a threshold is set at the maximum value minus noise tolerance
and the contiguous area around the maximum above the threshold is analyzed. marked .
Point Selection Displays a multipoint selection with a point at each maximum. Output Type
Can be seeProcess Find Maxima. . . outputs Single Points Results in one single point per
maximum. Segmented Particles Assumes that each maximum belongs to a particle and
segments the image by a watershed algorithm applied to the values of the image in contrast
to Process Binary Watershed. with the luminance dened as weighted or unweighted average
of the colors depending on how Weighted RGB to Grayscale Conversion is set in Edit
Options Conversions. Find Maxima.
Above Lower Threshold Thresholded images only Finds maxima above the lower threshold
only. . the area below the lower threshold is considered a background. but the
FindStackMaxima macro runs it on all the images in a stack and creates a second stack
containing the output images. The upper threshold of the image is ignored. Six outputs are
possible Single Points. List and Count. Exclude Edge Maxima applies to the maximum. .
Maxima Within Tolerance. as it is in the Cell Colony image in the illustration below. . Note
that Segmented Particles will usually result in particles touching the edge if Exclude Edge
Maxima is selected. . does not work on stacks. using an inverted or normal LUT depending
on the Black Background option in Process Binary Options.gov/ij/docs/menus/process.
ImageJ . Help Opens http//imagej. Light Background To be checked if the image background
is brighter than the objects to be found. The number of particles as obtained by Analyze
Analyze Particles. . . . . . If Segmented Particles is selected as Output Type. Output is a
binary image. .The ImageJ User Guide Process Process Find Maxima. Points at maxima
Multipoint selection Segmented Particles ROIs obtained with Analyze Analyze Particles. to
the ROI Manager. . Find Maxima. . . in the output image does not depend on the selected
Output Type. This option cannot be used when nding minima image with light background
and inverted LUT. . with foreground and background .htmlndmaxima.nih. Segmented
Particles. . not to the particle. Point Selection. The FindMaximaRoiManager macro
demonstrates how to add particles found by Find Maxima.s.
Use Stack Histogram If checked. See also Brightness/Contrast. Normalize All n Slices. for
oat images. Enhance Contrast Enhances image contrast by using either histogram stretching
or histogram equalization. Create a selection and the equalization will be based on the
histogram of the selection. Increasing this value will increase contrast. Saturated Pixels
Determines the number of pixels in the image that are allowed to become saturated. Uses a
modied algorithm that takes the square root of the histogram values. normalization will be
applied to all slices in the stack. ImageJ will recalculate the pixel values of the image so the
range is equal to the maximum range for the data type. and thus this option will not be
available on RGB images. If checked. is displayed.The ImageJ User Guide Process . XI .
ImageJ will use the overall stack histogram instead of individual slice histograms. each slice
in the stack is adjusted independently. . . that allow optimal adjustments for each slice alone.
. Note that normalization of RGB images is not supported. The maximum range is for bit
images and for bit images. or . The Saturated Pixels and Normalize parameters are ignored
when Equalize Histogram is checked. Noise Use the commands in this submenu to add
noise to images or remove it. . Both methods are described in detail in the Hypermedia
Image Processing Reference Contrast Stretching and Histogram Equalization. ImageJ will
enhance the image using histogram equalization . The contrast stretch performed on the
image is similar to the Auto option in the Brightness/Contrast. according to the optimal for
that slice alone if Use Stack Histogram is unchecked. This value should be greater than zero
to prevent a few outlying pixel from causing the histogram stretch to not work as intended.
Equalize Histogram If checked. except that with stacks. C window. This command does not
alter pixel values as long as Normalize. Hold Alt to use the standard histogram equalization
algorithm. . This option may be specially relevant when performing enhancements based on
a ROI. C . Normalize If checked. Equalize Histogram or Normalize All n Slices in the case of
stacks are not checked. With stacks another checkbox.
. Add Noise and Remove Outliers. . This command only works with bit images. Exponential.
Despeckle. .. Add Noise Adds random noise to the image or selection. . . The noise is
Gaussian normally distributed with a mean of zero and standard deviation of . of the pixels
with black pixels and . Poisson and Uniform a Java package for image randomization by Erik
Meijering .. Despeckle This is a median lter. . for each pixel in the selection. with white pixels.
. Add Specied Noise. . Median lters are good at removing salt and pepper noise. the nine
pixels in the neighborhood must be sorted and the center pixel replaced with the median
value the fth. See also RandomJ Binomial. Adds Gaussian noise with a mean of zero and a
chosen standard deviation. Gamma.. . It replaces each pixel with the median value in its
neighborhood. This is a time consuming operation because.The ImageJ User Guide Process
Process Noise Salt and Pepper. Gaussian. Salt and Pepper Adds salt and pepper noise to
the image or selection by randomly replacing .
e. hot pixels or dead pixels of a CCD camera. Northeast. in raw uncalibrated units. . Radius
Determines the area uncalibrated. The commands use Convolve . in pixels used for
calculating the median. The illustration below shows four of the Shadows convolution
kernels. and West kernels. Replaces a pixel by the median of the pixels in the surrounding if
it deviates from the median by more than a certain value the threshold. Which Outliers
Determines whether pixels brighter or darker than the surrounding the median should be
replaced. Shadows Commands in this submenu produce a shadow eect. North.. Binary This
submenu contains commands that create or process binary black and white images. Run
Process Filters Show Circular Masks. e. They assume that objects are black and background
is white unless unless Black Background is checked in the Process Binary Options. ImageJs
convolution function. i. East. Remove Outliers. to see how radius translates into an area. .
South. Southeast. dialog box. Threshold Determines by how much the pixel must deviate
from the median to get replaced.The ImageJ User Guide Process .. . Southwest and West.
Original Shadows North. Northwest. See also Despeckle . . The Shadows Demo command
uses all eight kernels to demonstrate the speed of Convolve . . ..g. . Useful for correcting.
with light appearing to come from a direction corresponding to the command name East.
South. .
. otherwise the calculated threshold of the currently displayed slice will be used for all slices .
T. . If a threshold has not been set. . See also Edit Selection Convert to Mask. . . With stacks.
the depicted dialog is displayed. white background checkbox reects and sets the global Black
Background value of Process Binary Options. the depicted dialog is displayed. Note that for
nonthresholded images and stacks Make Binary and Convert to Mask behave similarly.
automatic threshold levels will be calculated cf. dialog box. If a threshold has not been set...
Note that for nonthresholded images and stacks Make Binary and Convert to Mask behave
similarly. T tool. The value of the Black foreground.The ImageJ User Guide Process
Summary of morphological operators Process Binary Original Make Binary Erode Dilate
Open Close submenu. Outline Skeletonize Adjust Threshold. . . Make Binary Converts an
image to black and white. . XVII . . With stacks the Convert to Mask dialog box is displayed. .
T Minimum. or of the entire image if there is no selection is present and set an automatic
threshold level to create the binary image Autothresholding is displayed in the Status bar. . If
a threshold has been set using the Image Adjust Threshold. grayscale grayscale Erode then
Dilate Dilate then Erode pixel wide outline pixel wide skeleton . . Calculate Threshold for
Each Image If checked. Make Binary will analyze the histogram of the current selection.
Maximum. . threshold levels will be calculated for each individual slice. Threshold. The mask
will have an inverting LUT white is and black is unless Black Background is checked in the
Process Binary Options. Make Binary. Convert to Mask Converts an image to black and
white. . cf.
. to perform grayscale dilation. . Dilate Adds pixels to the edges of black objects. . so that
black is and white is cf. . Use Filters Minimum. See also Make Binary. Process Binary Make
Binary .The ImageJ User Guide Process Black Background Denes whether the background
is black and the foreground is white. T Apply By default these commands will produce binary
images with inverted LUTs.. . Use Filters Maximum. . . . . Edit Selection Convert to Mask.
Edit Selection Create Mask . . See also Binary Options.e. . .. Process Binary Convert to
Mask . XVII XVII Creating Binary Masks Four ImageJ commands can be used to create
binary masks . Image Adjust Threshold. This choice can be conrmed when running Make
Binary and Convert to Mask on thresholded images. . Erode Removes pixels from the edges
of black objects. . before running the above commands i. . . to perform grayscale erosion. .
Note that the value of this checkbox reects and sets the global Black Background value of
Process Binary Options. This behavior can be reversed by checking Black Background in
Process Binary Options. . See also Binary Options. an inverting LUT will not be used black
will be and white . Invert LUT. It can also be imposed at startup see Settings and
Preferences.
The ImageJ User Guide
Process
..
Open
Performs an erosion operation, followed by dilation. This smoothes objects and removes
isolated pixels.
See also Binary Options. . .
..
Close
Performs a dilation operation, followed by erosion. This smoothes objects and lls in small
holes. The command has a tailing hyphen to dierentiate it from File Close w .
See also Binary Options. . .
..
Outline
Generates a one pixel wide outline of foreground objects in a binary image. The line is drawn
inside the object, i.e., on previous foreground pixels. .. Fill Holes
This command lls holes connected background elements in objects by lling the background .
.. Skeletonize
Improved in IJ .
Repeatably removes pixels from the edges of objects in a binary image until they are
reduced to single pixel wide skeletons topological skeletons.
See also SkeletonizeD plugin
..
Distance Map
Generates a Euclidian distance map EDM. Each foreground pixel in the binary image is
replaced with a gray value equal to that pixels distance from the nearest background pixel.
The output type Overwrite, bit, bit or bit of this command can be set in the Binary Options. . .
dialog box. Note that when selecting Overwrite or bit output, distances larger than are
labelled as .
The ImageJ User Guide
Process
..
Ultimate Points
Generates the ultimate eroded points UEPs of the EDM. Requires a binary image as input.
The UEPs represent the centers of particles that would be separated by segmentation. The
UEPs gray value is equal to the radius of the inscribed circle of the corresponding particle.
The output type Overwrite, bit, bit or bit of this command can be set in the Binary Options. . .
dialog box. .. Watershed
Watershed segmentation is a way of automatically separating or cutting apart particles that
touch. It rst calculates the Euclidian distance map EDM and nds the ultimate eroded points
UEPs. It then dilates each of the UEPs the peaks or local maxima of the EDM as far as
possible either until the edge of the particle is reached, or the edge of the region of another
growing UEP. Watershed segmentation works best for smooth convex objects that dont
overlap too much. Enable debugging in Edit Options Misc. . . and the Watershed command
will create an animation that shows how the watershed algorithm works cf. online example.
Original Segmentation Movie Watershed result
Process Binary Watershed running in Debug mode. See also Find Maxima. . .
..
Voronoi
Splits the image by lines of points having equal distance to the borders of the two nearest
particles. Thus, the Voronoi cell of each particle includes all points that are nearer to this
particle than any other particle. When particles are single points a Voronoi tessellation also
known as Dirichlet tessellation is performed. The output type Overwrite, bit, bit or bit of this
command can be set in the Process Binary Options. . . dialog box. In the output, the value
inside the Voronoi cells is zero the pixel values of the dividing lines between the cells are
equal to the distance to the two nearest particles. This is similar to a medial axis transform of
the background, but there are no lines in inner holes of particles.
The ImageJ User Guide
Process
See also DelaunayVoronoi plugin
Original Voronoi Ultimate Points
Original
Distance Map
Ultimate Points
Watershed
Voronoi
Process Binary
commands.
..
Options. . . Species several settings used by Binary mands. com
Iterations Species the number of times erosion, dilation, opening, and closing are performed.
Iterations can be aborted by pressing Esc . Count Species the number of adjacent
background pixels necessary before a pixel is removed from the edge of an object during
erosion and the number of adjacent foreground pixels necessary before a pixel is added to
the edge of an object during dilation. Black background If checked, binary images will be
created without using an inverted LUT cf. XVII and commands in the Process Binary
submenu will assume that images contain white objects on a black background. Macros can
set this option using the setOptionquotBlackBackgroundquot, true macro function cf. Settings
and Preferences. Pad edges when eroding If checked, Binary Erode does not erode from the
edges of the image. This setting also aects Binary Close, which erodes from the edges
unless this checkbox is selected. EDM output Determines the output type for the Binary
Distance Map, Ultimate Points and Voronoi commands. Set it to Overwrite for bit output that
overwrites the input image bit, bit or bit for separate output images. bit output has oating
point subpixel distance resolution.
nih. Close on the active image.. The dividebyzero value can be redened using Edit Options
Misc. Adds a constant to the image or selection. results greater than are set to . dividing by
zero results in Innity. . With stacks.. etc. . Help Opens http//imagej. . results greater than . . a
constant to each pixel in the active image or selection. . Math The commands in this
submenu add subtract. . are set to . . . Open.gov/ij/docs/menus/process.. . Dilate. Subtract.
Except for bit oat images. the dialog depicted on the left is displayed. Multiplies the image or
selection by the specied real constant. With bit signed images. With bit images. Choose Yes
to process entire stack or No to process only the active slice. . . attempts to divide by zero
are ignored. . multiply. Innity or NaN / pixels when the source pixels are positive. . See also
Memory amp Threads. . . With bit signed images. are set to . . This option is only available
when the active image is binary. With bit images. results less than are set to . . Add. negative
or zero.The ImageJ User Guide Process Do This dropdown menu allows to test the chosen
settings by previewing each binary operation Binary Erode.. results greater than are set to . A
Preview option is available for most operations. Divide. . Subtracts a constant from the image
or selection. With bit and bit images. results greater than . The dialog is not displayed if Hide
quotProcess Stackquot dialog is checked in Edit Options Misc. . Divides the image or
selection by the specied real constant. .htmloptions.. Multiply. . . With bit images.
. . .The ImageJ User Guide Process . XOR. the image min and max are used for scaling
instead of . where . / ln... Pixels in the image with a value greater than the specied constant
are replaced by the constant. For RGB images. this function is applied to all three color
channels. Does a bitwise XOR of the image and the specied binary constant. . .. For oat
images. . . See also GammaCorrectionTool macro . Does a bitwise OR of the image and the
specied binary constant. . . For RGB images.. . Max. For bit images. . . Min. Applies the
function f p p/ to each pixel p in the image or selection. . this function is applied to all three
color channels. For bit images. applies the function f p lnp / ln to each pixel p in the image or
selection.. the image min and max are used for scaling instead of . AND. . Fills the image or
selection with the specied value. Does a bitwise AND of the image and the specied binary
constant... . Pixels in the image with a value less than the specied constant are replaced by
the constant. Gamma. . . . .. no scaling is done. Log For bit images. . OR. . Set. multiply the
result of this operation by . . To calculate log of the image. .
. . the Apply option in Image Adjust Threshold..POSITIVEINFINITY f/f or Float.
NEGATIVEINFINITY f/f are ignored when making measurements on bit oat images. The
MathMacroDemo macro demonstrates the usage of this command. For oat images. T runs
this command.. NaN Background Sets nonthresholded pixels in bit oat images to the NaN
Not a Number value.. This command performs image arithmetic using an expression specied
by the user . . Only works with bit oat images. See also Expression plugin . . . Reciprocal
Generates the reciprocal of the active image or selection. It can be used to create
fullysynthetic images or to perform precise pixel manipulations on existing images. . Abs
Generates the absolute value of the active image or selection. Exp Performs an exponential
transform on the active image or selection. Square Performs a square transform on the
active image or selection. . Square Root Performs a square root transform on the active
image or selection. Macro..The ImageJ User Guide Process . .. .. . Pixels with a value of
Float. Works only with bit oat or signed bit image images. Float.NaN f/f..
the same spatial frequency appears twice in the power spectrum. If the mouse is over an
active frequency domain FFT window. Two FFT dedicated tutorials are available on the
ImageJ website FFT Measurements and FFT Filtering.g. All other ImageJ commands only
see the power spectrum. however. With ocenter selections. The frequency domain image is
stored as bit oat FHT attached to the bit image that displays the power spectrum. The angle
is expressed in degrees. possible to both lter and pass during the same inverse transform. at
points opposite from the center. . editing and processing. You can lter or mask spots on the
transformed frequency domain image and do an inverse transform to produce an image
which only contains the frequencies selected or which suppresses the frequencies selected. .
such as Inverse FFT. m. . They are based on an implementation of the D Fast Hartley
Transform FHT contributed by Arlo Reeves. . . P or Analyze Set Scale. It is not. . FFT The
commands in this submenu support frequency domain display.. Note that areas to be ltered
in the frequency domain image must be zero lled and areas to be passed must be lled with
..The ImageJ User Guide Process . mm/c if the spatial scale of the image was dened using
Image Properties. Commands in this submenu. The radius is expressed in units per cycle e.
FFT Computes the Fourier transform and displays the power spectrum. . You can verify that
this is the case by moving the cursor over a lled area and observing that the values displayed
in the status bar are either or . Bob Doughertys D Fast Hartley Transform plugin performs D
FHTs . Black areas pixel value cause the corresponding frequencies to be ltered removed
and white areas pixel value cause the corresponding frequencies to be passed. its location is
displayed in polar coordinates. not on the bit power spectrum. It is sucient to ll / clear only
one of these. . while the radius is expressed in pixels per cycle p/c. Polar coordinates of
measured point selections are recorded by Analyze Measure. Use ImageJs selection tools
and ll / clear commands to draw black or white areas that mask portions of the transformed
image. Inverse FFT Computes the inverse Fourier transform. operate on the bit FHT. the
author of the ImageFFT spino of NIH Image.
It consists of an bit image of the power spectrum and the actual data. . .. enhancing the
visibility of components that are weakly visible. FFT Options. . Display Fast Hartley
Transform The internal format used by the command. This command allows you to start over
after misediting the bit power spectrum image. which is based on a Hartley transform rather
than Fourier transform. The power spectrum image is displayed with logarithmic scaling. The
actual data are used for the Inverse FFT command. Displays the FFT Options dialog box.
Display Raw Power Spectrum The power spectrum without logarithmic scaling.The ImageJ
User Guide Process Original Power spectrum with mask that lters low frequencies Result of
inverse transform Power spectrum with mask that passes low frequencies Result of inverse
transform FFT Example of low frequencies ltering. The rst group of checkboxes species
which images are created by the FFT command Display FFT Window The standard output.. .
. which remain invisible for the user. Original Edited power spectrum Inverse transform
Power spectrum after ltering FFT Example of low frequencies ltering. Redisplay Power
Spectrum Recomputes the power spectrum from the frequency domain image bit FHT.
Note that these values are both half the spatial frequencies of the actual cuto. more than a
factor of or so. Autoscale After Filtering If checked. preserving all intensities. . the current
image is transformed immediately when closing the FFT Options dialog. Tolerance of
Direction This is for Suppress Stripes.The ImageJ User Guide Process Display Complex
Fourier Transform A stack with two slices for the real and imaginary parts of the FFT. Filter
Large Structures Up to Determines the amount of smoothing. . Removal of horizontal stripes
is similar to subtracting an image that is only blurred in the horizontal direction from the
original. Suppress Stripes Select whether to eliminate Horizontal or Vertical stripes. ..
Removes high spatial frequencies blurring the image and low spatial frequencies similar to
subtracting a blurred image. the image is extended in size by attaching mirrored copies of
image parts outside the original image. The cuto is very soft. Filter Large Structures Down to
Smooth variations of the image with typical sizes of bright or dark patches larger than this
value are suppressed background. puts the lowest intensity to and the highest intensity to .
Saturate Image when Autoscaling If checked. so the bandpass will noticeably attenuate even
spatial frequencies in the center of the bandpass unless the dierence of the two values is
large say. Saturate Image when Autoscaling only has an eect when Autoscale After Filtering
is enabled. It can also suppress horizontal or vertical stripes that were created by scanning
an image line by line . allows some intensities to go into saturation. and produces a better
visual contrast. Bandpass Filter. higher values remove shorter stripes and/or stripes that are
running under an angle with respect to the horizontal vertical direction. Do Forward
Transform If checked. The Bandpass Filter uses a special algorithm to reduce edge artifacts
before the Fourier transform. . thus no jumps occur at the edges. Objects in the image
smaller than this size are strongly attenuated.
. . It does this by converting Image and Image to the frequency domain. These three
operations in the frequency domain are equivalent to correlation. convolution and
deconvolution in the space domain. Otherwise. . This command does Fourier space ltering of
the active image using a usersupplied spatial domain nonFFT image as the lter. FD Math.
convolves or deconvolves two images. . This image will be converted to bit. see the
FFTCustomFilterDemo and FFTRemoveStreaks macros. This command correlates. artifacts
can occur. then converting the result back to the space domain. the corresponding spatial
frequencies will be blocked. Refer to the DeconvolutionDemo and MotionBlurRemoval
macros for examples. For pixels that have a value of . . . For some examples. shows the lter
generated. y height/ should have the same value. Custom Filter. . Note that the lter should be
symmetric with respect to inversion of the center Points that are opposite of the center point
dened as x width/.. performing conjugate multiplication or division. Pixel with values of should
be used for passing the respective spatial frequencies without attenuation.. Note that this
disables Undo of the lter operation on the original image.The ImageJ User Guide Process
Display Filter If checked.
not the actual FHT data. . . mean. Gaussian. editing an image with swapped quadrants for
ltering or masking may lead to undesired results. . the input image is eectively extended by
duplicating edge pixels outward. . . The destination pixel is calculated by multiplying each
source pixel by its corresponding kernel coecient and adding the results. Therefore.. A kernel
is a matrix whose center corresponds to the source pixel and the other elements correspond
to neighboring pixels. More information on image lters can be obtained by looking up related
keywords convolution. on the Hypermedia Image Processing Reference index. If needed.
dilate. . Convolve. NonFFT Original Swapped For Fourier transforms.. Does spatial
convolution using a kernel entered into a text area. Filters This submenu contains
miscellaneous lters including those installed by the Plugins Utilities Install Plugin. . etc.The
ImageJ User Guide Process . See also Memory amp Threads. . unsharp. Swap Quadrants
aects only the image displayed. erode. Original Swap Quadrants FFT Swapped This
command transforms between the user friendly display of Fourier transforms with the lowest
frequencies at the center and the native form with the lowest frequencies at the four corners.
Swap Quadrants swaps quadrants I with III and II with IV counterclockwise starting from
Northeast so that points near the center are moved towards the edge and vice versa. . There
is no arbitrary limit to the size of the kernel but it must be square and have an odd width.
command. Another way to see this command is to imagine that the image is periodically
repeated and the origin is shifted by width/ in x and by height/ in y direction. median.
Sigma is the radius of decay to e. .The ImageJ User Guide Process Rows in the text area
must all have the same number of coecients. Like all ImageJ convolution operations. See
also Accurate Gaussian Blur plugin.q. the standard deviation of the Gaussian this is the
same as in Adobe Photoshop . AnimatedGaussianBlur macro . . . Smooths the current image
by replacing each pixel with the neighborhood mean.. . The kernel shown is a Mexican hat.
Kernels can be pasted into the text area using Ctrl V .g.. Thus. with a blur radius of e. . the
rows must be terminated with a carriage return. Mean. Median..e. . . it assumes that
outofimage pixels have a value equal to the nearest edge pixel. when smoothing with very
high blur radius. the image will be replaced by the average of the four corner pixels. . .
preserving image brightness. .. This lter uses convolution with a Gaussian function for
smoothing . Gaussian Blur. . See also ConvolutionDemo macro . Note that kernels can be
saved as a text le by clicking on the Save button. scaled to a reasonable size using Image
Adjust Size.java. the lines rows or columns of the image are downscaled before convolution
and upscaled to their original length thereafter. the output will be dominated by the edge
pixels and especially the corner pixels in the extreme case. . cf. . Reduces noise in the active
image by replacing each pixel with the median of the neighboring pixel values. i. . Checking
Normalize Kernel causes each coecient to be divided by the sum of the coecients. but
dierent from ImageJ versions till . . and plotted using Analyze Surface Plot. except for small
blur radii. in which radius was . . and the coecients must be separated by one or more
spaces. . displayed as an image using File Import Text Image. which does both smoothing
and edge detection in one operation. and higher weight to corner pixels than noncorner
pixels at the edge. GaussianBlur. For increased speed. This gives higher weight to edge
pixels than pixels inside the image.
Gaussian Blur. . Minimum. . Unsharp masking subtracts a blurred copy of the image and
rescales the image to obtain the same contrast of large lowfrequency structures as in the
input image. whereby M askW eight would be an innite weight of the highpass ltered image
that is added. . .. and Variance. cf. Radius The standard deviation blur radius. .. . . Maximum.
.. . . Binary Dilate . . Mean. . . This lter does grayscale erosion by replacing each pixel in the
image with the smallest pixel value in that pixels neighborhood.. Unsharp Mask. Generates a
stack containing examples of the circular masks used by the Median. Increasing the Mask
Weight value will provide additional edge enhancement. . This is equivalent to adding a
highpass ltered image and thus sharpens the image. . . . . . Maximum. Highlights edges in
the image by replacing each pixel with the neighborhood variance. . . . . Increasing the
Gaussian blur radius will increase contrast. . .The ImageJ User Guide Process . Binary
Erode . Sharpens and enhances edges by subtracting a blurred version of the image the
unsharp mask from the original. . This lter does grayscale dilation by replacing each pixel in
the image with the largest pixel value in that pixels neighborhood.. Minimum. . lters for
various neighborhood sizes. . . Show Circular Masks. Mask Weight Determines the strength
of ltering. of the Gaussian blur that is subtracted. Variance.
. In the case of TIFF images saved with active selections measurements are performed on
the ROI and not the whole image. m command in all images of the chosen directory. ..
Selects the destination folder where the processed images will be stored. Three critical
aspects to keep in mind when performing batch operations that modify processed images
Files can be easily overwritten since the batch processor will silently override existing les
with the same name. Input. i. In the case of nonnative formats. See also Analyze Set
Measurements.. Selects the source folder containing the images to be processed.. This
command measures all the images in a userspecied folder.. . . batch operations will be
inuenced by the behavior of the reader plugin or library cf. Convert. Measure.e. .. . . Batch
converts and/or resizes multiple images from a specied folder. . . Output. . .. Batch
commands are nonrecursive. . The destination Output folder should have adequate disk
space to receive the created images. Nonnative Formats. by running the Analyze Measure.
Nevertheless a directory hierarchy can be transversed using ImageJ macro language cf.
Note that measurements are performed on non thresholded images. Batch This submenu
allows the execution of commands in a series of images without manual intervention.The
ImageJ User Guide Process . Batch Macro.. . . they are applied to all the images of the
chosen Input folder but not its subfolders. BatchProcessFolders macro.
.. Other statements can be pasted from the macro recorder or ImageJs editor while the
dialog box is opened . Add Macro Code This dropdown menu contains macro snippets that
can be combined to create the processing macro. E. E. GIF. FITS. ZIP or Raw cf. . Selects
the source folder containing the images to be processed. .. Interpolation The resampling
method to be used in case Scale Factor is not .. . PNG. Text Image. . cf. Output Format
Species the output format that can be set to TIFF. Selects the destination folder where the
processed images will be stored. Output. Runs a macro over all the images in a specied
folder. folder the processed image will be displayed. When editing the macro beware of any
statements that may interfere with the normal operation of the batch processor such as Close
or Open calls. . Image Size. Open.htmlraw. Input. . bit TIFF. . JPEG. Saves the assembled
macro. PNG. FITS. . Image Scale. . Test Tests the macro on the rst image of the Input.
Image Types and Image Formats and File Save As submenu. . . BMP. Previously written
macros can be imported using Open. . . Macro. JPEG. . Scale Factor Species if images
should be resized cf. and Image Scale.The ImageJ User Guide Process Output Format
Species the output format that can be set to TIFF. . . bit TIFF. . Help Opens http//imagej. Text
Image. PGM.nih. BMP. PGM. Imports previously written macros. Save. Image Types and
Image Formats and File Save As submenu. GIF. ZIP or Raw cf.gov/ij/docs/menus/le...
. . BatchProcesser.. If both are stacks. Batch Virtual Stack. . . . . Click Process to create the
cropped virtual stack Note that cropped images are not loaded into memory but are saved to
disk as they are cropped see Virtual Stacks.java. that shares the same interface of Batch
Macro. . cf. The dividebyzero value can be redened in Edit Options Misc. . . Operation
Selects one of the thirteen available operators see Image Calculator.The ImageJ User Guide
Process See also Plugins Macros Record. the result of the operation replaces some or all of
Image. Select an Output folder and Output format . operations.. . Edit the macro code as
needed and press the Test button to verify the macro . a new image or stack will be created
to hold the result. With bit oat images. Select Crop from the Add Macro Code dropdown
menu . . . Create New Window If checked. . Image and Image do not have to be the same
data type or the same size. . E. Run Process Batch Virtual Stack.g. pixels resulting from
division by zero are set to Innity. Virtual Stack. Image or both Image and Image can be
stacks. they must have the same number of slices. Performs arithmetic and logical
operations between two images selected from popup menus. . . Cropping a virtual stack can
be performed by executing the following steps . . . allows virtual stack manipulations. . This
command. Otherwise. . . Image Calculator. or to NaN Not a Number if a zero pixel is divided
by zero. Open a virtual stack .
Image Calculator. . command. Note that calculations between images can also be
performed using copy and paste and the Edit Paste Control. . img Max img maximg. On
these examples source and destination images bit grayscale are displayed with inverted
LUTs White . operations. .nih. the source images will be converted to bit oating point before
the specied operation is performed.htmlcalculator.gov/ij/docs/menus/process. Black cf. Help
Opens http//imagej. Lookup Tables submenu. img Average img img img/ Dierence img img
img Copy img img Transparentzero Result .The ImageJ User Guide Process bit oat Result If
checked. Source image img Operator Add img img img Subtract img img img Multiply img
img img Divide img img img AND img img img OR img img img XOR img img img Result
Destination image img Operator Min img minimg. .
Rolling Ball Radius The radius of curvature of the paraboloid. Imagine a D surface with the
pixel values of the image being the height. the radius should be inversely proportional to the
pixel value range e. for bit or RGB images it should be at least as large as the radius of the
largest object in the image that is not part of the background. The sliding paraboloid typically
produces more reliable corrections since the rolling ball. Create Background can be also
used for custom background subtraction algorithms where the image is duplicated and ltered
e. for bit images pixel values .g.g. The sliding paraboloid algorithm does not use downscaling
and thus produces no downscaling artifacts. the command will use a more robust
implementation of the algorithm that uses an approximation of a paraboloid of rotation
instead of a ball. Removes smooth continuous backgrounds from gels and other images.
typical values of the radius are around . removing holes in the background before creating
the background and nally subtracting it with Process Image Calculator... Light Background
Allows the processing of images with bright background and dark objects.The ImageJ User
Guide Process . the operation will only aect the brightness. The rolling ball algorithm requires
a radius of at least . Larger values will also work unless the background of the image is too
uneven. the output is not the image with the background subtracted but rather the
background itself. . Subtract Background. Separate Colors RGB images only If unchecked. If
Sliding Paraboloid is checked. . to . since it does not really use a paraboloid an exact
implementation . leaving the hue and saturation untouched. This option allows any value of
the radiusgt . the rolling ball is replaced by a paraboloid that has the same curvature at the
apex as a ball of that radius. Nevertheless. to reduce the computing time the rolling ball
algorithm downscales the image in a way that is not really consistent.g. As a rule of thumb.
IEEE Computer. then a ball rolling over the back side of the surface creates the background.
a legacy algorithm. Biomedical image processing. This option is useful for examining the
background created in conjunction with the Preview option. Jan . Create Background Dont
Subtract If checked. E. the sliding paraboloid is also an approximation. Sliding Paraboloid If
checked. . Based on the rolling ball algorithm by Stanley Sternberg see Sternberg S. is prone
to edge artifacts. . For bit and bit images with pixel value ranges dierent from .
gov/ij/docs/menus/process.htmlbackground. Lan dini. The Edit Undo and File Open
commands are skipped. images are maximumltered pixels to remove outliers such as dust
and then smoothed to reduce noise average over pixels. Help Opens http//imagej. Disable
Smoothing For calculating the background rolling the ball.nih. Repeat Command R Reruns
the previous command. Check this option to make sure that the image data after subtraction
will never be below the background. See also Undo and Redo . With Disable Smoothing
checked. command. Background subtractor. . The radius should be set to at least the size of
the largest object that is not part of the background. the unmodied image data are used for
creating the background. Rolling Ball Background Subtraction the plugin that implemented
this command in versions up to . See also How to correct background illumination in brighteld
microscopy by G.The ImageJ User Guide Process would require a great computing eort but
it rather slides parabolae in dierent directions over the image. This command uses a sliding
paraboloid or a legacy rolling ball algorithm that can be used to correct for uneven illuminated
background as shown in the proles Analyze Plot Prole k below each image.e Original Image
Corrected Image Process Subtract Background. . . Auto Local Threshold.
Intensity statistics Mean. Point Tool. Line Selection Tools length and angle straight lines only
are also calculated. . m will paint invasively a mark over the measured point in foreground
color unless Mark Width in the Point Tool options dialog box is set to zero cf.The ImageJ
User Guide Analyze Analyze This menu contains commands related to statistical
measurements on image data. the following parameters can be recorded Length. For Point
selections cf. line lengths and angles. See also The Results Table. amp Max. . Shape
Descriptors. etc. Centroid. With line selections. . Kurtosis and Area Fraction. Analyze
Particles. Bounding Rectangle. results are calculated using brightness values. Measure. With
area selections. . Batch Measure. . Performed measurements can be specied in the Set
Measurements. Ferets Diameter. are calculated from the values of the pixels along the line.
Set Mea surements. . Summarize. With RGB images. blue if Weighted RGB Conversions is
checked in Edit Options Conversions. The mean. . . Skewness. Center of Mass. . . prole and
histogram plotting and plugins related to image analysis. . . and Bounding Rectangle. cf.
Perimeter. Median. . dialog box. Note that Measure. calculates and displays on the Results
table either area statistics. Tools. red . m Based on the selection type. Distribution. Point Tool
and Multipoint Tool. Standard Deviation and Integrated Density can be performed on area.
line and multipoint selections. Segmented and Freehand lines. . . Area statistics are
calculated for the complete image if there is no selection or for a selected subregion dened
by one of the rst four tools in the toolbar cf. . the X and Y coordinates are recorded. Min.
Gray Value. . . Angle straight lines only. RGB pixels are converted to brightness values using
the formula value red green blue/ or value . green . For linear selections Straight. or point
coordinates. . standard deviation. Fitted Ellipse. . . the following parameters can be recorded
Area. Modal. .
measures it using the Measure. . . It then outlines the object using the Wand Tool. ... Size
Circ. .. .. T or Color Threshold. . Particle Analyzer Analyze Analyze Particles. Size Circ. For
spatial scaled images cf. Original thresholded Size Circ. Improved in IJ . . Values may range
between and Innity. . . Analysis is performed on the existing area selection or on the entire
image if no selection is present. Analyze Particles. . Exclude on Edges Include Holes Size
Circ. . . Set Scale.The ImageJ User Guide Analyze . . . It works by scanning the image or
selection until it nds the edge of an object. Features of thresholded images can be extracted
by specifying suitable Size and Circularity ranges and/or by choosing if particles should be
traced by their outer edge or by ood lling Include Holes checkbox. . Press Esc to abort this
process. . lls it to make it invisible. . . This command counts and measures objects in binary
or thresholded images Image Adjust Threshold. Size Particles with size area outside the
range specied in this eld are ignored. . m command. then resumes scanning until it reaches
the end of the image or selection.
Set Measurements. Ellipses bit binary image containing the best t ellipse cf. Labels . Note
that with IJ . Outlines bit image containing numbered outlines of the measured particles
graylevels Outlines . . . Overlay Masks Displays lled outlines of the measured particles in the
image overlay. Circularity P erimeter . Bare Outlines bit image containing simple outlines of
the measured particles without labels graylevels Outlines .e and later. Summarize If checked.
Background . average particle size. the particle analyzer will display a blank image when the
count of detected particles is zero and Show is not Nothing. Enter a single value and
particles smaller than that value will be ignored. the measurements for each particle will be
displayed in the Results table. If In situ Show is checked. the particle count. any previous
measurements listed in the Results table will be cleared. If In situ Show is checked. the
original image will be replaced by this image. area fraction and the mean of all parameters
listed in the Set Measurements. Edit Selection Fit Ellipse of each measured particle
graylevels Ellipses . Overlay Outlines Displays outlines of the measured particles in the
image overlay. New in IJ . If In situ Show is checked. Masks bit binary image containing lled
outlines of the measured particles graylevels Masks . total particle area. dialog box will be
displayed in a separate Summary table.The ImageJ User Guide Analyze values are
expressed in physical size square units or in pixels if Pixel Units is checked. stack
Summaries are printed New in IJ . Clear Results If checked. the original image will be
replaced by this image. If In situ Show is checked. Show This dropdown menu species which
image or overlay should ImageJ display after the analysis. the original image will be replaced
by this image. Circularity Particles with size circularity values outside the range specied in
this eld Area are also ignored. Background . the original image will be replaced by this
image. the original image will be replaced by this image. . Count Masks bit image containing
lled outlines of the measured particles painted with a grayscale value corresponding to the
particle number. . Note that previously added overlays will be removed. cf. ranges from
innitely elongated polygon to perfect circle. Background . Display Results If checked. . New
in IJ . Background . If In situ Show is checked. Note that previously added overlays will be
removed. Nothing Neither images nor overlays will be displayed. Note that while single
images Summaries are output to the same Summary table.
. . Exclude on Edges If checked.The ImageJ User Guide Analyze in dedicated tables named
Summary of stack title.gov/ij/docs/menus/analyze. When this option is enabled. . the original
image will be replaced by the binary mask specied in the Show dropdown menu. interior
holes will be included. This command is also available by rightclicking on The Results Table.
/Connected Particle Analysis New in IJ . In situ Show If checked. . . Summarize For each
column in the results table. ImageJ nds the extent by ood lling. . . ImageJ nds the extent of
each particle by tracing the outer edge. the measured particles will be added to the ROI
Manager. Include Holes If checked.htmlap. Note that this option does not apply to Overlay
Outlines and Overlay Masks that are always displayed as nondestructive image overlays on
the measured image. The CircularParticles macro demonstrates how to use this feature.nih.y
macro function. note that descriptive statistics on Results measurements can be obtained at
any time using the Summarize command. Also. . See also Particle Remover plugin. Disable
this option to exclude interior holes and to measure particles enclosed by other particles.
standard deviation. Record Starts This option allows plugins and macros to recreate particle
outlines using the doWandx. Help Opens http//imagej. calculates and displays the mean.
Distribution. . When it is disabled. particles touching the edge of the image or selection will
be ignored. Add to Manager If checked. See also Analyze Particles. minimum and maximum
of the values in that column.
Produces a relative frequency histogram from the data of a chosen column of the Results
table . Use the List or Copy buttons to save the histogram data. . Parameter Species the
parameter in the Results table to be analyzed. Distribution. Optimal and databased . Mouse
over the histogram bars to read the counts for each bin on the windows lower right corner.
This command is also available by rightclicking on The Results Table. . . . Analyze Histogram
h describes in more detail ImageJs histogram window. ImageJ will use the method described
by David Scott to assess the optimal histogram bin width see Scott DW.l. Data points The
number of rows that will be analyzed informative Automatic binning If checked. .The ImageJ
User Guide Analyze Original thresholded Outlines Bare Outlines Masks Ellipses Count
Masks Overlay Outlines Overlay Masks Display options of Particle Analyzer Analyze Analyze
Particles. . IJ .
measurements can be restricted to highlighted pixels if Limit to Threshold is checked. . Label
This command labels the active selection with the current measurement counter value. i. . If
unchecked.e. XIV . .. . . Use this dialog box to specify which measurements are recorded by
Analyze Measure. . the number of bins can be set with Specify bins and the starting and
ending limits of the histogram with range. See also Distribution Plotter. Biometrika. . This
command is also available by rightclicking on The Results Table. For thresholded images. .
ROI Manager. See also Color Picker. As for Edit Draw d. or Measure. the entire active image
if no selection is present. . . command. Jan . or double click on the line tool. to change the
width of selections outline. Use the Edit Options Line Width.The ImageJ User Guide Analyze
histograms. the number of rows present in the Results table. . m commands and the
parameter Centroid cf. a macro that plots relative and cumulative frequencies on a double
Yaxis graph . Set Measurements. Measurements are performed on the current selection. .
ROI Managers Measure command cf. Selection outline and label at the selection centroid are
drawn invasively using current foreground/background colors. m. The dialog contains two
groups of checkboxes The rst group controls the type of measurements that are printed to
the Results table. extracted in the Results table. . . Selections can be labelled if they were
previously analyzed Analyze Particles. Set Measurements. and Analyze Analyze Particles. . .
The second group controls measurement settings. Clear Results Erases the results table and
resets the measurement counter. . . . This command is also available by rightclicking on The
Results Table.
Width and Height. m . . Reported in calibrated units e. This is the average of the x and y
coordinates of all of the pixels in the image or selection. Uses the heading Mode.. the mean
is calculated by converting each pixel to grayscale using the formula gray red green blue/ or
gray . With IJ . There are several ways to view the tted ellipse Improved in IJ . Uses the
headings Major. blue if Weighted RGB Conversions is checked in Edit Options
Conversions.g. red . the perimeter of a composite selection is calculated by decomposing it
into individual selections. dialog is not . . Uses the headings BX. Min amp Max Gray Level
Minimum and maximum gray values within the selection. green .f and later. Minor and Angle.
The coordinates of the center of the ellipse are displayed as X and Y if Centroid is checked.
was used to spatially calibrate the image. Note that ImageJ cannot calculate the major and
minor axis lengths if Pixel Aspect Ratio in the Analyze Set Scale.. Standard Deviation
Standard deviation of the gray values used to generate the mean gray value. BY. Major and
Minor are the primary and secondary axis of the best tting ellipse. Corresponds to the highest
peak in the histogram. Uses the XM and YM headings. Mean Gray Value Average gray value
within the selection. was used to calibrate the image. etc. . Angle is the angle between the
primary axis and a line parallel to the Xaxis of the image. . This is the sum of the gray values
of all the pixels in the selection divided by the number of pixels. Uses the X and Y headings.
Uses the Results table heading StdDev. Fit Ellipse Fits an ellipse to the selection. Note that
the composite perimeter and the sum of the individual perimeters may be dierent due to use
of dierent calculation methods. if Analyze Set Scale. Modal Gray Value Most frequently
occurring gray value within the selection. These coordinates are the rst order spatial
moments. . . . For RGB images.. Bounding Rectangle The smallest rectangle enclosing the
selection.The ImageJ User Guide Analyze The eighteen checkboxes of the rst group are
Area Area of selection in square pixels or in calibrated square units e. Perimeter The length
of the outside boundary of the selection. Centroid The center point of the selection. where BX
and BY are the coordinates of the upper left corner of the rectangle. mm . Uses the heading
Perim. optical density if Analyze Calibrate. . Center of Mass This is the brightnessweighted
average of the x and y coordinates all pixels in the image or selection.g.. .
. .. Values may not be valid for very small particles. Uses the heading Kurt. it indicates an
increasingly elongated shape.c and later. . Uses the heading AR. Select Ellipses from the
Show dropdown menu in the particle analyzer Analyze Analyze Particles. indicating a perfect
circle. . Uses the heading Area Solidity Convex area . Note that the Edit Selection Convex
Hull command makes an area selection convex. Shape Descriptors Calculates and displays
the following shape descriptors Area Circularity P erimeter with a value of . The angle
degrees of the Ferets diameter is displayed as FeretAngle. Uses the heading Skew. Uses
the heading Area. If M inor Fit Ellipse is selected the Major and Minor axis are displayed.
Uses the heading Circ. For nonthresholded images is the percentage of nonzero pixels..
Ferets Diameter The longest distance between any two points along the selection boundary.
This is equivalent to the product of Area and Mean Gray Value. also known as maximum
caliper. i. and it will draw the ellipse for each particle in a separate window. As the value
approaches . T.The ImageJ User Guide Analyze . Area M ajor axis or the inverse of Aspect
Ratio. Skewness The third order moment about the mean. The documentation for the
Moment Calculator plugin explains how to interpret spatial moments. Raw integrated density
sum of pixel values is displayed under the heading RawIntDen when Integrated density is
enabled. The length of the objects projection in the X FeretX and Y FeretY direction is also
displayed. . M ajor Axis . Area Fraction For thresholded images is the percentage of pixels in
the image or selection that have been highlighted in red using Image Adjust Threshold. With
IJ . The DrawEllipse macro draws destructively the best t ellipse and the major and minor
axis. Median The median value of the pixels in the image or selection. as well as the
minimum caliper diameter MinFeret. Axis Aspect Ratio The aspect ratio of the particles tted
ellipse. The Edit Selection Fit Ellipse command replaces an area selection with the best t
ellipse. .e. Roundness Round. Integrated Density The sum of the values of the pixels in the
image or selection. . The Dot Blot Analysis tutorial demonstrates how to use this option to
analyze a dot blot assay. Uses the heading Feret. Improved in IJ . Kurtosis The fourth order
moment about the mean.
b. Angle is recorded even if Fit Ellipse is unchecked. channel and frame in the stack or
hyperstack of the selection. e. Also. .The ImageJ User Guide Analyze Stack Position The
position slice. measurements are displayed in scientic notation. . . For line selections the
heading Length is created. . This setting aects only thresholded images see Settings and
Preferences.gifmySelection. Display Label If checked. For straight line selections.g. note that
measurements that do not apply to certain selection types may be listed as NaN. e. the
image name and slice number for stacks are recorded in the rst column of the results table.
This feature allows you to outline a structure on one image and measure the intensity of the
corresponding region in another image. only thresholded pixels are included in measurement
calculations. Decimal Places This is the number of digits to the right of the decimal point in
real numbers displayed in the Results table and in Histogram windows. commands. . . .. . .
Redirect To The image selected from this popup menu will be used as the target for
statistical calculations done by Analyze Measure. m and Analyze Analyze Particles. n. e.g.E.
For renamed selections Edit Selection Properties. mristack.tif. Invert Y Coordinates If
checked. . The second part of the dialog controls measurement settings Limit to Threshold If
checked. . Innity or Innity.. T to set the threshold limits. Uses the headings Slice. . the XY
origin is assumed to be the lower left corner of the image window instead of the upper left
corner see also Image Properties. y or selections measured via ROI Managers measure
command see ROI Manager.gif or blobs. blobs.g. P. Use Image Adjust Threshold. the
selection label is appended. Scientic Notation If checked. Ch and Frame. . . See also Ferets
Diameter macro ..
Setting Pixel Aspect Ratio to a value other than . . Enter the known width in Known
Distance. The CopyPixelSize plugin . . dialog. Click to Remove Scale resets Distance in
Pixels eld and Know Distance to zero and the Unit of Length to pixel. Enter the measured
width in pixels in Distance in Pixels. bring up the Set Scale. ImageJ will have automatically
lled in the Distance in Pixels eld based on the length of the line selection. Set Scale. for
example radioactive isotope standards or a calibrated optical density step tablet. pixels/cm
horizontally and pixels/cm vertically. . see XVIII. Then. Before using this command. . enables
support for dierent horizontal and vertical spatial scales.The ImageJ User Guide Analyze .
use the straight line selection tool to make a line selection that corresponds to a known
distance. the scale dened in this dialog is used for all opened images during the current
session instead of just the active image. Use this dialog to dene the spatial scale of the
active image so measurement results can be presented in calibrated units. Use this dialog
box to calibrate an image to a set of density standards. Calibrate. To set the Pixel Aspect
Ratio . . Note that to create a calibration curve. Calculate the aspect ratio by dividing the
width by the height and enter it in Pixel Aspect Ratio When Global is checked. . . enter the
Known Distance and unit of measurement. Measuring DNA Contour Lengths and Spatial
Calibration Fiji. .. e.g. Measure the width and height in pixels of a digitized object with a
known aspect ratio. then click OK. such as mm or m. See also Three tutorials showing how
to use this command Examples of Image Anal ysis Using ImageJ by Larry Reinking. . The
ImageJ web site has a tutorial on Optical Density Calibration explaining how to calibrate an
image to an optical density step tablet. the left column must contain a list of measured mean
pixel values and the right column must contain the same number of calibration standard
values.
. pixel width and height . . height and voxel depth. P pixel width. two other functions are
available that do not require any measurement of OD standards Uncalibrated OD Causes
ImageJ to convert gray values from bit images to uncalibrated optical density values using
the function Unc. temporal frame interval and luminance brightness information can be set
globally. If the calibration function is not satisfactory. . select Analyze Curve Fitting. bring up
the Calibrate. . . In addition to the fourteen functions that can be chosen from the dropdown
menu described in Curve Fitting.e. . When nished making the measurements. The Global ag
can be set in three dialog prompts . Pixel Inverter Linear function dened by Inverted pixel
Bitdepth Pixel value.The ImageJ User Guide Analyze XVIII Global Calibrations Calibration
settings related to spatial pixel width. . OD log /Pixel value. . to display the Calibrate dialog
box. m to record the mean gray value of each of the standards. To calibrate the image. frame
interval . The left column will be already populated with the measured mean gray values.
pixel intensity Once Global calibration is set. . can be applied to all images opened during the
current session instead of just the active image. height. . ignoring the calibration of the newly
open image. . dialog box again and select a dierent curve tting method. voxel depth. Choose
Disable Global Calibration to stop using global settings or Disable these Messages to keep
respecting global settings. enter the known standard values in the right column. A warning
message is displayed when a calibrated image with conicting calibration is opened and the
Global option is enabled. with Bitdepth being for bit images or for bit images. . a G is
displayed in all image titles until ImageJ is closed. Analyze Set Scale. . . . . use Analyze
Clear Results to reset the measurement counter and use one of the selection tools and
Analyze Measure. Image Properties. and click OK. i. .. Analyze Calibrate. . Before using this
command. enter the unit of measurement. Select a curve tting method from the popup menu.
ImageJ will then display the calibration function on a separate window.
Curve Fitting. Calculates and displays a histogram of the distribution of gray values in the
active image or selection. maximum Max and modal Mode gray value.The ImageJ User
Guide Analyze See also XVIII.e. Value / Count pairs i. The Xaxis represents the possible
gray values and the Yaxis shows the number of pixels found for each gray value. . Click on
Log to display a logscaled version of the histogram overlaid in gray. Image Types and Image
Formats. Histogram h Improved in IJ . The total pixel Count is also calculated and displayed.
. standard deviation StdDev . grayscale value corresponding to the Xaxis cursor position / the
number of pixels that have that intensity are displayed on This shortcut is not listed on Mac
OS X since it conicts with the system wide shortcut for the Hide command. . as well as the
Mean. .. H is a convenient shortcut for this command . Use the List or Copy buttons to save
the histogram data. It is shown on Windows and Linux and the H shortcut without holding
down Cmd does work on OS X. The horizontal LUT bar is scaled to reect the display range
of the image . minimum Min.
M . With bit images. red .getValues macro functions can be used to get the value and Count
data displayed when you click the List button cf. If unchecked. the range of gray values
between the Min and Max values is divided into bins.bits quot . length . // . run quot
Histogram quot . // . Obtaining Histogram Lists.The ImageJ User Guide Analyze the bottom
right while mousing over the histogram window. i print values i . . counts . quot stack quot . . f
o r i . . i lt values . . counts i . Listing Obtaining Histogram Lists with getHistogram and Plot.
counts i . getValues values . i print values i . With any image type. . this dialog can be called
with Alt H or by holding Alt while clicking on Histogram h. Bins Species the number of bins.
the Xaxis range is determined by the minimum and maximum values in the image or
selection. the number of bins is specied in the depicted dialog box. length . Use min/max If
checked. With RGB images. The getHistogram and Plot. With bit images. f o r i .getValues.
Plot . i lt values . Plot Prole k . Y Max Fixes the Yaxis range. blue if Weighted RGB
Conversions is checked in Edit Options Conversions. getHistogram values . Type Auto to
have the range determined by the largest bin count. Entire stacks run quot T Head . X Min
and X Max values can be or specied to x the Xaxis range. green . Single images run quot
Blobs K quot . the histogram is calculated by converting each pixel to grayscale using the
formula gray red green blue/ or gray . . counts .
StackProlePlot macro . or Copy. . Draw Axis If checked. .The ImageJ User Guide Analyze
Displays a twodimensional graph of the intensities of pixels along a line within the image. .
Surface Plot. In this case. the plot is drawn with a black background. For rectangular
selections or line selections wider than one pixel.. .. Radial Prole Extended plugins. lighter
areas in the source image will represent lower elevations valleys while darker areas in the
source image will represent higher elevations peaks. displays a column average plot. . where
the Xaxis represents the horizontal distance through the selection and the Yaxis the vertically
averaged pixel intensity. . Polygon Multiplier Adjusts the number of proles used to generate
the plot. . dialog box. Displays a threedimensional graph of the intensities of pixels in a
grayscale or pseudo color image nonRGB images. To average horizontally. . Draw
Wireframe If checked. Use Edit Options Prole Plot Options. Surface Plot. . The Xaxis
represents distance along the line and the Yaxis is the pixel intensity. The plot is based on
the existing rectangular selection or on the entire image if no selection is present. Radial
Prole Plot. the three axis will be drawn and labeled. A stack of plots can be produced when
the source image is a stack or hyperstack. Shade If checked. . closing the plot stack window
will abort the plotting process. Oval Prole Plot. hold down Alt or check Vertical Prole in the
Edit Options Prole Plot Options. . Fill Plot Background with Black If checked. a shaded plot
will be generated using the LUT of source image.. to adjust how plots are generated. Use the
List. otherwise white will be used. See also Plot Zaxis Prole. Dynamic Proler. buttons to view
and save the prole data. . . Source Background is Lighter If checked.. the outline of each
prole will be drawn in black. Save.
Gels Use the commands in this submenu to analyze onedimensional electrophoretic gels.
See also Plot Prole k. D Color Inspector/Color Histogram . . perspective. Note that all
selections must have the same dimensions.The ImageJ User Guide Analyze One Polygon
Per Line If checked.. scale. drawing lines to enclose peaks of interest. sharp uctuations will
be smoothed. lighting and smoothing can be interactively adjusted. and then measuring peak
areas i. . denite integrals using the Wand Tool. . Note that some plots can be further
improved by adjusting the contrast of the source image or smoothing it. These commands
use a simple graphical method that involves generating lane prole plots. The commands
listed in the this submenu are Select First Lane Requires a rectangular selection. Note that
lanes are assumed to be vertical unless the width of the initial selection is at least twice its
height. Smooth If checked. all polygons will be drawn. Select Next Lane To be used after the
rst rectangular ROI is moved over the adjacent lanes. . Interactive D Surface Plot plugin it
works with all image types and viewing angle.e. Note that this technique cannot be used to
compare bands on dierent gels unless gels are calibrated to known standards.
ImageJ will convert gray values to uncalibrated optical density values using the function
Unc. the Label Peaks command will print to the Results table the peak percentage and use it
to label the plot. Use this dialog to control the behavior of the Gel Analyzer. . . To recreate
plotted proles use the Replot Lanes command. This setting does not change the analysis see
Image Lookup Tables Invert LUT. ImageJ assumes that only one plot is created per analysis.
peaks will be inverted. Reset Resets the analysis. command.g. rerunning this command
more than once within the same analysis will cause an error message You must rst use the
Select First Lane command . Note that images can be calibrated to. Replot Lanes Recreates
the lane prole plots. Gel Analyzer Options. . . bands darker than background will have
positive peaks. . The percentage value is obtained by dividing the area of each peak by the
sum of all measured peaks from all lanes. If Plot Lanes has not yet been run an error
message is displayed The data needed to replot the lanes is not available. a calibrated
optical density step tablet using the Analyze Calibrate. Label With Percentages If checked.
Label Peaks Uses the area measurements obtained with the Wand Tool to label lane peaks
see Gel Analyzer Options. Invert Peaks If checked. Vertical / Horizontal scale factor Specify
the scale factor at which the lane prole plots are displayed.e.The ImageJ User Guide
Analyze Plot Lanes Generates the lane prole plots. .. As a consequence. Uncalibrated OD If
checked. i. . OD log /pixel value. e. . bands lighter than background will have negative peaks.
. . Dot Blot Analysis. SinglePanelGelAnalyzer macro. . . .The ImageJ User Guide Analyze
For practice. Tools This submenu provides access to various image analysis plugins. Dot
Blot Analyzer toolset . The selected lane is outlined and labeled. . To access to all the lanes.
. scroll the image vertically by holding down the space bar and dragging. Use the Straight
Line Selection Tool to draw base lines and/or drop lines so that each peak of interest denes
a closed area ImageJ will automatically switch to the Straight Line tool. refer to the video
tutorial on the ImageJ wiki page and use the File Open Samples Gel sample image D gel to
perform the following steps. . . and Lane n selected is displayed in the status bar. . For each
peak. . it may be necessary to scroll the image vertically using the Scrolling Tool Hold down
the space bar to temporarily switch to this tool. Select Gels Select First Lane and the lane will
be outlined and Lane selected displayed in the status bar. measure the size by clicking inside
the peak with the Wand Tool. Select Gels Label Peaks to label each measured peak with its
size as a percent of the total size of the measured peaks. This should be the left most lane if
the lanes are vertical or the top lane if the lanes are horizontal. Note that a copy of the gel
image with the lane outlines can be created at any point using the Image Overlay Flatten F
command. Note that you can hold Shift to constrain lines to be either horizontal or vertical.
See also Calibrate. Select Gels Plot Lanes to generate the lane prole plots. Video tutorial on
ImageJ wiki. Use the rectangular selection tool to outline the rst lane. Repeat the previous
step for each remaining lane. Move the rectangular selection right to the next lane or down if
the lanes are horizontal and select Gels Select Next Lane . If necessary. Luke Millers tutorial.
.
e. Fractal Box Count. J Neurosci Methods. This command is used to estimate the fractal
dimension D of a binary image. separated by spaces.. D slope. G.. green and blue. Refer to
the source code for additional information. red. textures. G. Smith. writes ve values per line
x.. . B. Background is assumed to be the value of the pixel at the upper left corner of the
image. i.. Fractal Methods and Results in Cellular Morphology. y. The number and
percentage of nonbackground pixels is printed to the Log window if Suppress Log output is
not checked. For grayscale images. D. Marks. Writes to a text le the XY coordinates and
pixel value of all nonbackground pixels in the active image. and is specially relevant in cases
in which Euclidean measures such as diameter or length are not good descriptors of
complexity. Jr. . A plot is generated with the log of size on the Xaxis and the log of count on
the Yaxis and the data is tted with a straight line.. y. Save XY Coordinates. etc. For RGB
images. See also Fractal Dimension and Lacunarity plugin . . vascularization. D can be used
as a measure of pattern complexity cell shape.The ImageJ User Guide Analyze . and value.
The origin of the coordinate system is at the lower left corner of the image. Lange and W.
writes three values per line x.. . Size S and count C are printed to the Results table. The
slope S of the line is the negative of the fractal dimension. The command counts the number
of boxes of an increasing size needed to cover a one pixel binary object boundary and
implements the method described in T. .
. . . . .The ImageJ User Guide Analyze . Curve Fitting. T tool Shift T . ImageJs curve tter
Analyze Tools Curve Fitting. The typical usage of this command is listed below.. . . . and
background is white. . Open the image containing the graph. ImageJ . K. Color Picker. cf.
Improved in IJ . use the File Open Samples Line Graph sample image. . Click on Apply make
sure foreground is black .. Adjust the threshold so the graph is highlighted in red. ImageJs
curve tter provides a very simple tool for tting various functions to X. . For practice. Select the
curve by clicking to the left of it with the Wand Tool. Use Analyze Tools Analyze Line Graph
to get the XY coordinates. Steps and are not necessary for binary black and white graphs.
Use Edit Clear Outside to erase everything but the curve. . . .l. . Open the Threshold.
Analyze Line Graph ImageJ can be used to recover numeric coordinate data from scanned
line graphs using the following procedure.and Ydata. . Use the Elliptical Selection Tool as an
eraser press Backspace to erase to isolate a single curve NB background color must be
white.
add and draw by pressing and add and advance to the next slice by pressing . . Click Apply
to create a bit copy of the current image transformed with the chosen function. . Delete
Deletes the selected ROIs from the list. Values may be separated by spaces. builtin functions
are available. commas or semicolons. The function to be t is selected from the dropdown
menu. The ROI manager creates a three part label.. Formula and Fitting Options must be
specied by the user. or press T . The rst part stacks only is the slice number. Renames the
selected ROI. Tabular data is entered or copied in the input window or alternatively. User
dened functions with up to six parameters are also possible by choosing Userdened. Deletes
all the ROIs if none is selected. . Improved in IJ . . including points. lines and text. from
dierent slices of a stack or from dierent images. . In this case. Add Click Add to add the
current selection to the list. Hold down Shift while clicking Add to Add and Draw. tabs.
Update Replaces the selected ROI on the list with the current selection. With stacks. . ROI
Manager. . Hold down Alt while clicking Add to Add and Rename. the second is the
Ycoordinate of the selection and the third is the Xcoordinate. Click on a label to restore the
associated selection to the current image. See also Prole Plot Options. Once the Fit button is
pressed. The ROI Region of Interest Manager is a tool for working with multiple selections. . .
add and rename by pressing . Rename. This is usually a modied version of a selection from
the ROI Manager list. are supported. . CurveFittingDemo.The ImageJ User Guide Analyze .
Install the ROIManagerMacros macro set and you will be able to add a selection by pressing
. the selection is restored to the slice it came from. The selections can be from dierent
locations on an image. the keyboard shortcut for the Edit Selection Add to Manager t
command. a two column text le is opened by clicking on the Open button. ImageJ displays a
graph of the data with the tted curve as well as a log window containing information about the
t and the values of the tted parameters if Show Settings is checked. All selection types. .
RodbardSigmoidFit and PlotSig moidDerivatives macros .
or if none is selected. . Properties. Measure. Deselect Deselects any selected ROIs on the
list. to specify the parameters to measure. FRAPProler plugin y a ebx c Measure Measures
the selected ROIs. you will be given the option to measure all the slices if all ROIs are
associated with the rst slice have labels like xxxxyyyy or all have labels in the form xxxxyyyy.
. all ROIs on the list. Via the Userdened option y a ebx c y a b a e xc d cf. Click Show All a
second time to remove the overlay. Delete. . . ..The ImageJ User Guide Analyze Summary of
ImageJs CurveFitter functions. See Edit Selection Properties. Function Straight Line nd
Degree Polynomial rd Degree Polynomial th Degree Polynomial th Degree Polynomial
Exponential Power Log Gamma Variate Rodboard Exponential with Oset Gaussian
Exponential Recovery Formula y a bx y a bx cx y a bx cx dx y a bx cx dx ex y a bx cx dx ex f
x y a ebx y axb y a lnbx y a x bc e y dad x b c xb d Comments cf. Click on a label selection
number in the overlay to activate the corresponding selection. y.nih. Pixel Inverter Calibrate..
. . That selection can then be moved or edited and the overlay will be dynamically up .html.
and More Combine work with all ROIs on the list when none are selected. Use Analyze Set
Measurements.gov/ij/developer/api/ij/measure/CurveFitter. More Save. With a stack. ..
Flatten F See Image Overlay Flatten F. Show All Displays a nondestructive overlay that
outlines and labels all ROI Manager selections. The complete documentation for the
CurveFitter class is available at http//imagej.
roi le. . Use the Open All macro to add all the . . . . New in IJ . saves all the ROI Manager
selections as a ZIP archive. Opens a . Edit Mode Disables / enables selection labels More
Displays a dropdown menu with several additional commands this dropdown menu is also
available when rightclicking on any listed ROI Open. AND Uses the conjunction operator on
the selected ROIs to create a composite selection. Saves the selected ROI as an . XOR
Uses the exclusive or operator on the selected ROIs to create a composite selection . If no
ROIs are selected.The ImageJ User Guide Analyze Show All Show All in Edit Mode
Xcoordinate Ycoordinate Slice number Options Deselect/Select All Show All with/without
labels More drop down menu also available when rightclicking on list area The ROI Manager
Analyze Tools ROI Manager. New in IJ . Draw Alias for Edit Draw d. The color and behavior
of the Show All overlay can be changed in the More Options dialog box. Save.l. . OR
Combine Uses the union operator on the selected ROIs to create a composite selection.
dated. All ROIs are considered if none is selected.roi le and adds it to the list or opens a ZIP
archive .roi les in a folder. Fill Alias for Edit Fill f. All ROIs are considered if none is selected.
ImageJ . . .zip le and adds all the selections contained in it to the list. Combines all the ROIs
if none is selected.
and to have the ROI Manager restore ROIs to the center of the image. . .htmlmanager
Options. it is possible to select contiguous ROIs with a single Shiftclick. Sort Sorts the list in
alphanumeric order. . .. . Requires that Record Starts be checked in the Analyze Analyze
Particles.The ImageJ User Guide Analyze Split Splits the current selection it must be a
composite selection into its component parts and adds them to the ROI Manager. Add
Particles Adds objects segmented by the particle analyzer to the ROI Manager. b. Particle
analyzer objects can also be added to the ROI Manager by checking Add to Manager in the
Analyze Particles dialog box. to measure all ROIs in manager one would press Deselect then
Measure. Displays a dialog box that allows you to set the Show All color. Add Selection. . to
associate Show All ROIs with the stack slices. . See also Selection Properties. ROI Color
Coder macro XIX Selecting Multiple ROIs in the ROI Manager For most ROI Manager
operations Deselect works as a Select All button. .g. . XVI.gov/ij/docs/menus/analyze.nih. In
addition. . . creating a Results table with either one row per image if One Row Per Slice is
checked in the dialog or one row per measurement . . Specify. A B A AND B A OR B A XOR
B Logical operations using the ROI Manager Analyze Tools ROI Manager. . . Noncontiguous
ROIs can be selected by Ctrlclick Commandclick on Mac OS X. dialog box. e. Multi Measure
Measures all the ROIs on all images in the stack. See Edit Selection Specify. . y. . Remove
Slice Info Removes the information in the ROI names that associates them with particular
stack slices Help Opens http//imagej.
. Scale Bar. If there is a selection. Background Adjusts the lling color of the label text box.
Bold Text / Serif Font Specify if label should be typeset in boldface / serif typeface. Draws a
labeled spatial calibration bar. See also Set Scale. .. . Font Size Adjusts the labels font size.
XIV. Hide Text If checked the bar is drawn without label. . . . Width Length of the bar in
calibrated units. Color Adjusts the text color cf. . Creates an RGB copy of the current image
and displays a labeled calibration bar on it. XVIII . the bar is initially drawn at the
selection.The ImageJ User Guide Analyze . . Height Height of the bar in pixels.. Calibration
Bar. Location Adjusts the position of the calibration bar.
See also Calibrate. The Calibration Bar Macros can be used to add a calibration bar to a
stack or to all the images and stacks in a folder. the bar is initially drawn at the selection.
Font Size Adjusts labels font size labels are drawn bold if Bold Text is checked Zoom Scale
Zooms the entire calibration bar. Label Adjusts the text color. . . Number of Labels Adjusts
the total number of values displayed. .The ImageJ User Guide Analyze Location Denes the
position of the bar. Fill Color Denes the bars background color. XVIII . Decimal Places Adjust
the number of decimal places present in the labels. If there is a selection.
open the recorder.The ImageJ User Guide Plugins . Loads and runs a macro without
opening it in The ImageJ Editor. When the recorder is open.. Click on Auto or Set in the
Image Adjust Threshold. . Opens the ImageJ command recorder. . . Install. . To run a macro.
Adds one or more macros contained in a le to the bottom of this submenu. . in the macros
folder. The run function has one or two string arguments. . and at the same time view their
source code. . then click Create. and on Reset to generate a resetThresold call. newly
opened macro sets with two or more macros are also automatically installed in this menu.
The rst is the command name.txt. open the macro le with File Open and use The ImageJ
Editors Macros Install Macros command. .txt. . . Macros contained in a le named
StartupMacros. To create a macro. use one or more ImageJ commands. . as well as any
macro commands added by Plugins Macros Install. Run.. Examples Create a rectangular.
Similarly. Plugins Macros This submenu contains commands for installing. makeOval or
makeLine function call. . Macros in the le ImageJ/macros/StartupMacros. are automatically
added to this submenu when ImageJ starts up.txt are automatically installed when ImageJ
starts up. T window to generate a setThresold call. Opens ImageJ/macros/StartupMacros.f
and later. with ImageJ . . The optional second argument contains dialog box parameters.
oval or line selection and the recorder will generate a makeRectangle. . open it with File
Open and use the editors Macros Run Macro command.. The same le can be opened by
holding Shift while selecting Startup Macros from the dropdown menu. To install a set of
macros. . running and recording macros. and at the same time view its source code. Startup
Macros. Record. .. . each menu command you use generates a macro run function call.
Improved in IJ .
K window to generate setForegroundColor and setBackgroundColor calls. . . See also
Keyboard Shortcuts. Note that. . Click in the Image Color Color Picker. to open an image
press O File Open. Extending ImageJ. List Shortcuts. Create Shortcuts. as mentioned
previously. Note that you can interact with the recorder window by deleting or commenting
lines of code or pasting text from The ImageJ Editor. you do not have to hold down Ctrl to
use a keyboard shortcut.g. .. E. . This command generates a table with the ImageJ keyboard
shortcuts in one column and the commands they call in another. . See also The ImageJ
Editor. Commands prexed by refer to shortcuts created with Create Shortcuts. you would
start the Recorder and let ImageJ keep track of the performed actions by generating macro
code.The ImageJ User Guide Plugins Select an image from the Window menu to generate a
selectWindow call. The ImageJ Macro Language Pro grammers Reference Guide . This may
be specially useful when writing your own macros or to generate simple Session Logs.
Commands prexed by refer to installed macros listed in Plugins Macros submenu and
override default ImageJ hotkeys.. . In this case. . . . Shortcuts This submenu contains
commands for creating keyboard shortcuts and for installing and removing plugins. . . .
The ImageJ User Guide
Plugins
..
Create Shortcuts. . . Assigns a keyboard shortcut to an ImageJ menu command and lists the
shortcut in the Shortcuts submenu. Select the command from the popup menu and enter the
shortcut in the text eld. A shortcut can be a lower or uppercase letter or F through F. Use
Plugins Utilities List Shortcuts. . . to get a list of shortcuts that are already being used.
..
Install Plugin. . . Installs a plugin in a userspecied submenu. Plugins with a showAbout
method are also automatically added to the Help About Plugins submenu. Use the rst popup
menu to select the plugin and the second to select the submenu it is to installed in. The
command must be dierent from any existing ImageJ command. Shortcut optional must be a
single letter or F through F. Argument optional is the string that will passed to the plugins run
method.
..
Remove. . .
Removes commands added to the Shortcuts submenu by Create Shortcuts. . . Also removes
commands added by Install Plugin. . . and removes plugins installed in the Plugins menu.
The menus are not updated until ImageJ is restarted.
The ImageJ User Guide
Plugins
.
..
Utilities
Control Panel. . . U This command opens a window containing ImageJ commands in a
hierarchical tree structure. Click on a leaf node to launch the corresponding ImageJ
command or plugin. Double click on a tree branch node folder to expand or collapse it. Click
and drag on a tree branch node folder to display its descendants in a separate child window.
In a child window, click on Show Parent to reopen the parent window.
Improved in IJ .
See also Command Finder
..
ImageJ Properties. . .
This command displays various ImageJ properties Java version, OS name and version, path
separator, location of directories, screen size, etc. in a text window. Holding Alt lists all Java
properties
See also Status bar, Help About ImageJ. . .
..
Threads. . .
This command lists, in a text window, the currently running threads and their priorities. ..
Benchmark
Runs image processing operations on the current image and displays the elapsed time in the
ImageJ status bar. Additional benchmarks, test results, and source code are available in the
Benchmarks package of plugins.
See also FAQs on the ImageJ Documentation Wiki
..
Reset. . . Use this command to unlock a locked Image, or to reclaim memory used by the
clipboard and undo buers cf. Undo and Redo.
The ImageJ User Guide
Plugins
..
Monitor Memory. . .
Displays a continuously updated graph of ImageJs memory utilization, which can be useful
for detecting memory leaks. Ideally you should be able to open several images, process
them, close them, and the amount of memory used will be the same as when you started.
Clicking on ImageJs status bar, which forces the Java garbage collector run, may help
reclaim unused memory cf. Status bar. Starting the memory monitor holding down Alt will
have it use a window that simulates how a frame grabber plugin would work .. Search. . .
Described in Finding Commands. .. Capture Screen g
Copies the screen to an RGB image and displays that image a new window. Holding Ctrl
Shift G will capture the screen while a modal dialog box is active if the dialog is based on
ImageJs GenericDialog class. .. Capture Image
Copies a WYSIWYG version of active image to an RGB image and displays that image a
new window.
See also Flatten F
..
Find Commands. . . l
Described in Command Finder.
.
New
This submenu contains commands opening editor windows that can be used to edit and run
macros, scripts and plugins. It also has a command that opens a text window of a specied
size and a command that opens a table that macros can write to. The editor windows opened
by Plugin, Plugin Filter and Plugin Frame contain prototype Java code for the three types of
plugins supported by ImageJ.
See also The ImageJ Editor, Extending ImageJ
Plugin Opens an editor window containing a prototype plugin that implements the PlugIn
interface. Clock and ProgressBar are examples of macros that write to a text window. Note
that the name you choose for the plugin should include at least one underscore. See also
Scripts. Another example is the Image Inverter. .. Plugins of this type open.. File New Text
Window N . capture or generate images. The prototype displays quotHello worldquot in the
ImageJ window.. Another example is the IP Demo plugin. Plugin Filter Opens an editor
window containing a prototype plugin that implements the PlugInFilter interface.. . .The
ImageJ User Guide Plugins .txt. The prototype inverts the active image twice. . Text Window.
The prototype opens a window containing a text area. Plugin Frame Opens an editor window
containing a prototype plugin that extends the PlugInFrame class. Plugins of this type
displays a window containing controls such as buttons and sliders.. See also Macros. .
Plugins of this type process the active image. JavaScript Opens a blank editor window with
the title Script. Press Ctrl R File Run Macro to compile and run it. Another example is the
Step Maker plugin. See also Plugins New Macro. Macro Opens a blank editor window with
the title Macro. Opens a text window of a specied size that macros can write to.js. . .
PrintToTextWindow. The ImageJ Editor . Text Window. The ImageJ Editor. .. File New Text
Window N .
See also Plugins New Text Window. adds the BioFormats plugin locitools. Requires that
ImageJ be running on a Java Virtual Machine that includes the javac compiler. Runs a plugin
if the name of the selected le ends in .gov/ij/ macros/SineCosineTable. .The ImageJ User
Guide Plugins . Since ImageJ . Improved in IJ . . . . Tools. and it is preinstalled on Mac OS X.
which is contained in the Tools. . SineCosineTable http//imagej. command can be used to
congure the javac compiler.jar archive. Compile and Run. Compile and Run. . .nih.jar to the
Java compilers classpath.. Compiles and runs a plugin. .c and later.jar is included with the
Windows and Linux versions of ImageJ bundled with Java.class. that macros can write to.
Troubleshooting information can be found under Compiling Plugins in the Linux and
Windows release notes.txt is an example of such a macro. . . Opens a blank table. The Edit
Options Compiler. Table. . similar to the Results table. .
pull down this menu and select the window by name. To activate a window. . Tile Shrinks all
open image windows and repositions them to t on the screen without overlapping. Put
Behind tab Displays the next open image. slightly oset from each other. . Cascade Moves all
open images to the left side of the screen. . .The ImageJ User Guide Window Window This
menu contains four commands plus a list of open ImageJ windows. and displayed in the
order they are listed at the bottom of this menu. Note that pressing Enter on any image will
bring the ImageJ window to the foreground. See also I . The currently active image will have
a checkmark next to its name. Repeatedly press the tab key to cycle through all open
images. Show All Makes all the windows associated with ImageJ visible.
ImageJ News. Opens the Developer Resources section of the ImageJ website. Installation.
refox. . macros. Use this page to nd plugins. Resources. Mac OS X or Windows. Opens the
Installation section of the ImageJ website specically dedicated to the OS in which ImageJ is
running. . Worth reading are the sections Known Problems and Troubleshooting. Mac OS .
Opens the News section of the ImageJ website.The ImageJ User Guide Help Help Many of
the commands in this menu use ImageJs BrowserLauncher to open a Web page using the
users default browser. . Search Website. opera. or update options. Opens the
Documentation section of the ImageJ website. mozilla. post a message to the list. . epiphany
or lynx and uses the rst one it nds. . Opens the ImageJ Interest Group page on the NIH
LISTSERV facility. .e either Linux. . On Linux. . . . . . ImageJ Website. . List Archives. join or
leave the list. . . Opens the Search page on the ImageJ website. . Opens the ImageJ home
page. . Dev. i. . or messages that have been posted to the ImageJ mailing list.
BrowserLauncher looks for netscape. . . konqueror. Here you can search the mailing list
archives. . . Documentation.
.nih. Opens the macros directory on the ImageJ website. Opens the Macro Functions
reference page. . Update ImageJ. .nih. .b this command was named Update Menus. Opens
the Plugins page on the ImageJ website. . . To be included in this submenu.jar at
http//imagej. . There is an example at rsb.The ImageJ User Guide Help .jar.
Macros.gov/ij/upgrade/. See also Macros .gov/ij/plugins/jardemo. a plugin must be packaged
as a JAR le. which contains more than ImageJ macros. Upgrades ImageJ to the latest ij.
Prior to ImageJ . See also Maintaining ImageJ Changed in IJ . . Refresh Menus Use this
command to update ImageJs menus after adding or removing plugins or macros to the
plugins folder.html. or downgrades to one of the earlier versions at http//imagej.gov/ij/ij.
Plugins.info. . . . which lists more than ImageJ plugins. nih. . Select daily build from the
dropdown menu and ImageJ will be upgraded to the latest daily build at http//imagej. an
indispensable guide to the built in functions that can be called from the ImageJ macro
language. Macro Functions.nih. . About Plugins This submenu displays information about
some of the plugins in the ImageJ plugins folder.gov/ij/download/ jars/.
the author. the website. Java version and memory available. . See also Plugins Utilities ageJ
Status bar ImProperties. . Note that clicking in the status bar is a quicker way to show this
information. Opens an image containing information about the ImageJ version. .The ImageJ
User Guide Help . . . About ImageJ. .
.gov/ij/docs/shortcuts. . . p Edit Undo z Cut x Copy c Paste v Clear Fill f Draw d Invert I
Selection Select All a Z X C V Backspace F D Shift A I N Shift N Shift V O Shift O Shift B W
S R P Shortcut Description Create new image or stack Create new text window Create
image from system clipboard Open le any format recognized by ImageJ Open next image in
folder Opens the Blobs.Part VI Keyboard Shortcuts The following table summarizes the
keyboard shortcuts built into ImageJ. or override builtin ones. You can create additional
shortcuts. . A similar list can be obtained using ImageJ Plugins Shortcuts List Shortcuts. Edit
Options Misc. . . . . .txt. Except when using the text tool. you do not need to hold down the
control key to use a keyboard shortcut cf. This table is also available at http//imagej.
command. See also Shortcuts and Modier Keys. You can also assign a function key to a
menu command using Plugins Shortcuts Create Shortcuts. Open Next O Open Samples
Blobs K Close w Save s Revert r Print. command.html. . n New Text Window N New System
Clipboard V Open. . . .nih. . This table can be obtained within ImageJ using the Plugins
Shortcuts List Shortcuts. by creating simple macros and adding them to the StartupMacros.
builtin shortcuts. . Command / Operation File New Image. Macro Tools List of ImageJ .gif
example image Close the active window Save active image in Ti format Revert to saved
version of image Print active image Undo last operation Copy selection to internal clipboard
and clear Copy selection to internal clipboard Paste contents of internal clipboard Erase
selection to background color Fill selection in foreground color Draw selection Invert image or
selection Select entire image . . Finding Commands.
. .The ImageJ User Guide List of ImageJ . . . builtin shortcuts. P Color Color Picker. m
Histogram h Plot Prole k Gels Select First Lane M H K Shift S Shift R Shift C Shift T I Shift P
Shift K gt or lt or / Shift H Shift Z gt or lt or Ctrl gt Ctrl lt Alt gt Alt lt Shift X Shift D E or or
Shortcut Shift A Shift E Y T Description Remove selection Restore previous selection Denes
selection properties Add selection to ROI Manager Adjust brightness and contrast Adjust
threshold levels Display information about active image Display image properties Open Color
Picker Go to next stack slice Go to previous stack slice Reslice stack Toggle orthogonal view
display Start/stop stack animation Open the Channels tool Next hyperstack channel Previous
hyperstack channel Next hyperstack slice Previous hyperstack slice Next hyperstack frame
Previous hyperstack frame Crop active image or selection Duplicate active image or
selection Scale image or selection Make image larger Make image smaller Revert to original
zoom level Zoom to unweighted smoothing Repeat previous command Display statistics of
active image / selection Display histogram of active image / selection Display density prole
plot of active selection Select rst gel lane Select None A Restore Selection E Properties. C
Adjust Threshold. . . . . E Zoom In Zoom Out Zoom Original Scale Zoom View Process
Smooth S Repeat Command R Analyze Measure. command. T Show Info. . D Scale. . . . . Z
Hyperstacks Hyperstacks Hyperstacks Hyperstacks Hyperstacks Hyperstacks Crop X
Duplicate. . . Command / Operation Selection Selection Selection Selection Image Adjust
Brightness/Contrast. . . . y Add to Manager t . i Properties. K Stacks Next Slice gt Stacks
Previous Slice lt Stacks Reslice. / Stacks Orthogonal Views H Stacks Tools Start Animation
Hyperstacks Channels. . . This table can be obtained within ImageJ using the Plugins
Shortcuts List Shortcuts. . . . .
. nd and launch commands Make all windows visible Switch to next image window Bring
ImageJ window to front Alt Key Modications File Open Next Open Previous File Revert Dont
show dialog Edit Copy Copy to system clipboard Image Color Split Channels Keep original
image Image Stacks Add Slice Insert before current slice Image Stacks Next Slice Skip nine
slices Image Stacks Previous Slice Skip nine slices Image Stacks Start Animation Show
options dialog Image Duplicate Dont show dialog Image Overlay Add Selection Dont show
dialog Process Equalize Do classic histogram equalization Analyze Histogram Show dialog
Analyze Plot Prole For rectangular selections. generate row average plot Analyze Plot Prole
For wide straight lines. . command. . display rotated contents Analyze Gels Select First Lane
Assume lanes are horizontal Analyze Tools Analyze Line Graph Show intermediate image
Analyze Tools Roi ManagerAdd Name and add selection Plugins Utilities ImageJ Properties
List all Java properties . l Window Show All Put Behind ImageJ Tab Enter Shift U Shift G L
Shortcut Description Select next gel lane Plot gel lanes Open Control Panel Grab screenshot
List. . builtin shortcuts. U Utilities Capture Screen g Utilities Find Commands. Command /
Operation Gels Select Next Lane Gels Plot Lanes Plugins Utilities Control Panel. This table
can be obtained within ImageJ using the Plugins Shortcuts List Shortcuts.The ImageJ User
Guide Alt Key Modications List of ImageJ . . .
The ImageJ User Guide Space Bar Plugins Utilities Monitor Memory Simulate frame grabber
Any user plugin Load using new class loader Area selection tools Subtract this selection from
the previous one Rectangle and Oval selection tools Current aspect ratio is maintained while
resizing Polygon selection tool Altclick on a node to delete it Straight line tool Keeps the line
length xed while moving either end of the line. Forces the two points that dene the line to
have integer coordinate values when creating a line on a zoomed image Segmented line tool
Altclick on a node to delete it Point tool Altclick on a point to delete it Color picker tool Altclick
to pickup background color All tools Show location and size in pixels Shift Key Modications
Image Adjust Threshold Adjusting Min also adjusts Max Image Adjust Brightness/Contrast
Apply adjustments to all channels of a composite image Installed Macros and Scripts Open
instead of run Rectangle and Oval selection tools Forces aspect ratio Area selection tool Add
this selection to previous one Polygon selection tool Shiftclick on a node to duplicate it
Straight line tool Forces line to be horizontal or vertical Segmented line selection tool
Shiftclick on a node to duplicate it Point selection tool Shiftclick to add a point Ctrl Key or
Cmd Key on Macs Modications Rectangle and Oval selection tools With Alt Current aspect
ratio is maintained while resizing Rectangle and Oval selection tools Selection is resized
around the center Straight line tool Rotate/resize the line about its center Space Bar Any
Tool Switch to the hand tool .
If there is a selection. The set of macros listed below taken from the Rename and Save ROI
Sets toolset exemplify the use of the setTool function by assigning the numeric keys to the
rst four area selection Tools.The ImageJ User Guide Keyboard Shortcuts for ImageJ Tools
Arrow Keys Moving Selections The four arrow keys move selection outlines one pixel at a
time Resizing Selections Rectangular and oval selections are resized by holding Alt while
using the arrow keys Stacks Navigation The and keys substitute for lt and gt for moving
through a stack. setTool quot brush quot . getToolName . exit . If there is a selection. you
must also hold Shift Hyperstacks Navigation The and keys change the channel. requires the
user to memorize as many shortcuts as the number of tools in the toolbar. it may be dicult to
assign so many hotkeys without . Once copied to the to the ImageJ/macros/StartupMacros.
macro quot Refine Area Selection quot tool IJ . i f flags amp setTool tool . Listing Assigning
Keyboard Shortcuts to ImageJ Tools / This set of macros exemplifies how to use the setTool
function to assign hotkeys to ImageJ tools . Hold Ctrl to move through the slices and Alt to
move through the frames Zooming The and keys zoom the image in and out. y . z . In
addition. / macro quot Rectangle quot setTool quot rectangle quot . shortcuts can be
assigned to macros that use the setTool function. This approach. however. macro quot
Polygon quot setTool quot polygon quot . Once the mouse is released the previously
selected tool is restored. macro quot Freehand quot setTool quot freehand quot . The macro
Rene selection activates temporarily the brush selection tool when is pressed. However.
flags . macro quot Ellipse quot setTool quot elliptical quot . you must also hold either Shift or
Ctrl Keyboard Shortcuts for ImageJ Tools Keyboard shortcuts cannot be used directly to
activate tools in the ImageJ toolbar with the exception of the Magnifying Glass and the
Scrolling Tool.txt le ImageJ will automatically install them at startup. while true getCursorLoc
x.
quot freehand quot . macro quot Cycle Tools Fwd F quot setTool tools tIndx .quot freeline
quot . macro quot Cycle Tools Rwd F quot tIndx . .quot polyline quot . It is composed of two
macros activated by F and F that iterate through the toolbar items from left to right forward
cycle and right to left reverse cycle. quot arrow quot . quot point quot . quot text quot .. quot
angle quot . length . The next example demonstrates such an approach. length tIndx . / var
tIndx . Listing Cycling Through ImageJ Tools Using Keyboard Shortcuts / These two macros
loop through the tools listed in an array using quot F quot and quot F quot as keyboard
shortcuts forward and reverse cycling . setTool tools tIndx . .quot multipoint quot . Probably a
more ecient way to control the toolbar using the keyboard is to create macros that can cycle
through all the tools in the ImageJ toolbar. quot dropper quot . tIndx . quot ellipse quot . i f
tIndx lt tIndx tools . quot line quot . var tools newArray quot rectangle quot . .The ImageJ
User Guide Keyboard Shortcuts for ImageJ Tools conicting with previously dened ones see
List Shortcuts. quot wand quot . quot roundrect quot . . i f tIndx tools . quot polygon quot .
quot oval quot . quot brush quot .
added connected and connected tracing with tolerance to the Wand Tool.
.edu/chernov/cl/MATLABcircle. . E. . C The macro editors Function Finder Macros Find
Functions. . . was written by Michael Castle and Janice Keller of the University of Michigan
Mental Health Research Institute MHRI. . C The Edit Selection Fit Circle command. . .
command. command implements Gabriel Landinis Threshold Colour plugin. based on a
MATLAB script by Nikolai Chernov http//www.. C The Elliptical Selection Tool was
contributed by Norbert Vischer.uab. C The Image Hyperstacks Reduce Dimensionality. .m.
Michael Doube added support for XZ and YZ view control as well as mouse wheel control. C
The Image Stacks Tools Make Substack. command is based on the Substack Maker plugin
by Anthony Padua. and Image Scale. command is based on Jrme Mutterers Im C Michael
Schmid contributed improvements to the AVI reader and AVI writer plugins. .Credits C The
Command Finder was written by Mark Longair. . . C The Color Picker Image Color Color
Picker.. . . Daniel Barboriak and Ved Sharma. portResultsTable macro. C The File Import
Results. C The Image Stacks D Project. a intern from BethesdaChevy Chase High School. C
Michael Schmid. . C The dierent thresholding methods available in the Image Adjust
Threshold. C Karen Collins contributed improvements to the FITSWriter File Save As FITS. .
. was written by Jrme Mutterer. T tool were implemented by Gabriel Landini. Bill Mohler
added suport for hyperstacks and /bit images in IJ . . C The Image Stacks Orthogonal Views
H command is based on Dimiter Prodanovs StackSlicer plugin and Albert Cardonas Updater
class. C The Reslice and the ZProject plugin Image Stacks Reslice. command is based on
Jrme Mutterers Reduce HyperStack macro. C Michael Schmid contributed improvements to
the downsizing kernel used by Image Adjust Size. E as well as undo support for Image
Scale. . was contributed by Michael Doube and Ved Sharma C The Edit Selection Create
Selection command is based on the ThresholdToSelection plugin written by Johannes
Schindelin. C The Image Adjust Color Threshold. San Diego. C The Brush Selection Tool is
based on the ROI Brush Tool plugin from Tom Larkworthy and Johannes Schindelin. . .math.
K was written by Gali Baler. . . . . / and Z Project. .html. commands were contributed by
Patrick Kelly and Harvey Karten of the University of California. .
C The Rodboard and Gaussian functions implemented in Analyze Tools Curve Fitting. Scale
Bar Tools for Microscopes. Karen Collins. Kai Uwe Barthel. . C The Control Panel Plugins
Utilities Control Panel. C The Process Binary Fill Holes algorithm was contributed by Gabriel
Landini. Erik Meijering. C The ROI ManagerMulti Measure command Analyze Tools ROI
Manager. Uwe Walschus. Dimiter Prodanov.class used by the Process Batch Macro. Michael
Schmid. . . Joachim Wesner. Norbert Vischer. Stephan Saalfeld. . . was added by Johannes
Schindelin. . . C The Process Find Maxima. C The Process FFT Bandpass Filter.
respectively. Andreas Maier. Robert Dougherty. Reinhard Mayr. Frederic Hessman. Jan
Funke. Wilhelm Burger. C The Process Math Macro. Mark Longair. . Adrian Daerr.txt.txt. C
The scaled color bar implemented in Analyze Histogram h was contributed by Bob
Dougherty. Olaf Freyer. . C The NonBlockingGenericDialog. . . .C The Image Zoom Set.
Magic Montage. command is based on a plugin contributed by Michael Schmid. C Macro
Toolsets distributed with ImageJ have been contributed by Gilles Carpentier Arrow Labelling
Tools. Tiago Ferreira. Kevin Moll. . Stefan Starke. command was added by Johannes
Schindelin. were contributed by David Rodbard NIH and Stefan Wrz DKFZ. U was written by
Cezar M. Christian Moll. Tigare. .txt. . Ulf Dittmer. implemented in ImageJ . improvements
and bug xes have been contributed by Albert Cardona. Julian Cooper. Johannes Hermen.txt.
C Other additions. Michael Ellis. Shannon Stewman. . is a built in version of Joachim Walters
FFT Filter plugin. Gabriel Landini. Tseng Qingzong.txt. Duncan Mak. command is based on
Albert Cardonas Zoom Exact plugin. Juan Grande. C The equalization code implemented in
Process Enhance Contrast was contributed by Richard Kirk. . Divakar Ramachandran.
command is modeled after Ulf Dittmers Expression plugin. C The faster and more accurate
version of Process Filters Gaussian Blur. Matthew Smith. Jrme Mutterer Example Icons.
Tiago Ferreira Toolset Creator. command was written by Gabriel Landini. Ved Sharma.
Michael Doube.r and later was contributed by Michael Schmid. C The Analyze Distribution. is
based on Bob Doughertys MultiMeasure plugin. Alden Dima. . . Nico Stuurman. . Johannes
Schindelin. C The ROI ManagerXOR command Analyze Tools ROI Manager. Jay Unruh. . . .
Barry DeZonia.
Pavel Tomancak. Chapter Unit. Masayuki Itoh. Jan . Y LahbibMansais. and James A
Kavanaugh.ImageJ Related Publications The following references are a small sample of the
bibliography directly related to ImageJ. Adam Fraser. Bioinformatics Oxford. Quantication of
pancreatic islet distribution in situ in mice. Junghyo Jo. and T Boudier. Michal M Klosowski.
Nick E Leininger. Mark E Bastin. Johannes Schindelin. Ron Vale. Pavel Tomancak. . Nenad
Amodaj. Kevin Miller. and Hiroshi Takano. Atsuko Kobayashi. A highlevel D visualization API
for Java and ImageJ. Am J Physiol Endocrinol Metab. Takumi Fujigaya. c American Institute
of Physics. Christof Karmonik. Takahisa Taguchi. the standard in scientic image analysis.
and Martin Heisenberg. . Jan . Albert Cardona. Feb . Ute Klinkhardt. German Kilimnik.
Reinhard Schneppenheim. Robert Grossman. Arthur Edelstein. Abraham Kim. Polarization
Imaging and Insect Vision. Curr Protoc Mol Biol. Stephan Saalfeld. These publications
include technical articles and books describing routines implemented in ImageJ. and
Sebastian Harder. Benjamin Schmid. Ignacio ArgandaCarreras. BMC Bioinformatics .
research articles that have made extensive use of ImageJ as a scientic tool or reviews that
discuss ImageJ pertinently. Albert Cardona. Nature Methods. An integrated micro. . Nicholas
Hamilton. Suzanne Duce. Stephan Preibisch. and Nico Stuurman. John R Hutchinson. M
Yerle. England. An image analysis pipeline for the semiautomated analysis of clinical fMRI
images based on freely available software. Karl Hoover. NEMO a tool for analyzing gene and
chromosome territory distributions from DFISH experiments. Dec .. . Michael Doube. Robert
P Dougherty. PLoS Biol. Dec . Fabrice P Cordelieres. Jim Pulokas. Ekta Kakkar. and Volker
Hartenstein. Bone. Benjamin Schmid. . and David King. Jan . Jurgen E Schneider.
Ultramicroscopy. SupplS. Benjamin Schmid. . Computer control of microscopes using
Manager. Computers in biology and medicine. E. and Manami Hara. . Technical note a tool
for determining rotational tilt axis with or without ducial markers. and Sandra J Shefelbine.
Dec . Krutina Patel. Mar . Sascha Meyer Dos Santos. Adam S Green. Anchi Cheng.
Visualization of image data from cells to organisms. Platelets. Mark A Ragan.and
macroarchitectural analysis of the Drosophila brain by computerassisted serial section
electron microscopy. F Mompart. The Physics Teacher. Oct . E Iannuccelli. Using ImageJ for
the quantitative analysis of owbased adhesion assays in realtime under physiologic ow
conditions. Mark Longair. Michele York. Richard Baldock. This list appears in chronological
order rather than alphabetical and is particularly biased towards the life sciences. Paul R
Ohmann. Anne E Carpenter. Hani Haykal. Jan . J Gellin. Jonathan S Jackson. and
JeanKarim Hrich. Thomas Walter. Jan Ellenberg. David W Shattuck. BoneJ Free and
extensible bone image analysis in ImageJ. Jan . Steve Pieper.
David J Barry. and Timothy J Levesque. Lilian Kisiswa. P Arenberger. Jnos Szllosi. . Michael
J Ophir. Albert Cardona. Aug . Stephan Saalfeld. Henk J Groenewegen. and O Zoras. T
Ruzicka. . Nov . and JeanMichel Deniau. Jonathan T Erichsen. Zebrash. free image
processing and analysis software. Evaluation of intensitybased ratiometric FRET in image
cytometryapproaches and a software solution. Image analyses of the kinetic changes of
conjunctival hyperemia in histamineinduced conjunctivitis in Guinea pigs. Skin Res Technol.
Bioinformatics Oxford. Jason R Swedlow and Kevin W Eliceiri. Nicola Goodall. CATMAID
collaborative annotation toolkit for massive amounts of image data. Suzanne N Haber. I
Navrozoglou. . A new method of assessing the size of mandibular cysts on
orthopantomograms projection area fraction. Sep . . Krish Singh. Motionbased angiogenesis
analysis a simple method to quantify blood vessel growth. . Dhammika Menike Dissanayake.
J Anat. Trends in Cell Biology. Dimensional modelling of chick embryo eye development and
growth using high resolution magnetic resonance imaging. Richard L Mort. Emel Bulut and
Bnyamin Sahin. Oct . G Messer. and Gwilym A Williams. . Open source bioimage informatics
for cell biology. E N Stathopoulos. Philip D Manos. T Vrekoussis. Nov . Jul . Nov . Dec . A
Simple Quantitative Bedside Test to Determine Methemoglobin. Atsuki Fukushima and
Tsutomu Tomita. Farrah M Laliberte. Dec . Fathima Shihana. Oct . J Hegyi. Georey C
Collins. Cytometry A. and Pavel Tomanck. J Neurosci Methods. Willi Halfter. A D multimodal
and multidimensional digital brain model as a framework for data sharing. . Anticancer Res.
Sep . Clayton M Costa and Suann Yang. England. J Ind Microbiol Biotechnol. V Chaniotis.
Oct . Dec . Confocal laserscanning capillaroscopy a novel approach to the analysis of skin
capillaries in vivo. . . Morphological quantication of lamentous fungal development using
membrane immobilization and automatic image analysis. Image analysis of breast cancer
immunohistochemistrystained sections using ImageJ an RGBbased model. Nicholas Allan
Buckley. Jez Guggenheim. Philippe Mailly. Ankush Prashar. Joseph A Lee. and Michael A
Wride. J Craniofac Surg. . Jun . . Volker Hartenstein. Julia L Chen. Counting pollen grains
using readily available. Ann Bot. Quantitative analysis of patch patterns in mosaic tissues
with ClonalTools software. Exp Eye Res. and Andrew Hamilton Dawson. and Gyrgy Vereb.
Cecilia Chan. Jnos Roszik. Pawe Tokarczuk. . Ann Emerg Med. V Hegyi. Kyle M Judkins.
Cornea. April E GreeneColozzi. Stuart Faulkner. . Duarte Lisboa. and C Berking. K Pavlakis.
V Dousias. Edmund Y Tong.
D Batchelor. Major orthogonal dimensions measurement of food grains by machine vision
using ImageJ. Ian C Hallett. Res. Ricardo B Medeiros. Daniel B Hawcutt. L. Jan .
Anteriorposterior bending strength at the tibial shaft increases with physical activity in boys
evidence for nonuniform geometric adaptation. Brian Hoium. Lourdes Estrada. Automated
tracking of migrating cells in phasecontrast video microscopy sequences using image
registration. Julio E Herrera. . J Voice. Automated classication of Plasmodium sporozoite
movement patterns reveals a shift towards productive motility during salivary gland infection.
Jenny A Pennack. Jan . Priya D Krishna. A J Hand. Evan C Crawford and James K
Mortensen. and Daisy Vanrompay.. D R Hose. Ashley Smith. James Osborne. O Pordesimo.
Computers amp Geosciences. Kristen Coley. Anuratha Elayaperumal. A rapid method of fruit
cell isolation for cell size and shape measurements. Tech. and HsiaoTzu Ni. . Yoonseok
Kam. Jan . Jan . Properties of secondary and tertiary human enteric nervous system
neurospheres. . Audrey Karperien. Stephan Preibisch. Journal of microscopy. Jan . A novel
method for analyzing mitochondrial movement inhibition by paclitaxel in a
pheochromocytoma cell model. J Mol Neurosci. SaikKia Goh. Geert Meesen. BMC Res
Notes. Jun . and Simon E Kenny. Alexander R Anderson. Brandy Weidow. D C Barber. and
H A McKay. Mar . Anabel R Learte. Osteoporos Int. . and S MacNeil. Patrick Van Oostveldt.
and Pavel Tomancak. Nest expansion assay a cancer systems biology approach to in vitro
invasion measurements. Novel sequential ChIP and simplied basic ChIP protocols for
promoter cooccupancy and target gene identication in human embryonic stem cells. BMC
Biotechnol. Jun . England. Stephan Saalfeld. DeadEasy Caspase Automatic Counting of
Apoptotic Cells in Drosophila. David H Edgar. . . Digital titration automated image acquisition
and analysis of load and growth of Chlamydophila psittaci. J Pediatr Surg. and Robert J
Schaer. Joy Jadrich. May . Kate J Papenfuss. . Plos One. Biotechnol J. . Globally optimal
stitching of tiled D microscopic image acquisitions. Stephan Hegge. . Jason W Johnston.
Delphine S A Beeckman. Food Res Int. Noel Jabbour. D M L Cooper. . Plant Methods. Peter
A McAtee. Apr . and Friedrich Frischknecht. C Igathinathane. and Clark A Rosen. Richard M
Lindley. and W. T Sun. . Bioinformatics Oxford. . Jan . discussion . Jan . e. and Vito
Quaranta. Tal Shprung and Illana Gozes. Microsc. and Alicia Hidalgo. M Gwen Connell. A
new approach to geometrical measurements in an animal model of vocal fold scar. . Manuel
G Forero. An ImageJ plugin for the rapid morphological characterization of separated
particles and an initial application to placer gold analysis. H M Macdonald. Ernesto Resnik.
Mikhail Kudryashev. . Feb . Jun .
Int J Radiat Oncol. Zhuang Tian. Feb . Gina Lockwood. and S. and J. Jan . Jnos Szllosi.
Pentacam tomograms a novel method for quantication of posterior capsule opacication. Jan .
Thomas Haustein. W. Publications of National Astronomical Observatories of China ISSN .
and Alyson E Fournier. Benjamin M Chain. Neelufer Bana. Madeline Pool. Jan . van
Hylckama Vlieg. Christopher A Myrick. Jan . E Mols. Jan . Dilraj Grewal. Sep . Cytom Part A.
. S Sieuwerts. . Patrick Card. Amit BarOr. AccPbFRET an ImageJ plugin for semiautomatic.
Astronomical Research and Technology. May . and Laura A Dawson. Point analysis in Java
applied to histological images of the perforant pathway A users account. Masoom A Haider.
Springer. and Chuanlai Xu. . Rajeev Jain. M de Vos. Gagandeep Singh Brar. A new
development of measurement of Nortestosterone by combining immunochromatographic
strip assay and ImageJ software. . Jan . Lett Appl Microbiol. Jun Xu and Dong Chen. Giorgio
A Ascoli. . A simple and fast method for determining colony forming units. . J Neurosci
Methods. Zhenxing Chen. . and Gyrgy Vereb. Dora Brites. M Math. W. F. Digital image
processing An algorithmic introduction using Java. BMC Bioinformatics. Li Qiang Liu. . and
Wolfgang Alt. Ruggero Scorcioni. . J. Invest Ophthalmol Vis Sci. . and German Barrionuevo.
Jan . Robert F Miller. Automated Analysis of NeuronJ Tracing Data. Food Agr Immunol. and
Satinder Pal Singh Grewal. J N Am Benthol Soc. Susan N Wright. and Lorene M Lanier. A
lowcost system for capturing and analyzing the motion of aquatic organisms. and David R
Katz. . E. Desing and Implementation of the Image Format BatchConversion Software Based
on ImageJ. Image analysis of timelapse moviesa precision control guided approach to
correct motion artefacts. P Columbus. Comput Electron Agr. A. E. Karl Schilling. Chifang
Peng. Jan . Perry Choi. Shape identication and particles size distribution from basic shape
parameters using ImageJ. Jan . Anna Kirilova. J Neurosci Methods. Quantitative imaging
assay for NFB nuclear translocation in primary human macrophages. L. R Methuku. fully
corrected analysis of acceptor photobleaching FRET images. T. NeuriteTracer a novel
ImageJ plugin for automated quantication of neurite outgrowth. Mahdad Noursadeghi.
Alexander Glassmann. Jan . Jul . Joachim Thiemann. Kristy K Brock. Cynthia Eccles. C
Igathinathane. O Pordesimo. . Jonathan Popko. Wilhelm Burger and Mark James Burge.
Threedimensional motion of liver tumors using cinemagnetic resonance imaging. J Immunol
Methods. D Batchelor. Joachim Kappler. ISBN . A. Jnos Roszik. Jhen Tsang. David Hecker.
M de Bok. Adelaide Fernandes.
Commun. . Jan . Sep . Martha L Narro. and Donald M Bers. World J Surg. Tony J Collins.
Brian A Irving. and Ch Klopp. Glenn A Gaesser. Jan Willem W M Greve. Obesity Silver
Spring. and I Esteve.. C Nelson. Bioinformatics. Eur J Nucl Med Mol I. FRETcalc plugin for
calculation of FRET in noncontinuous intracellular compartments. Jacques Malet. T Carlier.
and Cornelis H C Dejong. and Linda L Restifo. and Mark T Madsen. Kevin M Schartz. A
Lisbona. Feb . Virginie MonnetCorti. Jan . Microsc. and Joachim Walter. ImageJ based.
Christopher K Davis. Development of a novel CASA system based on open source software
for characterization of zebrash sperm motility parameters. Root coverage assessment
validity and reproducibility of an image analysis system. . Ultramicroscopy. Per Olav
Johnsen. . NIH ImageJ and SliceOMatic computed tomography imaging software to quantify
soft tissue. . Journal of microscopy. Cell Physiol. V Portillo. . . David W Brock. . Mar . Nov .
AGScan a pluggable microarray image quantication software based on the ImageJ library.
Simon A W G Dello. Y Tsunashima. R Carmona. Aug . Theriogenology. J Clin Periodontol.
Kevin S Berbaum. Robert T Caldwell. Feb . A Sol. . Feb . Jan . David Stepensky. Sep .
Philippe Thvenaz and Michael Unser. F Lopez. WorkstationJ workstation emulation software
for medical image perception and technology evaluation research. Aug . and R MuozChpuli.
Eckard Picht. NeuronMetrics software for semiautomated processing of cultured neuron
images. Jules J G Slangen. R Cathelin. Pt .. J Mas. BioTechniques. An imageJ plugin to
create whole body transmission scan using CT scanner a validation study. Stephen J
Wigmore. SparkMaster automated calcium spark analysis with ImageJ. Marcel C G van de
Poll. . Robert Kraft. Mar . A new method based on image analysis for determining
cyanobacterial biomass by CLSM in stratied benthic sediments. Res. Nov . Robert
Dougherty. Medical Imaging Image Perception. Quantication of the D microstructure of SC
surfaces. Suppl. and M Bardies. . Alon Efrat. J M PrezPomares. Brain Res. Gary Chinga.
Francis Mora. and Philippe Bouchard. J A Guadix. and Arthur Weltman. Tech. Biophys.
Userfriendly semiautomated assembly of accurate image mosaics in microscopy. Stphane
Kerner. Daniel Etienne. Am J Physiol. Biochem. S S. web accessible tool for treatment plan
evaluation. D Macas. and P Balter. ImageJ for microscopy. Aleksey V Zima. L Ferrer. Carola
Wenk. Fan Yang. . Med Phys. B Choi. C . Elisabeth Lunden Berli. Pt . Lothar A Blatter. Judy
Y Weltman. Jonas G WilsonLeedy and Rolf L Ingermann. Ronald M van Dam. Journal of
microscopy. Open source. Liver volumetry plug and play do it yourself with ImageJ. Marc H A
Bemelmans. . A simple technique of image analysis for specic nuclear immunolocalization of
proteins. Jul . Regina G H BeetsTan. Res.. Jan .
JeanLuc Galzi. Lab Invest. J Bloom. AA. O Rampado. and K. Spectral unmixing of
multicolored bioluminescence emitted from heterogeneous biological sources. and G
Gandini. Jason Moat. Jan . and S M Kurtz. and K. Olivier Marchal. and David PiwnicaWorms.
Biol Cell. J C Grochowsky. and Gianandrea Pasquinelli. T Bloom. R Ropolo. Ravikanth
Nathani. Computeraided meiotic maturation assay CAMMA of zebrash Danio rerio oocytes in
vitro. and Sandra Lecat. page . . . Pt . Jan . Automated quality control in computed
radiography. R. Cdric Messaoudi. a useful tool for biological image processing and analysis. .
AA. Jamie Walker. . L Savio. Quantifying the intercellular forces during drosophila
morphogenesis. May . Res. O Davini. BMC Bioinformatics. TomoJ tomography software for
threedimensional reconstruction in transmission electron microscopy. Charles A Lessman.
Nov . Thomas Boudier. Joel B Sheeld. Sabrina Valente. T Bloom. . and Sergio Marco.
Pascale DupuisWilliams. a free image analysis software package. Nov . Erik V Rencs.
Analysis and documentation of progression of Fuchs corneal dystrophy with retroillumination
photography. R Siskey. Raque Uddin. Carlos Oscar Sanchez Sorzano. Thomas Boudier. and
David M Sabatini. Jan . . Jan . Polina Golland. W Matthew Leevy. David G Emmert. Tech.
Cornea. Thouis R Jones. Nol Converset.. Anne E Carpenter. Radiol Med. and Sergio Marco.
Muriel HachetHaas. A Hii. . Nicole Garreau de Loubresse. A Hii. . J Biomed Mater Res Part
B Appl Biomater. Hans Matthes. Color separation of IHC stained slides using ImageJ. P
Isoardi. Jan . and Gregory W Schmidt. D Helling. Laura Foroni. a freely available software
package. An algorithm for counting IHC stained nuclei using ImageJ. L W Alaways. John D
Gottsch. Michael R Lamprecht. Dec . Cdric Messaoudii. Joo Han Chang. Multipleaxis
tomography applications to basal bodies from Paramecium tetraurelia. Mar . . Digital
photogrammetry for quantitative wear analysis of retrieved TKA components. Colin Clarke.
Walter J Stark. Jul . . A Izzo. Francesco Alviano. Microsc Microanal. Journal of microscopy.
In Han Kang. J Bloom. Clement J Cheng. A guided tour into subcellular colocalization
analysis in light microscopy. X. R De Lucchi. Microsc. Ma and M. Robert A Lindquist. and
Jianxiong Liu. Seth T Gammon. Shimon Gross. David A Guertin. S. . Mar . Dec . Dec .
Ultrastruct Pathol. Francesca Papadopulos. Modern Pathol. Hutson. American Physical
Society. S Bolte and F P Cordelires. Sophie Gioria. Anal Chem. Genome Biol. Cellproler
image analysis software for identifying and quantifying cell phenotypes. E Most. Catia Orrico.
T Cammarota. Olof H Sundin. Mol Reprod Dev. D Helling. Matthew Spinelli. George W
Gokel. FRET and colocalization analyzera method to validate measurements of sensitized
emission FRET acquired by confocal microscopy and available as an ImageJ Plugin.
Common tasks in microscopic and ultrastructural image analysis using ImageJ. Jan .
ImageJ. Ola Friman.
Tech. Microsc. Daniel Sage. M Doube. Writing ImageJ PluginsA Tutorial. Creation of
DICOMaware applications using ImageJ. David Gandara. Ludovic Ferrer. Y Grealou. Pierre
Loonis. and Christopher Coulon. and James R Macfall. c American Geophysical Union.
American Geophysical Union. Neuroinformatics. Jan . Apr . P Steiner. Apr . PixFRET. . . . J
Parasitol. Dec . Eben Gering and Carter T Atkinson. of Media Technology and Design
Hagenberg. Duncan E Donohue. J Uszkoreit. Batrice Desvergne. S Gaudaire. Luko Laptalo.
Scanning. M Jacob. Cytometry. I Resche. . and M BardiAs. Jan . Aug . Res. A colourmap
plugin for the open source. . Jrme N Feige. . Eur J Nucl Med Mol I. . for astronomy. image
processing package. A new ImageJ plugin to correct for partial eect volume. Design and
validation of a tool for neurite tracing and analysis in uorescence microscopy images. J Digit
Imaging. E Meijering. Walter Wahli. and Laurent Gelman. and Olivier Couturier. Edited by
Flynn. and Michael Unser. an ImageJ plugin for FRET calculation that can accommodate
variations in spectral bleedthroughs. de/ konen/ WPFBV/ tutorialImageJV. ImageJ. Este
Geraghty. Medical Imaging Physics of Medical Imaging. astroph. Austria. . Computerassisted
image analysis of bronchioloalveolar carcinoma. Jan . M Bell. T Carlier. and M Unser. K
Parton. and Giorgio A Ascoli. . Jean B Berruchon. . . Quality controls for gamma cameras
and PET cameras development of a free opensource ImageJ program. Clin Lung Cancer.
Florence Hediger. Derick Lau. A Lisbona. IEEE Trans Image Process. A rapid method for
counting nucleated erythrocytes on stained blood smears by digital image analysis. ImageJ.
Kerry M Brown. D Autret. Sep . Daniel P Barboriak. EarthTutor An Interactive Intelligent
Tutoring System for Remote Sensing. SS. Automatic tracking of individual uorescence
particles application to the study of chromosome dynamics. Jan . http// www. Clin
Neuropathol. Automated nuclear segmentation in the determination of the Ki labeling index in
meningiomas. Jan . Regis Cuissard. Java based. C Rousseau.. Jan .gm. Susan M Gasser.
Mar . ImageJ and analysis of correlated confocal and BSESEM imaging. . Jennifer L West
and Ian D Cameron.pdf . Computers amp Geosciences. Jan . . Thomas Carlier. W
Bailer.fhkoeln. Upper Austria University of Applied Sciences Dept. and W Feiden. G Brunet.
and E Smith. Daniel Sage. Gerald E York. Giampaolo DAlessandro. Sep . Part A the journal
of the International Society for Analytical Cytology.. Y J Kim. Using the medical image
processing package. Anthony Seibert. G Delpon. Anthony O Padua. Franck R Neumann. H
Hirling. B Bridji. arXiv. Jun . Adeline Martineau. A. A crossplatform freeware tool for digital
reconstruction of neuronal arborizations from image stacks. L Ferrer. B F M Romeike. JC F
Sarria. K Moodley and H Murrell.
Biophotonics International available at http//webeye. M. .pdf. .J Magalhaes. .ophth. and SJ
Ram. P.edu/dept/biograph/abramo/ imagej.uiowa. Image Processing with ImageJ.D Abramo.
. FITS . . . . . . . . . . ASCII . . . Java ARchive. Frames Per Second. . CT . URL . Option or
Meta key. . . . . . . . . . . . . Operating System. . . . . . voxel . . NaN . . . . . . . . . . . . . . . . . FFT . .
. . RAM . . . . . . HTML . . . . DICOM . . . . . . Computed Tomography. . . FAQ . . . . . American
Standard Code for Information Interchange. . Shift . . . . . . . MIP . . . . . . Bits per pixel. CCD .
. . . . . . . . Alt. . . . . . . . . . . . . . . . . . . . . . . . Pixels per cycle. . . . . . . . EDM . . . . MJPG .
Ultimate Eroded Points. . . . p/c . . . . Tagged Image File Format. . . . Hue Saturation
Brightness. . LempelZivWelch. . . Portable BitMap. . . . . pixel . GUI . Lookup table. . . . .
Uniform Resource Locator. UEPs . . . . . . . . . . . . Fast Fourier Transform. . . . . Region Of
Interest. . bpp . HSB . . . . MotionJPEG. . Digital Imaging and Communications in Medicine. .
. . . . Maximum Intensity Projection. . . . AVI . Audio Video Interleave. . . . regex . . . . Picture
element. RGB . . . . . . . . . . . . . . . . API . . . . . . . . . ROI . . . . . CP . . . . HyperText Markup
Language. . . . . . . . . . . . . . . . . . . JPEG . . . . . . . FHT . Color Picker. . . . . . Hexadecimal. . .
ppi . Dots Per Inch. . Portable PixMap. . . . . . . . Fast Hartley Transform. . . What You See Is
What You Get. . . . . . . . . ImageJ. RandomAccess Memory. Ctrl . . Pixels per inch. . . LZW . .
. . . . . . . . Volumetric pixel. . . . . . . . . Graphical User Interface. . . . . . . . . . . . . . . .
CommaSeparated Values. . . . . . . . fps . . Joint Photographic Experts Group. . . . . . . .
Euclidian Distance Map. . . . . . . . HDR . . . . . . . . . . . JAR . . . . . . . . . . . . . . In this guide also
the Command key in Apple keyboards. . . . . . . Binary digit. OS . . . ChargeCoupled Device.
DPI . . . . . . . . . . PBM . . . . . Control key. . . LUT . . . . . . . . . . . . . . . . . . . HEX . . . . Regular
expression. . . . Shift key. . . . . . . . . Not a Number. . . . . . . . . . . . . . PNG . . TIFF . . . . . . . . . .
. PGM . . . . Portable GrayMap. . bit . CSV . . . Graphics Interchange Format. . IJ . . . . PPM . .
. . . . Flexible Image Transport System. . Application Programming Interface. . . . . . . . . Red
Green Blue. . High Dynamic Range. Frequently Asked Questions. . . . . . WYSIWYG . GIF
.List of Abbreviations and Acronyms Alt . . . Portable Network Graphics. . . . . . . . . .
. D Dead pixels. . Curve tting. Background pixels. . Angle tool. Bio. . Models. . Display range.
. AND see Logical operations. . . Benchmark. . Animation. . . . . . Convolution. Batch
processing. Add see Math. Channels. CodeBar. . Brush selection tool.Index A ActionBar.
Developer resources. . .hyperpage. Elliptical selection. Distribution. DICOM. Balance. Crop. .
. Color Background. Area under the curve see Denite integral. . . CIE Lab. Convex hull. AVI.
Grayscale images. CatmullRom see Interpolation CCD. Blindness. Calibration bar.
Appearance. Concatenate. Canvas. . . Bicubic interpolation see Interpolation. Spatial. . . .
Capture image. Optical density. B Background see Subtract Background. Color lter array.
Erosion. . Aspect ratio. AutoRun. Centroid. . DPI. . Coordinates. . . . . . . C Calibration.
Brightness/Contrast. Blend. Dilation. Despeckle. . Cell Counter plugin. Control Panel. .
Coronal see Orthogonal views. Area. Black background. . Compile. Bilinear interpolation see
Interpolation. . CT. . Bug reporting see also Debug. Duplicate. Center of mass. Analyze.
Distance map see EDM. . . . CellProler see Interoperability. Bounding box. . . . CIE. . . . . Add
images see Image calculator. . Downsizing. Settings. Color quantization. Dirichlet see
Voronoi. Foreground. E Editor. . Threshold. . Command key. Clipboard. Conversions. Divide
see Math. Deconvolution see Convolution. BeanShell. . . Caliper length see Feret. Drag amp
Drop. Dot blot analysis. Annotations. Combine. . Bitwise operations. Debug. Counting
objects. Composites. Bioformats see LOCI. . Arrows. . . Clojure. Delaunay see Voronoi.
Euclidian distance map. Color Picker. Circularity. Binary. Eroded points. . Divide images see
Image calculator. CSV. . . . Contextual Menu.
JFileChooser. Find see Search. D Gel analysis. G Gamma correction. . Manager. Graph.
Math. IsoData see Threshold. Global calibration see Calibration. Huang see Threshold. K
Kurtosis. . Ellipse. . MinError see Threshold. LZW compression. LUT. Quality. Fractal box
count. . Macro Tools. Layers see Image overlays. Curve see Curve tting. . LOCI BioFormats.
Image types. JPEG. Hot pixels. J Java. . Image sequence. Frame interval. Jython see
Python. Install. . Flatten. Mask. Transparency. Log. . Grouped Z Projection. . . . .
Hexadecimal Hex colors. . Median cut algorithm see Color quantization. MIP see Projection.
JPEG. Linear regression see Curve tting. Frequency domain. . MBF ImageJ. Memory. .
Image formats Native. FITS. ROIs. . Heckberts median cut algorithm see Color quantization.
M Macro functions. . Logical operations Images. Cubic spline. . . Hyperstacks. . . Fit Circle.
.Exponential transformation. Minima. . Li see Threshold. Eye dropper. Max. . Holes. Lossy
compression. . H HandleExtraFileTypes. . GIF. Installation. . Metadata. F Fast Fourier
transform. L Lanes see D Gel analysis. Levels see Brightness amp Contrast. . Freehand line
selection. Lossless compression see LZW and PackBits. . Magenta Green Blue MGB. .
Interoperability. . . ImageJ for Microscopy see MBF ImageJ. I Image calculator. Mailing lists
see Help resources. MATLAB see Interoperability. MaxEntropy see Threshold. Maxima.
Macro Toolset Switcher. . Fiji. Filters. . Fast Hartley Transform. . Histogram measurements.
Measure. Heatmaps. . HSB. Feret. Measurements. . Gaussian Blur. . . Help resources.
Macro recorder. Macros. . Min. . Grayscale morphology. Magnifying Glass Tool. Integrated
density. MIJ see Interoperability. . Histogram. . Freehand area selection. . . Import. .
Nonnative. JavaScript. . Interpolation.
. . Screenshot. Sliding paraboloid see Rolling ball. . Polygon selection. Reset. Renyi see
Threshold. . Resampling see Interpolation. Proxy. Results table. PPI. Paste. . SalsaJ. Noise.
Processing. Transparency. . Segmented Line selection. Perimeter. Plugins. . . Popup menu
see Contextual menu. Revert. Regex. Skewness. Sample Images. ROI Manager. Options
see Settings. Rolling ball. Scale. . Outline. Moments see Threshold. Performance see
Memory. Shadows. Rotate. Restore. . . R R GNU S see Interoperability. . Q Quit. Multiply
images see Image calculator. Nonbackground pixels. ROI Manager. OR see Logical
operations. Polar coordinates. Otsu see Threshold. PNG. Shape descriptors. Square root
transformation. . Preferences see Settings. . Shanbhag see Threshold. Polynomial
regression see Curve tting. Python. Settings. . .MJPG. Oval selection. Scale bar. Multiply see
Math. Redo. . Sobel edge. Rene. Search. S Sagittal see Orthogonal views. . . . . Outliers.
Spatial scale. Sharpen. xi. . Morphological operators. P PackBits compression. Raw density.
Power spectrum. . Solidity. Montage see Stacks Montage. Rectangular selection. Scrolling.
Reex angles. . Overlay. . Point tool. Planar views see Orthogonal views. . . Progress bar. . . .
Record see Macro recorder. Modier keys. Plot prole. RAM see Memory. . Multipoint tool.
Composite. Projection. Reduce. ROI see Selection. Properties. Orthogonal views. bit. . xi.
Smooth. Panel gures see Stacks Montage. . . RGB. . Pixel size. Shortcuts. Round rectangle.
Modier Keys. . Ruby. O Optical density see Calibration Optical density. Reciprocal. . . .
Precision. . Skeleton. Print. Scientic notation. . PGM. . . . . Raw. . N NaN. Roundness. .
Selection.
Transform. Voxel depth. . Threshold. Status bar. Hyperstacks. Color Picker. Web browser.
TIFF. xi Synthetic images. . . . U Undo. Compressed TIFF. . . ZIP. Oval. Labeling. Virtual. . .
Macro Toolset Switcher. StartupMacros. Time stamper. Y Yen see Threshold. Voronoi. . .
Straighten. Point. . Magnifying Glass. . Tracing see Wand tool. . D Projection. W Wand tool. .
Text. . Segmented Line. Toolset. Color. Substacks. Wand. . Montage. Binary images. . . T
Tessellation see Voronoi. . Window management. . Brightness/Contrast. Reduce. Macro
Tools. . Zoom. . . From List. . V Variance. Text. Statistics. Line Selection Arrow. . Surface.
Export. Round Rectangle. Tools Angle. Subtract Background. . Syntax highlighting. Polygon.
X XOR see Logical operations. Toolbar. . . Subtract see Math. . . Tolerance Wand Tool.
.Square transformation. Subtract images see Image calculator. Fit to Screen. . Threads.
Stacks. Rectangle. Unsharp mask. Straight Line. Updates. ZProle. Z Z Projection see
Projection. Straight line selection. Prole. YUV. D viewer. . Tools. Multipoint. Scrolling. . Area
Selection Brush. Translate. . Virtual stacks see Stacks Virtual. Freehand Line. Projection see
Projection. Freehand. Watershed. Ellipse. .
P. February . available at http//webeye..pdf .mcgill. Magalhes. has been intentionally
omitted.b. . de/guide. there are two possible ways to reference ImageJ . Nevertheless. .
Maryland. National Institutes of Health.J.ca . depicted on the front page inspired the ImageJ
icon for Mac OS X.git.uiowa.nih. because there has never been accompanying
documentation for some of the described commands.J. About the Cover The Hartnack
microscope ca. QC. Fiji webpage or Tony Collins ImageJ for Microscopy manual.About This
Guide The contents of this guide have been retrieved using htmltext from the ImageJ website
and updated where necessary using either information posted on the ImageJ mailing
list.D.mpicbg. Schindelins Tutorial Maker plugins. ImageJ Documentation Portal. nih. Abrmo.
Rasband. ImageJ. Canada tiago. The ImageJ User Guide Version . W. the L TEX and LYX
source les of this document are available through a Git version control repository at
http//pacic. Bethesda.gov/ij/. The HTML version may use icons from the Tango Desktop
Project under a Creative Commons license.. To reference this document ..S. U. W.S.
Landinis IJ Robot and J. Montreal. Image Processing with ImageJ. S. All other images in the
guide were created with Apple Grab . and ImageJ . some parts of this guide were written
from scratch based on the relevant ImageJ source code and/or authors own
experience.gov/ij/docs/userguide. Legacy nomenclature that became obsolete with version .
and Rasband.ophth. Due to ImageJs heavy development this guide will always remain
incomplete. More information about the original picture can be found on the ImageJ
website.q.pdf. Comments and Suggestions Tiago A. USA. .edu/dept/
biograph/abramo/imagej. loaded with G. and Ram. As explained on the ImageJ web site. A
This is a free content guide. . Biophotonics International. http//imagej. T. Ferreira. You are
encouraged to contribute to the ImageJ documentation resources. preferentially by maturing
the ImageJ Documentation Portal or by committing changes directly to the Git repository.
Thanks to Johannes Schindelin. M.ferreiramail. Ferreira Centre for Research in
Neuroscience McGill University.. http//imagej.
.This document was typeset with TEXLive on Mac OS . . HTML version produced with
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