Essen BioScience
Product Reference
Version
Windows Compatibility
2012A
7, Vista, XP/SP3; 32 and 64-bit
2013A
7, Vista, XP/SP3; 32 and 64-bit
2013B
Win8; Win7, Vista: 32 and 64-bit;
XP/SP3: 32-bit; XP/SP2: 64-bit
2014A
Win8; Win7, Vista: 32 and 64-bit;
XP/SP3: 32-bit; XP/SP2: 64-bit
2015A
Win8; Win7, Vista: 32 and 64-bit;
XP/SP3: 32-bit; XP/SP2: 64-bit
Instrument:
Reference Name:
Document Number:
Date:
IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
Release and Revision Dates
24 Aug 12 – Base software release
10 Oct 12 – GUI Revision 1 / Controller Revision 1
15 Oct 12 – Controller Revision 2
27 Nov 12 – Controller Revision 3
11 Jan 13 – Controller Revision 4
06 Mar 13 – Base software release
03 Apr 13 – Controller Revision 1
20 May 13 – GUI Revision 1 / Controller Revision 2
13 Jun 13 – GUI Revision 2 / Controller Revision 3
19 Nov 13 – Base software release
24 Feb 14 – GUI Revision 1 / Controller Revision 1
01 May 15 – Controller Revision 2
09 May 14 – Base software release
22 Sep 14 – GUI Revision 1 / Controller Revision 1
01 May 15 – Controller Revision 2
23 Feb 15 – Base software release
04 May 15 – GUI Revision 1 / Controller Revision 1
This document contains an overview of IncuCyte ZOOM® Software Releases. The table above contains a list of
major version releases in the first column. We refer to the major version as the “base” version from which
revisions are made. The 2nd column holds the Windows version compatibility list for the IncuCyte ZOOM®
Graphical User Interface (GUI). The 3rd column summarizes the release dates for the base and any revisions to GUI
and/or Controller software.
On the following pages are a list of ZOOM® features and fixes implemented in the base releases and revisions
starting with the 2012A version. Within each version section the revision details follow chronologically.
Page | 1
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
2012A Software Release -- 24 August 2012
GUI
Controller
Firmware
Motion Controller
20121.1.4622.xxxxx
20121.1.4609.xxxxx
20121.1.3.0
20121.1.1
Initial Software Release for IncuCyte ZOOM®

Windows Compatibility
o Windows 7 (32-bit or 64-bit)
o Windows Vista (32-bit or 64-bit)
o Windows XP Service Pack 3 (32-bit only)
o Not compatible with Windows 2000 or Windows Server
2012A Software Revisions
2012A GUI Revision 1 / Controller Revision 1 -- 10 October 2012
GUI
Controller
Firmware
Motion Controller
20121.2.4666.xxxxx
20121.2.4666.xxxxx
20121.2.15.0
20121.1.1
GUI Fixes and Improvements
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The tooltips on Image Blender slider controls no longer block the image refresh
The Image Blender mask weight slider is now disabled when the Blend Mode is set to Overlay
The Image Blender weight slider now properly weights the Phase channel when it is the only channel
displayed
The default mask colors provided by the Image Blender can now be restored via the Color Picker
control under “Custom Colors”
The “Add to image collection” utility was not correctly clearing its state in between uses, leading to
improper selected channels, etc.
When using the “Add to image collection” utility from a ScratchWound scan type, the Analysis Job
type is now set to “ScratchWound” by default
When using the “Add to image collection” utility from a TiledFOV scan type, the Analysis Job type is
set to “Angiogenesis” by default
In the Processing Definition editor, a user is prompted to retrain if an image collection used for phase
analysis training has been changed since last trained. Retraining was occurring regardless of the
answer; now if the answer is “No”, the job is left unchanged
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Instrument:
Reference Name:
Document Number:
Date:
IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
When an Angiogenesis or NeuroTrack Processing Definition is edited, the Image Blender now selects
the correct channels automatically based on the definition’s “Analyze” channel settings
The numeric up/down controls found in the Processing Definition editor now work correctly when a
number other than a whole number is typed in manually. Example: the “Adjust Size” control in the
Basic Analyzer
Search Grids now display the Edit Filter control and column headings in red when using the Auto Filter
feature (1st row)
The Analysis Job launch form now correctly displays the scan pattern based on the selected times
Improvements were made to the NeuroTrack Analysis Job:
 The algorithm was improved to detect high-contrast neurites more reliably
 The Processing Definition editor controls improve upon the usability
The Scheduler’s drawer view now correctly handles the drawing and reloading of the largest (3x
standard) trays
The acquisition time controls in the Scan On Demand interface now work correctly when the
scheduler is refreshed following an on-demand scan
When using the Add Vessel utility in the Scheduler, the drawing of the Tray at the base of the form
now updates correctly when using the grid Auto Filter feature (1st row)
Scan patterns are now correctly restricted to having a maximum 255 images per well
The Scan On Demand Unique ID now appears in the main window “View Scans” vessel properties
The lower bound of the Passage control in the Vessel View is now correctly set to 1 instead of 0
Improved the bulk image export progress window behavior when an export error is encountered
Movies exported in WMV format no longer have the last frame repeated 3 times
When a user account is deleted and recreated, it no longer retains its original Permission Level
The contents of the “Help | About” window is now included as a header in an exported GUI log
Improvements were made to the login speed
Controller Fixes and Improvements
o
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The camera now operates more reliably at very short exposure times (less than 0.2 msec), which are
often encountered with phase imaging at 4x magnification
The scan time estimates in the Scheduler have been corrected for Wide-Mode ScratchWound scans
that acquire more than one image per well
A bug was fixed that was reporting Spatial Calibration tests as having Passed even though the belt
calibration portion of the test was in fact Failing
The Fluorescence calibration was improved:
 The analysis of camera “hot pixels” is now correctly handling a special case that was overlooked
and can cause the procedure to fail with an error
 The calibration is no longer prone to fail if the middle and rear trays have not been spatially
calibrated
When a Self Test is stopped via the Eject button, the control software no longer blocks upcoming
activities like scans that are requested to start before the original Self Test completion time
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Reference Name:
Document Number:
Date:
IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
Cancelling the Auto Warmup function via the Eject button or the LCD panel now functions reliably
Logic was added to the control software to block certain activities like Self Tests and Auto Warmups
under certain device conditions (drawer open, handling an Eject button press, etc)
A post-activity delay was added to the function that checks the optics board and filter module for
excessive (> 50 degrees C) temperatures
When manually stopping the gantry fans using the control software, a timer is used to restart the fans
later. The period of this timer was extended to 5 minutes
Controller motherboard sensors are now correctly updated periodically before testing against
warning thresholds
A function was added to the control software user interface for on-demand motherboard sensor
readings
The MCU reprogramming tool was made more robust via longer delays and retries
All tiled image sites are now logged to scan folders on the controller
Invalid characters are filtered prior to entering database logs
Improvements were made to the drawer leveling utility used by manufacturing and service
A bug was fixed that was resulting in over-quantization of GCU and RCU levels, especially when very
long acquisition times are used
A bug was fixed that was could potentially mark an open-ended Analysis Job as having failed
catastrophically (unrecoverable) when it interrupts an already-running job post-scan
2012A Controller Revision 2 -- 15 October 2012
GUI
Controller
Firmware
Motion Controller
20121.2.4666.xxxxx
20121.2.4666.xxxxx
20121.3.1.0
20121.1.1
Controller Fixes and Improvements
o
o
o
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Fixed a bug that was launching Open-Ended Analysis jobs too rapidly at the end of a scan, leading to
database lock errors and Job Processor terminations. These in term could lead to a job getting
marked with a Catastrophic Failure status
After adding a 1-minute, post-startup delay, Job Processors now launch more reliably when the
instrument control code starts after a Controller boot
Fixed a problem associated with applying more than one Scan Type while first scheduling a vessel.
The control code now correctly configures the instrument to scan per the last-scheduled Scan Type.
This was particularly common when scheduling 96-well Corning scans on systems with an
Angiogenesis license, for which Tiled FOV is the default scan type
The 2012A Rev1 controller upgrade package was not correctly deploying a 3rd-party library required
for bundling information collected via the “Setup Files” diagnostic retrieval function
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
2012A Controller Revision 3 -- 27 November 2012
GUI
Controller
Firmware
Motion Controller
20121.2.4666.xxxxx
20121.2.4666.xxxxx
20121.4.7.0
20121.1.1
NOTE: this controller revision was triggered by an unexpected new version of the firmware running on the
ZOOM® camera. This change forced an adjustment in the ZOOM® control software to work with the new camera
firmware. Cameras with a Camera Device Version of 105601-06 require this controller upgrade. Older cameras
running 105601-05 do not require this revision (optional), but will function correctly if the revision is applied.
Controller Fixes and Improvements
o
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Adjusted the device control software to work correctly with newer cameras that are running Camera
Device Version 105601-06 firmware as opposed to 105601-05
The camera driver/API version is now reported in the GUI “Help | About” window
The fluorescence calibration procedure was improved to handle better the lower black level in the
newer (105601-06) cameras
The calibration data are no longer lost when a new scan starts within a few seconds of the end of the
previous scan. Lost calibration data usually results in fluorescence images with incorrect calibrated
values
Scans that experience numerous, consecutive exposure time issues during focusing no longer
terminate and reboot the controller
Spatial calibrations that fail during the confirm procedure no longer appear with a “Pass” status in the
GUI
The chance of a motion error during three-axis moves was significantly reduced
2012A Controller Revision 4 -- 11 January 2013
GUI
Controller
Firmware
Motion Controller
20121.2.4666.xxxxx
20121.2.4666.xxxxx
20121.5.0.0
20121.1.1
Controller Fixes and Improvements
o
Improved the nightly MCU reset function to eliminate the possibility of an undesirable watchdogtimer reset of the controller occurring after the MCU reset.
Page | 5
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
2013A Software Release -- 06 March 2013
GUI
Controller
Firmware
Motion Controller
20131.1.4819.261xx
20131.1.4800.329xx
20131.1.7.0
20131.1.0
Windows Compatibility
 Windows 7 (32-bit or 64-bit)
 Windows Vista (32-bit or 64-bit)
 Windows XP Service Pack 3 (32-bit only)
 Not compatible with Windows 2000 or Windows Server
Overview of Major Features
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Vessel Archives
 Scope
 Archives hold one or more vessels and their associated jobs.
 Archives can be written to ZOOM®-attached hard-drive storage via eSata or USB connections.
 Archives can be written to folders that can be browsed to from the user’s PC.
Opening Archived Vessels
 When browsed to from the user’s PC, archives can be connected to like ZOOM® devices.
 Alternatively, vessels can be opened individually in vessel views.
Management
 Archives can be deleted.
 Archive size can be retrieved.
 Archive errors can be viewed.
Limitations
 Archives cannot be opened while storage is still attached to ZOOM®.
 Processing definitions and image collections cannot be viewed.
 Analysis Jobs cannot be run on archived vessels.
Vessel View
 Improved organization of metrics via tree-based lists.
 Double-clicking a plot point will launch the vessel view.
 Improved warning messages surrounding spectral un-mixing.
 Improved Min / Max increments when adjusting image viewer settings.
Miscellaneous
 Graphics added to buttons throughout.
 Limitations placed on editing and deleting other users’ processing definitions, image collections,
analysis jobs, etc.
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Instrument:
Reference Name:
Document Number:
Date:
IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
Detailed List of GUI Improvements and Fixes
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Schedule Scans
 Changing the scan pattern after the first scan has completed no longer affects the scheduled
Analysis Job.
 After a vessel is added, it remains highlighted to show it is selected.
 The spectral un-mixing warning tooltip now appears only when it should (based on the channel
selection).
 There is now better enforcement of immutable scan parameters when one tries to apply an
invalid schedule after a vessel has been scanned at least once.
 A typical example is an attempt to change Channel Selection or Scan Type after the scan has
commenced or even completed.
 If a scan pattern is in use in either of the schedules, then edits to this pattern are now blocked if
the edits put one of those two schedules into an invalid state.
 In the case of switching to another connection when there are unapplied schedule changes, the
connection is now correctly set back to the current connection if the user decides to cancel the
connection switch.
Vessel View
 A warning is now issued when a dual-color Analysis Job is launched with no spectral un-mixing.
 A warning is now issued when attempting to exit the Vessel View with unsaved spectral un-mixing
parameters.
 When no spectral un-mixing is set in a two-color vessel, the un-mixing controls are now placed in
a warning state with a warning bubble and a red controls background.
 When using “Export Current Image” with an open Analysis Job, the GUI no longer generates an
error if there are missing masks due to processing errors.
 The Info bubbles are now active when Job Details are viewed.
 The Analysis Job notes are no longer losing “new line” characters.
 The NaN replacement value for metric export now accepts a blank field by inserting a space
character.
 The correct image is now exported if one navigates to a new time or image site without actually
currently viewing the “Image” tab in the Vessel View.
 The single-image export tool was improved by providing default file names that identify key
pieces of information required for diagnosis: Vessel ID, Scan Time, and Image Site.
Graph/Export
 The graph window now offers a menu option that allows you to edit the x- and y-axis plot labels.
 Plot title separator characters were changed from “/” to “-“.
 User customization of the Analysis Job object properties table found at the bottom of the Vessel
View is now stored as a preference and recalled across vessel views, connections and from
session to session.
 Corrected a bug associated with the “Smooth Lines” and “Estimate Rate of Change” graph tools.
When graphing data where the metric cannot be evaluated (e.g., a divide-by-zero condition that
generates a NaN metric value), these tools no longer generate large, erroneous values.
Page | 7
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Instrument:
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015



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The unnecessary “N.A.” subtitle was removed from Basic Analyzer histogram plots.
The “Raw Data To Document” drag-and-drop function is now functional.
The mouse-over tooltip that shows the x-axis time value now works when the mouse is placed in
the lower portion of a plot.
 “Object Mean Intensity” histogram plots now have correct x-axis units.
 Image Sharpness scan metrics were added for all channels. These diagnostic metrics can now be
viewed by users with Administrator credentials.
Processing Definitions
 Editor
 The sort order of the Preview and Training image collections is now reversed so the newest
appear at the top.
 The user is now warned if he attempts to close the GUI with unsaved changes.
 The “Save” button is now disabled if you are not the owner of the processing definition.
 The “Save as” button is now enabled if the processing definition has a valid phase model,
circumventing the need to Preview before saving.
 “File | Open” and “File | New” menu items were added.
 User customization of the object properties table is now stored as a preference and recalled
each time the editor is used; these are the same preferences that are recalled when an
Analysis Job is opened in the Vessel View.
 The ownership of the “Save as” processing definition is now correctly assigned to the user
requesting the “Save as” operation.
 The uniqueness of user-defined Phase Object Names in the Basic Analyzer is now enforced.
 Job Details
 Information and warning bubbles are now displayed even when they are members of a group
box in which all other controls are disabled.
 Read-only Definitions
 A number of new processing definition attributes were added, including some that might be
used in the future. For instance, a “Read Only” field now prevents any user from editing the
definition, but does allow a user with Administrator credentials to delete it.
 Read-only processing definitions were introduced in the form of “DEMO USE ONLY”
definitions.
Image Collection Editor
 A “File” menu was added, making this editor behave a little closer to the Processing Definition
editor, which offers Open, New, Save, and Save As menu items.
Administer
 A device tests viewer now allows users to navigate to each test and view the test history:
 Images were added for all of the tests, the most important of which are the Optics Test and
Fluorescence Calibration images.
 Rotation and dirt checks were added to the Optics Test.
 Users with Administrator privileges can now reset/change another user’s password.
 Deleting larges sets of data (Analysis Jobs, sets of vessels, etc.) no longer generates an error. The
GUI now returns a message that the task is continuing in the background.
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Instrument:
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Date:
IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015

o
The selected vessels in the grid on the Delete tab no longer lose their selected state when
navigating away from this grid.
 The database export tool no longer fails when connected to a ZOOM® by IP address rather than
by name.
 New user accounts can no longer be created using reserved user names.
 Maintenance log entries can now be made by users with Administrator credentials.
Miscellaneous
 A new Neurite Outgrowth metric was added: "Neurite Branch Points / [Cell-Body Cluster Area]".
 Grid cells can now be copied to the clipboard via Ctrl-C, and grid rows can be copied using a rightclick in the leftmost column of a grid.
 The Free Space reporting in the lower left of the GUI was improved; the % report is always Free
Space, and the RAID Free Space calculation in now more accurate.
 Temperature graphs no longer continue to request updates after a connection is terminated.
 Additions were made to the GUI’s Help | About menu:
 Essen C++ Library and Job Processor version numbers
 Network NIC IP address
 The RAID cache policies
 Drive Image build ID
Detailed List of Controller Improvements and Fixes
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Scanning
 Sweep Mean errors no longer lead to scan cleanup issues and a subsequent scan-hang reboot of
the controller.
 Fixed an issue that made some instruments susceptible to rebooting (control software crash) after
a Scan On Demand scan completes.
 Color images are now saved when the first frames (or frames) are completely saturated and
image cropping is required [ImageLock and standard-mode ScratchWound].
 An issue was addressed for scans of ImageLock plates using cameras with a Camera Device
Version of 105601-06. The camera was generating errors that led to excessive retries and
extremely long scan times.
Spatial calibration at 4x magnification no longer fails on the bottom calibration tray windows when
the initial estimated coordinates are biased toward the rear of the instrument.
The Boot Warmup no longer runs if the drawer is open.
Attempts are now made to Park the gantry whenever a reboot or shutdown is requested.
Some regularly-scheduled Windows tasks are now suppressed. The most important of these is the
weekly disk defragmentation task, which is highly disruptive to scans.
The dskchk function is now disabled at boot for all partitions but the C: drive.
The Windows Start Repair tool (which can run at boot) is now disabled.
The z-axis travel limit was expanded by 2-3 mm, which helps with accessing an adjustment screw on
the z-axis assembly.
System sensor checks are now run at startup as well as daily.
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
The accelerometer sensor now takes single-axis readings before and after scans and looks correctly
for mechanical jolts during long-exposure color acquisition.
The RAID alarm is now disabled in a way that allows the control software to raise the alarm
periodically. Logic was added to raise the alarm daily (during working hours) if the RAID is in a
prolonged, non-optimal state.
The RAID diagnosis tools were enhanced to handle an arbitrary number of physical drives.
The motherboard watchdog timer refresh function now runs on a dedicated timer and performs the
refresh every 15 sec rather than every 2 minutes.
A background task now runs when the device is Idle that looks for old, filtered-object Analysis Job
databases and compresses these files.
Shutdown and Restart button were added to the embedded control software interface.
The Restart and Shutdown signals from the GUI are now correctly received by the control software.
2013A Controller Revision 1 -- 3 April 2013
GUI
Controller
Firmware
Motion Controller
20131.1.4819.261xx
20131.2.4833.248xx
20131.2.5.0
20131.1.0
Controller Fixes and Improvements
o
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The Optics Test dirt detection algorithm was improved: the dirt detection strategy was refined, and
detections are now categorized as Strong, Moderate or Weak. After studying the imaging
performance over a wide range of production-unit cameras, the Pass/Fail criteria were relaxed slightly
to adapt to the changing detection strength across all magnifications.
The source options (Phase LED and Color LED) for image results from calibration tests are now correct.
For instance, the Phase LED source is no longer an option when viewing Fluorescence Calibration Test
results. The erratic behavior of the Source droplist was unpredictable and depended on the order
that the various calibration tests were run.
The scan order for 384-well plates no longer rasters down the 24 columns of the plate. Each jump
between columns was triggering a long, wide-range autofocus operation that increased scan times by
10-12 seconds per column. When scanning every column, this can lead to an extra 4-5 minutes of
scan time.
Users with Administrator privileges are no longer blocked from adding to another user’s image
collections.
The device control software now blocks certain commands associated with the 2013A MCU software
if the MCU is not up to date.
The device configuration tool [aka, the “Configurator”] now correctly creates the Archive Jobs
database via the “Update DB Structure” menu item [SERVICE ONLY].
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
2013A GUI Revision 1 / Controller Revision 2 -- 20 May 2013
GUI
Controller
Firmware
Motion Controller
20131.2.4876.287xx
20131.3.4868.214xx
20131.3.0.0
20131.1.0
GUI Fixes and Improvements
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Fixed a problem that prevents the opening and viewing of archives when the GUI is running on a
computer with a date/time format that differs from the one used by the ZOOM® controller. The
format used by one’s computer is found in the Region and Language settings.
A Processing Definition that is opened via the Processing Definition Editor’s File | Open menu can
now be used correctly to run a Preview over collections of images. In addition, the Preview Image
Collection group box label no longer grows in length with each Processing Definition that is opened.
The Calibration Test image viewer now properly handles the display of images that have a negativevalued initial minimum intensity setting. A negative value for the Minimum was causing the viewer to
crash when opened.
The Vessel Scheduling table no longer contains an “Item Color” column, which should have been
hidden.
Controller Fixes and Improvements
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In support of the ZOOM® GUI archive date/time format fix (see above), the controller now uses a
fixed archive data/time format that is independent of the controller’s Region and Language settings.
An extra delay of 2 video frame periods was added between the Start Video and Stop Video calls used
in the camera configuration function. This was added based on observations and diagnoses of a few
rare system crashes.
The focus retry logic was improved to recognize more cases of receiving an insufficient number of
frames from the camera.
The controller is no longer susceptible to losing scan schedule changes when back-to-back schedule
changes are sent closely spaced in time. This can occur, for instance, when a scan pattern used in the
schedule is edited, causing the instrument to lose the scan pattern change.
Additional time was added at startup for establishing communication with the camera. We found
that some systems require extra time and can get into a restart loop when the camera-discovery
period is too short.
The 14-day reboot no longer interrupts the device when it is scanning and/or self testing.
The nightly MCU resets were restored.
When an optics filter module is installed in the system, the temperature sensor on the filter module
does not function correctly until the MCU is reset. This can lead to spurious warnings about the
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Document Number:
Date:
IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
sensor in the GUI logs. To mitigate these warnings, the sensor is now checked after the nightly MCU
reset.
2013A GUI Revision 2 / Controller Revision 3 – 13 June 2013
GUI
Controller
Firmware
Motion Controller
20131.3.4910.278xx
20131.4.4903.21xxx
20131.3.0.0
20131.1.0
GUI Fixes and Improvements
o
Prior to this improvement, Processing Definitions were tied strongly to Filter Modules and were
restricted to training and previewing with Image Collections from the same Filter Module.
Furthermore, Analysis Jobs run on data collected with a particular Filter Module were restricted to
using Processing Definitions tied to that same Filter Module. This was restrictive for customers who
upgraded from a No Fluorescence Filter Module (Model 4460) to a Dual Color Filter Module (Model
4459) in that their 4460 Processing Definitions could not be used to analyze new data collected with
the 4459 Filter Module. With this change:
 4460 No-Fluorescence Processing Definitions can be used to analyze phase images from the 4459
Dual-Color Filter Module.
 4460 Image Collections can be used as phase-channel Training Image Collections in 4459
Processing Definitions.
 4460 Image Collections can be used as both Training and Preview Image Collections with 4459
Processing Definitions for which only the phase channel is required.
Controller Fixes and Improvements
o
See GUI Fixes and Improvements above. The issue addressed above requires an upgrade to both
controller and GUI software components.
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Essen BioScience
Product Reference
IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
2013B Software Release -- 19 November 2013
GUI
Controller
CppLib
Firmware
Motion Controller
20132.1.5071.176xx
20132.1.5070.265xx
20132.1.6.1
20132.1.17
20132.1.0
Windows Compatibility
 Windows 8
†
 Windows 7 (32-bit or 64-bit)
†

Windows Vista (32-bit or 64-bit)


Windows XP Service Pack 3 (32-bit ); Windows XP Service Pack 2 (64-bit)
Not compatible with Windows 2000 or Windows Server
†
†
A 64-bit operating system is required to access the full feature set associated with Whole-Well scanning
and related viewing, analysis, marking, and export tools.
Overview of Major Features
o
o
o
Whole Well scan type
 100% coverage at 4x magnification for qualified vessels
 6-well , 12-well, 24-well, and 96-well microplates
 35mm dishes
 Counting and confluence calculations through Basic Analyzer
 Per-well metrics utilize a customizable processing region
Dilution Cloning scan type
 100% coverage at 4x magnification for qualified 96-well plates
 Special autofocus and imaging strategy for sparsely-seeded wells
Whole-Well and Dilution-Cloning utilities
 Zoomed Navigation tools
 Whole-well survey with keyboard shortcuts and auto-play
 An overview graphic in the vessel navigator orients the user within the well
 Points of Interest (POIs)
 Areas of interest are stored as POI “bookmarks”
 Customization and categorization: Groups, Labels, Notes, Time Span
 Convenience tools: Jump To, Filter, Tally, Export as Overlay, Show/Hide, etc.
 Printing Marks
 Identify large regions of interest to mark with choice of shapes
 Draw marks on vessel bottom with Zoom® Marking Tool pen
Page | 13
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
Detailed List of GUI Improvements and Fixes
o
o
o
Vessel View
 The new Zoomed Navigation tool designed for Whole Well and Dilution Cloning scans is also
available when zoomed into images from all other scan types.
 An overview rectangle was added to the vessel navigation graphic to help orient the user within
the image and within the well / sector.
 The vessel navigation graphic now resizes more sensibly when the upper pane and/or overall
window size is adjusted.
 Well / sector navigation within the vessel can now be accomplished via the keyboard shortcut of
Shift + Arrow key.
 The auto-scale algorithm now prevents the Min and Max settings from getting too close to one
another, reducing color-scale stretching when a color-channel image has no content of interest.
 The Tools and Spectral Unmixing control groups no longer disappear after (a) maximizing the
window, then (b) restoring the window to its former size.
 The metric label and metric shading view options were split into independent menu selections,
allowing one to view the metric shading without the label interfering.
Movie and Image Export
 New movie formats
 MPEG-4 video format
 Improved AVI compressed format
 AVI uncompressed format
 Improved Designer Tool
 Designer first opens with Vessel View zoom and crop settings
 Scan-time selection allows user to choose a specific scan to use for Preview operation
 Points of Interest can be added to exports as overlays
 JPEG, TIFF and PNG image format choices now provided whenever possible.
 Image-set export updated for compatibility with the latest version of MetaMorph
 Meta Image Series TIFF Format (Single/Multi-Plane) v1: this format now uses file splitting
when necessary to overcome individual file-size restrictions of 2 GB
 MetaMorph Multi Dimensional File v2.0 (ND files): individual TIFF filenames are formed
correctly in support of the “Review Multidimensional Data” tool. An overall ND file is created
along with one ND file per combination of image site and channel.
 24-bit TIFF images are no longer saved when an 8-bit TIFF is sufficient
 Practical limits on movie export sizes are enforced.
 An error is no longer generated when a movie of just an analysis job mask is exported.
Basic-Analyzer Analysis Jobs
 The Object Name fields in Basic-Analyzer processing definitions can now be edited via the Job
Details form, thereby allowing one to edit the per-channel object names after an analysis
completes.
Page | 14
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Date:
IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015

o
o
o
Metrics Modifications
 Added the “Average Object Mean Intensity” color-channel metric.
 Added two “Total Object Area” color-channel metrics (per-image and per-well).
 Dropped “/Image” from the “Average Object Integrated Intensity” metric units.
 Confluence was promoted to the first phase-channel metric in metrics lists.
 Processing definitions from phase-only filter modules are now available for all dual-color filter
module scans that contain a phase channel, not just phase-only scans.
 The “Count (1/Well)” metric is no longer available for vessels (like flasks) that are not comprised
of wells.
 This was hidden by default in metrics grids and was not available for graphing and export.
Processing Definition Editor
 The Preview operation can now be canceled.
 The pane that holds the metrics table is now both labeled and wider, making it easier to discover
and use. Furthermore, if one closes the pane after a Preview operation, then the table is no
longer shown again after subsequent Preview operations complete.
 The results from the last Preview operation are no longer found in the metrics table after a new
Processing Definition is opened using the File | Open menu.
Metric Graph and Export
 The ordering of metrics lists is now consistent between the Vessel View and the Graph/Export
window.
 The NaN (“Not a Number”) string no longer appears in metrics tables.
 The scan pattern spatial scope is now correctly shown at the selected time.
 A more sensible method for choosing plot markers and colors was implemented.
 The handling of missing data is improved
 Graphs displayed with errors bars that also contain missing time points no longer incorrectly
shift in time when toggling the x axis from Calendar mode to relative time.
 The computation of the y-axis scale on graphs now correctly ignores missing-data placeholder
values.
 The graph time axis no longer comes up in Calendar mode by default.
 After editing a graph title and/or labels, the x-axis label is no longer lost.
Scan Scheduler
 A table of Supported Vessels can now be accessed through the Add Vessel window. The table also
holds the supported magnifications and scan types for each vessel.
 The Scan Pattern Manager is improved
 The Scan Type can be selected when designing scan patterns, accurately displaying the image
size and location within the vessel.
 A reminder about images-per-well scan pattern limits for Scratch Wound scans is displayed.
 An unnecessary “Save changes?” confirmation request has been removed.
 A table of Supported Vessels can now be opened. The table also holds the supported
magnifications and scan types.
Page | 15
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Instrument:
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015

o
o
Scan On Demand is improved
 Scan-On-Demand vessels are now assigned the scheduler’s user account instead of the builtin System account.
 The grid of historical Scan-On-Demand vessels is now sorted by scan time, and the vessel
Unique ID appears in the first column with color highlighting.
User Preferences are improved and expanded
 The Image Drag and Drop preference is no longer required.
 New User-Settable preferences have been added:
 Auto-Scale histogram thresholds used for determining the color-channel Min and Max display
scale values
 Zoomed-Navigation Step Overlap and Play Speed
 Memory Limit Warning message show/hide
 New Automatic preferences have been added:
 The Brightness, Contrast, and Weight image-display settings are stored and recalled in the
Vessel View, Processing-Definition editor, and Image-Collection editor.
 The customization of grid columns for some of the more important grids is stored.
Miscellaneous
 A table of Supported Vessels can now be accessed through the Help menu in the main window.
The table also holds the supported magnifications and scan types for each vessel.
 The Help | About window was expanded to include more GUI and PC details as well as 3rd-party
software license information.
 A problem associated with browsing to a folder containing a mix of archives at different version
levels was fixed. This problem will be observed in the 2013A GUI if archives are written by a
2013B GUI to the same folder.
 A PlateMap editor issue was fixed: color customization was lost in certain cases where a group of
wells was originally deriving its color from a common compound or growth condition.
 An unnecessary “Save changes?” confirmation was removed from the Image-Collection editor.
 A more robust approach to vessel deletion avoids an error condition when metrics tables that
aren’t linked to the vessel are found in the database.
 The Setup Files export tool now includes job-processor error logs.
 The Description text in the Calibration Tests viewer is no longer editable.
 Feedback is given after a license update, and the Help | About menu contents are updated.
 Grids containing device-connected archives are now cleared when switching ZOOM® connections.
 The device time is no longer shifted to local time when connecting across time zones. Note that
the GUI does not function correctly when connecting to a ZOOM® in a different time zone.
Page | 16
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
Detailed List of Controller Improvements and Fixes
o
o
o
o
o
o
A number of scanning issues have been resolved:
 If the ImageLock crosshair is not in the field of view when a plate is scanned for the very first time,
a search for the crosshair is triggered. However, this search was not executed like expected when
using a scan pattern with just one image per well.
 When using an ImageLock scan pattern with more than one image per well, the grid of crosshairs
is checked once to verify that the microscope is positioned on the correct crosshair. The result of
this check is now saved to disk so future checks might be skipped after a system restart.
 If the Vessel Scheduling feature is used to change the vessel scan order from the default order
(left-to-right within a tray, front-to-back within the drawer), then a prematurely-terminated scan
might skip the loading of the results into the database for some of the vessels.
 When the “Sweep Mean Retries” attempts have been exhausted at a given well/sector, we no
longer skip the vessel if there are other wells/sectors defined in the scan pattern. There is a limit,
however, to the number of attempts made at other wells/sectors before skipping the vessel.
 The following issue was fixed: stopping a device activity like a scan or a warm up could block the
reading of the scan schedule. This could, in turn, lead to missed scans.
 The following issue was fixed: after a schedule containing a Scratch Wound scan was applied, the
toggling of the Wide Mode checkbox followed by another Apply could create an issue with locking
on the ImageLock crosshair. This could, in turn, lead to black bands (zero-valued pixels) in the
final images.
An issue with controller-side analysis job processing led to a gradual reduction over time of the
number of job processors working on a job. This, in turn, led to a significant drop in processing
throughput, especially on multi-hour analyses that were uninterrupted by device activity.
A new approach was implemented for establishing a USB connection to the microcontroller (MCU)
when the controller first starts up. The hope is to prevent the system from going into a reboot loop
because of repeated USB communication failures. The same approach is now applied to the MCU
reprogramming tool.
New MCU code contains minor fixes and improvements
 New belt-pitch values are now handled correctly through the command interface
 Triggered acquisition timing was improved to reduce the influence of I2C latencies
Both phase and color images are now saved in uncompressed TIFF format with custom headers
containing ZOOM® metadata.
IncuStore support was added in the form of handling more than one RAID virtual drive and enclosure
 Dynamic disks merge multiple virtual drives into a single drive letter
 The reporting of RAID capacity was expanded to handle multiple enclosures
 The reporting of RAID drive failures was expanded to handle multiple enclosures
Page | 17
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
2013B Software Revisions
2013B GUI Revision 1 / Controller Revision 1 – 24 February 2014
GUI
Controller
Firmware
Motion Controller
20132.2.5164.21xxx
20132.2. 5164.21xxx
20132.2.3.0
20132.1.0
GUI Fixes and Improvements
o
o
o
o
The Region of Interest (ROI) extraction tool used to generate Image Collections no longer generates
an error when zoomed and scrolled to a field of view for which the ROI is undefined. This can occur
when zoomed in too far near the border of the image. Instead of generating a software exception
error, the user is now prompted to adjust the field of view.
The Basic Analyzer metric “Count (1/mm2)” is now correctly set to a value of zero when there are no
objects in an image. Prior to this fix, the metric was incorrectly displayed with a “-“.
The launching of Analysis Jobs containing thousands of image sites to process no longer puts jobs that
are currently running at risk of termination with a “Catastrophic Error”. The database access timeout
that intermittently created this issue was eliminated.
The ability to open an Analysis Job at a specific scan time by double-clicking a point on a metric graph
was inadvertently lost in the 2013B Release, but is restored now.
Controller Fixes and Improvements
o
o
o
o
o
The 14-day nightly restart of the system is no longer suppressed according to the initial power-up
state of the system. The inadvertent suppression of the 14-day restart was responsible for the
appearance of “No USB comm link” messages in GUI logs between 3am and 7am, but did not interfere
with normal device activity.
The scan-to-scan tracking of well offsets associated with Whole Well and Dilution Cloning scans is now
done correctly, thereby reducing the likelihood of scan-to-scan image “bounce” in the left-to-right
direction.
Improvements were made to camera saturation handling to help find a suitable exposure time more
quickly. In addition, Dilution Cloning scans now correctly look for other wells to focus on at the
beginning of a scan after prior attempts in other wells encounter saturation errors.
The automatic boot warm-up function is now correctly time-limited to a maximum of 45 minutes.
The incorrect behavior was rarely seen when an instrument was placed in an incubator, but was
observed when powering up the instrument at room temperature.
The Analysis-Job processing timeout used when there are just a few image sites left to process was
extended to 5 minutes after discovering that the previous value of 1 minute was too small in certain
situations; for instance, when doing NeuroTrack analysis while the device is also scanning.
Page | 18
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
The Analysis-Job processing log maintained on the controller is no longer susceptible to issues
encountered when paring it down nightly. Problems are encountered when more than 5000
characters are written on a single line, which is an uncommon occurrence.
The following error-generating sequence was addressed:
 A microplate with a large footer depth (> 3 mm) is scheduled to scan with a 20x objective
 The microplate is not actually placed in the drawer to scan
 After detecting that there is no vessel to scan, an error is incorrectly generated when the
microscope attempts to scan the next vessel
 The next vessel must either be another microplate or any vessel placed in a different tray
The “Potential Microscope Collision” error is no longer generated in this case.
Incorrect log entries associated with the wrong tray being discovered are no longer made to the GUI
system log when a Microplates tray is scheduled.
2013B Controller Revision 2 – 01 May 2015
GUI
Controller
Firmware
Motion Controller
20132.2.5164.21xxx
20132.3. 5576.27xxx
20132.3.1.0
20132.1.0
Controller Fixes and Improvements
o
o
o
o
o
The “Disk Nearly Full” and “Disk Full” device status states are now displayed correctly in the GUI
status. Prior to this, the status was only shown on the LCD panel. However, the controller itself was
blocking activity once the “Disk Full” limit was reached.
The wide-range autofocus technique used with the 4x objective is no longer susceptible to data
processing errors that make it appear that no vessel has been placed in the system.
Archive Jobs are no longer blocked by the “Disk Nearly Full” and “Disk Full” device status states.
The incomplete cleanup of scan data and Analysis Job files and folders on the controller was
addressed as follows:
 The long-operation web service timeout was increased from its value of 7 minutes, 20 seconds.
We observed cases where it takes longer than this to delete vessels with large amounts of scan
data and Analysis Job data. In those cases, the file/folder deletion was terminated by the web
service after the timeout was reached, leaving behind “orphaned” file system artifacts.
 The device control software now uses idle time to seek out these “orphaned” file system artifacts
and remove them.
Added stitched-image diagnostic files (.ssf and .spf file extensions) to the list of valid web-service files
in order to suppress errors that are generated when trying to archive these files.
Page | 19
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Essen BioScience
Product Reference
IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
2014A Software Release -- 09 May 2014
GUI
Controller
CppLib
Firmware
Motion Controller
20141.1.5242.2xxxx
20141.1.5242.2xxxx
20141.1.7.0
20141.1.6
20141.3.0
Windows Compatibility
 Windows 8
†
 Windows 7 (32-bit or 64-bit)
†

Windows Vista (32-bit or 64-bit)


Windows XP Service Pack 3 (32-bit ); Windows XP Service Pack 2 (64-bit)
Not compatible with Windows 2000 or Windows Server
†
†
A 64-bit operating system is required to access the full feature set associated with Whole-Well scanning
and related viewing, analysis, marking, and export tools.
Overview of Major Features
o
o
o
o
o
Color Image Analysis using Background Subtraction
 Top Hat technique with adjustable radius parameter
 Estimates the background level at each pixel in the image
 Subtracts the background level from the image before finding objects
 Object properties that are based on intensity levels use background-subtracted values
 The background-subtracted image is available as a byproduct of the Analysis Job
 Available for any type of Analysis Job that offers color-image analysis
Color Neurite Analysis for NeuroTrack assay
 Kinetic quantification of labeled neurite dynamics
Support for ZOOM® Rack System with instrument console
 GUI runs on controller in a non-interfering , resource-friendly mode
Processing Definition management and portability enhancements
 Import / Export
 Import from file (including definitions exported from another ZOOM®)
 Export to file
 Management tools
 Rename
 Make a copy
 Make a read-only copy (locked)
Improved controller LCD menu interface with additional calibration/test options
Page | 20
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
Detailed List of GUI Improvements and Fixes
o
o
Vessel View
 Navigation Improvements
 The clickable area for a well now extends outside the well interior to the halfway point
between the well and its neighbors
 The use of the keyboard Shift+Arrow combination to navigate from well to well no longer
requires the user to click first on the image or vessel navigation graphic
 The image blending controls no longer disappear when navigating to a sector or well where
an image is not found for one or more of the selected blend channels
 The Zoomed Navigation tool behaves more intelligently, avoiding navigation to fields of view
that fall completely outside of the well boundary
 The image legend no longer moves as one pans and scrolls through an image
 The font size used for microplate row and column labels now depends on the well-to-well
spacing instead of the size of a well
 Spectral Unmixing
 The behavior of unsaved unmixing values was corrected in the case of certain use patterns
associated with opening/closing Analysis Jobs and navigating in time
 Unsaved unmixing values no longer propagate to Image Collections (via the Add to Image
Collection operation) nor Analysis Jobs (via the Launch operation)
 While waiting for an image to load, the wait spinner animation no longer disappears before the
image load truly completes.
 Images are now centered in the window instead of anchored to the left.
 The Points of Interest (POI) management tool is launched using the Manage POIs button. The
behavior of the tool’s table of POIs was improved by making the Start Time and End Time columns
read only.
 The rules for adding a Platemap to a vessel were made more flexible, permitting the addition to
the vessel of empty Platemaps and those containing only custom well colors and labels.
 The required memory when first opening a Vessel View or Analysis Job is no longer overestimated, thereby eliminating unnecessary warnings.
Analysis Jobs and Metrics
 Two new Analysis Job tools are offered via the table of jobs found on the “Analysis Jobs” tab in
the “Search” view: Rename and Export Processing Definition
 After selecting the job in the table, one can either use the new split button at the bottom
right or right-click on the job for options
 A “Hole Fill” parameter was added as color-channel analysis option for all Analysis Job types
except the Angiogenesis “Tube Networks” channel.
 Image blend controls are now placed in “Image Channels” and “Analysis Masks” rollup sections,
facilitating the reduction of scrolling through blender controls when many image channels and
masks are available.
 The tooltip displayed when placing your mouse over an Analysis Mask image now uses the actual
color (e.g., “Green”) rather than the more generic “Channel X”.
Page | 21
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015

o
A more consistent approach for the formatting of metrics was adopted, affecting both the
number of significant digits displayed as well as the use of scientific notation.
 The Vessel View table of metrics was updated to use the grid style found throughout the rest of
the software.
 The Launch tool now provides specific feedback to the user when the form is incomplete.
 Analysis Jobs should open a bit faster after eliminating redundant image blend operations.
 The controller memory used when running Whole Well and Dilution Cloning analyses was reduced
by up to 30% in some cases.
Processing Definitions: Preview and Edit
 Preview Improvements
 One can now Preview a single image stack at a time instead of the entire collection
 A Preview operation can now be cancelled while in the long Phase Training stage at the
beginning of the operation
 The processing of phase images during a Preview operation is up to 30% faster:
 This is a function of your computer’s CPU resources
 This only applies to the processing portion, and not to Phase Training
 Basic Analyzer, Scratch Wound and Neurotrack processing all benefit
 For optimization purposes, a bug was fixed that caused unnecessary phase re-training under
certain conditions where the Keepout mask parameter was not initialized correctly
 The upper-right portion containing the Preview split button and progress bar is no longer
clipped when the window is sized to its minimum width
 As a result of the software defects described below, a new version of the Phase Training algorithm
is now used behind the scenes
 Of note:
 All new processing definitions will use the new version
 Users will be given the option to update existing processing definitions to create new
versions that use correct and predictable phase training
 The defects:
 An issue was encountered on Windows 8 systems when training on Whole Well image
collections. An analysis of the problem during repair created concerns that other
versions of Windows were susceptible as well, despite the fact that issues were never
encountered. This bug can create unpredictable results during phase training
 A second bug that could produce undesirable results was also corrected. This bug
was triggered when (A) a standard image collection was used for Phase Training and a
Whole Well image collection was used to Preview , or (B) vice versa [e.g., the training
and preview collection types are reversed]
 When a Processing Definition is set to a state where a preview operation can’t be performed,
specific recommendations are now offered in the space where images are normally displayed.
These recommendations are customized to the Analysis Job type.
 Most of the numeric parameter controls were converted from Up/Down controls to more
standard numeric text controls. With the introduction of Whole Well analysis in the 2013B
release, Up/Down controls were no longer practical because of the sheer size of the numbers
required by certain filter parameters.
Page | 22
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Instrument:
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IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015
Image Collections
 Buttons consolidated into a single Split Button at bottom right of “Image Collections” tab in
“Search” view
 Management tools are accessible both from Split Button and via right mouse button click in row
of Image Collections table:
 Edit
 Rename
 Save Copy
 Delete
Movie and Image Export
 The legend used for exports no longer differs in style and behavior from the legend found
elsewhere in the software (Vessel View, Processing Definition Editor, etc.)
 The orientation of Points of Interest (POIs) is now correct in exported images. POIs are no longer
rotated all the time and only change orientation when close to the boundaries of the user-defined
export region.
 The “Select Preview Scan” option is no longer displayed in the export designer when using the
Export Current Image utility.
 Minor defects associated with the Metamorph image-set export status are fixed: the file count
and the progress messages could at times be erroneous.
Schedule Scans
 The various text controls on the “Properties” tab (Label, Cell Type, etc) can no longer be sized too
small when the window width is reduced.
 Any vessel that was copied onto the Schedule Scans clipboard is cleared now when a Configure
operation is performed via the ”Administer | Optics Reconfiguration” tab.
 The front of the instrument is now labeled as such in the “Drawer Setup” section.
 Information bubbles are now found next to the Scan Type and Scan Pattern droplist controls.
Archives
 Creation: by overcoming a database limitation, it is now possible to create an archive that
contains more than 2100 scan times.
 Updates: the archive update process no longer fails when attempting to handle numerical
formats associated with different Windows Region Settings.
Preferences
 Autoscale
 New values now propagate automatically to all open windows when the Preferences window
is closed
 A Use Default button was added, giving one the ability to reset to the recommended, factory
settings
 New Autoscale settings were added in support of background-subtracted color images, which
are a byproduct of Top-Hat color-image analysis
 A new “Black Level” setting was added to allow one to tune a computer monitor to optimize the
visibility of low-signal cells. Faint cells are often undetectable because they are mapped to black
when using the default settings of monitors, projectors, and other display devices.
Page | 23
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Document Number:
Date:
IncuCyte ZOOM®
ZOOM® Software Release Notes
8000-0190-E02
May 4, 2015


o
o
Existing preferences are no longer forgotten when upgrading the user interface.
The “Show Tray Labels” preference now correctly reverts back to its original value when the
Preferences window is closed via a Cancel request.
Controller Updates and Installers
 A Software License is now required for controller updates.
 Future controller updates can now be configured to require the scan schedule to be cleared.
 The current license is now backed up on the controller when a new license is uploaded.
Miscellaneous
 New sliders now display the numerical setting of the control instead of relying upon a tooltip.
 The “drag-and-drop” operation no longer fails under certain conditions: the use of a temporary
folder on the PC might be denied based on the user’s permissions, causing the drag-and-drop to
fail. A folder for which the user will always have write permissions is now used instead.
 Split Buttons are now used in a number of views to facilitate the introduction of more options (for
instance, see the lower right of the “Search | Processing Definition” tab).
 A Copy Grid button accompanies the table shown when the “Help | Supported Vessels” tool is
launched.
 The software was modified to reduce/eliminate the occurrences of windows getting covered up
or hidden behind other windows during normal usage.
 The details displayed in the “Help | About” window can now be searched using the “Ctrl + f” key
combination.
 The 48-well Nunc microplate column labels are now drawn correctly without clipping.
 Metadata added to exported images that are byproducts of Analysis Jobs (masks, for instance)
now contain the Processing Definition used in the analysis.
Detailed List of Controller Improvements and Fixes
o
o
Scans
 In instances where a scan encounters illumination problems across the field of view that can’t be
corrected by adjusting exposure time, the best HD phase image that can be acquired under the
circumstances is now saved. Prior to this change, the scan of that vessel would be terminated.
 After observing seams in a stitched image due to microscope positioning errors, the stitching
algorithm capture range was expanded from 110 µm to 151 µm.
 One in every 4000 or so fluorescence images could have an exposure-time error on the order of
20-25%. Logic was added to check for exposure consistency using the average signal. The
detection of a bad frame now triggers reacquisition.
 Vessels with a microplate footprint that have a different center-to-center spacing in the horizontal
and vertical directions are now supported and scanned correctly.
 Image diagnostics are now saved when lock errors occur during scans of ImageLock plates.
Calibration
 Fluorescence Calibration summaries now distinguish between errors due to insufficient channeldepth measurements versus those due to insufficient signal levels.
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May 4, 2015

o
o
o
o
o
A new option to run all calibration tests is found in the redesigned LCD menu. With three
calibration trays placed in the drawer and a loaded calibration slide in the front tray, the following
tests are run in succession:
 Optics Test
 Front Tray: Spatial Calibrate and Confirm
 Fluorescence Calibration
 Middle Tray: Spatial Calibrate and Confirm
 Rear Tray: Spatial Calibrate and Confirm
 Bad spatial calibration values can occasionally find their way into the recorded calibration data
file. When a subsequent calibration procedure is run to correct the bad data, the existing values
no longer influence the procedure.
 When logged into the controller and using the Firmware User Interface (FUI), the Optics Test is
now an option for tests than can be run automatically when three calibration trays are placed in
the drawer.
 When logged into the controller and running calibrations through the FUI, the spatial calibration
results are no longer reported twice if running an automated combination of Fluorescence and
Spatial calibrations.
 Calibration diagnostic images (which can be displayed in the GUI) that were previously saved in
JPEG and PNG formats are now saved as TIFF files.
The instrument warm-up sequence that runs at startup was improved:
 It is no longer susceptible to running over its time limit
 It no longer runs after the periodic 14-day restart of the instrument
The existence of the D: partition that holds image data is now checked regularly during run time in
case an IncuStore is inadvertently powered off.
The nightly log paring activity is now robust to reading log files with lines containing more than 5000
characters.
The accelerometer sensor is now checked for errors nightly like other sensors.
The Configurator tool’s information about the previous configuration is now preserved when running
a controller update.
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2014A Software Revisions
2014A GUI Revision 1 / Controller Revision 1 – 22 September 2014
GUI
Controller
Firmware
Motion Controller
20141.2.5373.xxxxx
20141.2. 5373.xxxxx
20141.2.1.0
20141.3.0
GUI Fixes and Improvements
o
o
o
Analysis Jobs and Processing Definitions
 This defect was triggered when an existing Processing Definition with the phase channel turned
off was loaded into the Processing Definition Editor. When turning the phase channel on, the
Whole Well Processing Keep-out parameter is now correctly injected into the phase training
process.
 Running a Neurotrack preview over Image Collections that do not contain a phase channel no
longer causes a crash. The software no longer looks for a phase neurite channel to analyze if that
channel is not on.
 When an Analysis Job is running its last set of images to analyze, there was a very small window of
opportunity (now eliminated) for an error. This error arose out of contention over access to the
image set by the controller-side job processors, leading to a Catastrophic Error for the Analysis
Job.
Metric Graph/Export
 The overwriting of a file during metric export no longer results in garbled formatting and incorrect
data in the updated file.
 Exporting metrics using either the “All scans in one file” or “Each scan in a separate file”
destinations now works correctly, taking into account “holes” in the data where metrics are
missing. These holes could lead to formatting errors when importing into other applications as
neighboring metrics shift in to fill the holes. Exporting to the Clipboard was already handling
holes correctly.
 Correct data are now graphed when requesting a red-channel Basic Analyzer histogram of the
object Eccentricity metric.
 Points of Interest (POIs) metrics now load much faster, preventing the possibility that the
Graph/Export window does not open because of a database timeout. Timeouts could occur for
vessels using several POI groups, where many images (i.e., all wells of a 96-well plate) and scan
times (dozens) have been acquired.
Regional Formatting
 Changes made in 2014A for displaying numerical data with consistent precision throughout the
GUI created issues on PCs with Region and Language Number settings that format numbers
differently than English formatting does (“Non-English Formatting” for the purposes of this note).
Specifically, the roles of the period and comma characters are reversed, affecting many PCs
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configured with European formatting. These issues, which are fixed in this revision, primarily
affected Processing Definitions as follows:
 Editing numerical fields in the Processing Definition Editor on a PC with Non-English
Formatting did not work correctly, in that the GUI did not interpret the role of the commas
and periods correctly
 Processing Definitions exported with a PC using English Formatting were not imported
correctly by a PC using Non-English formatting, and vice-versa.
 Many of the dialog windows throughout the GUI did not format correctly when viewed on PCs
running a Japanese installation of Windows. These formatting issues were resolved and
important buttons and checkboxes displayed in these windows are no longer hidden or partially
covered.
Miscellaneous
 The robustness of the drag-and-drop feature was improved to avoid creation and access errors
associated with the temporary folder used in this operation.
Controller Fixes and Improvements
o
o
o
o
A marking request using the Zoom® Marking Tool now runs successfully when the request is made for
the vessel that was the last vessel scanned On Demand.
The wide-range autofocus technique used with the 4x objective is no longer susceptible to data
processing errors that make it appear that no vessel has been placed in the system.
The Spatial Calibration no longer drives the microscope in the incorrect direction (causing the
calibration to fail) in cases where the drawer is offset by several millimeters from its typical position.
An “Upload Vesselware” tool was added to the Tools menu within the controller’s Configurator
application. The Configurator is regularly used by Service for managing the ZOOM® databases and
controller configuration.
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2014A Controller Revision 2 – 01 May 2015
GUI
Controller
Firmware
Motion Controller
20141.2.5373.xxxxx
20141.3. 5577.2xxxx
20141.3.0.0
20141.3.0
Controller Fixes and Improvements
o
o
o
o
o
o
The “Disk Nearly Full” and “Disk Full” device status states are now displayed correctly in the GUI
status. Prior to this, the status was only shown on the LCD panel. However, the controller itself was
blocking activity once the “Disk Full” limit was reached.
Archive Jobs are no longer blocked by the “Disk Nearly Full” and “Disk Full” device status states.
The HD image formation was improved for 10x imaging of rounded-up cells.
Reboot and Shutdown requests made via the GUI, the controller LCD panel, or the device control
software are all rejected if the RAID is rebuilding.
The incomplete cleanup of scan data and Analysis Job files and folders on the controller was
addressed as follows:
 The long-operation web service timeout was increased from its value of 7 minutes, 20 seconds.
We observed cases where it takes longer than this to delete vessels with large amounts of scan
data and Analysis Job data. In those cases, the file/folder deletion was terminated by the web
service after the timeout was reached, leaving behind “orphaned” file system artifacts.
 The device control software now uses idle time to seek out these “orphaned” file system artifacts
and remove them.
Added stitched-image diagnostic files (.ssf and .spf file extensions) to the list of valid web-service files
in order to suppress errors that are generated when trying to archive these files.
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ZOOM® Software Release Notes
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May 4, 2015
2015A Software Release -- 23 February 2015
GUI
Controller
CppLib
Firmware
Motion Controller
20151.1.5529.2xxxx
20151.1.5543.2xxxx
20151.1.5.0
20151.1.3.0
20151.1.1
Windows Compatibility
 Windows 8
†
 Windows 7 (32-bit or 64-bit)
†

Windows Vista (32-bit or 64-bit)


Windows XP Service Pack 3 (32-bit ); Windows XP Service Pack 2 (64-bit)
Not compatible with Windows 2000 or Windows Server
†
†
A 64-bit operating system is required to access the full feature set associated with Whole-Well scanning
and related viewing, analysis, marking, and export tools.
Overview of Major Features
o
o
o
o
Added capability of 384-well whole-well imaging
 Image the entire surface of every well using High-Definition phase contrast optics
 Perform dilution cloning studies in high throughput format with automated imaging and colony
detection
 High-Definition phase-contrast clarity enables clear detection of single cells even at well edges
enabling easy verification of monoclonality
Enhanced NeuroTrack™ fluorescence tools
 Improved sensitivity ensures fluorescently labeled neurons are accurately detected whether dim
or bright
 Enables the use of a wider range of neuronal labels with varying fluorescence intensities
New fluorescence analysis tools for co-culture scratch wound assays
 Monitor and measure migration of fluorescently labeled cells in co-culture models (e.g. test the
effect of stromal cells cancer cell migration)
 Correlate migration potential with gene expression or activation/inhibition of signaling pathways
Improved scheduling flexibility using the new Restore feature
 The “Restore” feature allows users to use individual tray positions for more than one experiment
at a time
 Interrupt experiments and resume at a later date using any tray position in the confidence that
your data will be automatically paired with previous scans
 Conduct an experiment over many days without tying up the instrument
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Detailed List of GUI Improvements and Fixes
o
Vessel View
Features
 The Image Blender channel selection controls are now more compact, requiring in less scrolling.
 Points of Interest (POIs) were improved as follows:
 POIs are now available for all scan types, not just Whole Well and Dilution Cloning.
 The POI labels are improved: there is better background shading, and the height of the labels
adjusts to the number of lines of text.
 POI groups can now be added to the vessel by double-clicking on a member of the Template
Groups list.
 The color-channel auto-scale of Whole-Well images now takes into account the well boundaries
and keep-out mask.
 The text on the Add to Image Collection hyperlink in the upper right was improved to make it
clear that this is also used to create a new Image Collection. This area was also enhanced by the
introduction of an Information Bubble and a logical separator.
 One can now pan through the full-screen view of the blended image (opened via a mouse doubleclick) using a click-and-drag operation.
Fixes
 The Zoomed Navigation survey mode no longer enters an infinite loop when run at certain high
zoom levels.
 When navigating from well to well (or sector to sector) using the keyboard, you can no longer
move to a well that is not part of the processing scope of an Analysis Job.
 Navigating in space or time when viewing a slide show no longer causes a failure.
 Whole Well scans of dishes no longer report a sector area as a vessel property.
o
Movie and Image Export
Features
 The export workflow was improved based on user feedback, making it more “wizard-like” for
walking one through the export process. More tooltips were added for Image Types as well.
Fixes
 When the number of images per well (sector) in the scan pattern changes over the export time
range, there was potential for entering a state that would prevent one from successfully
completing the export. Specifically, when dense patterns were used (more than 9 per well), the
controls used to select specific images within a well (e.g., the image index) did not function.
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May 4, 2015
o
Metric Graph/Export
Features
 The tab in the Vessel View was renamed to Metrics, and the tab controls were redesigned by
moving the metric-selection droplist tree control into a simple list tree control. This allows the
user to view all the available metrics simultaneously with the grid of metric values.
 More “Order By” flexibility was added to metric exports, allowing for “By Row”, “By Column” and
“By Replicate” export formatting.
 Custom Regions used during graph and export can now be saved and retrieved for later use.
Fixes
 The tracking of Analysis Job metrics grid preferences was improved, and the preferences for the
metrics grids found in the Vessel View and the Processing Definition Editor were synched.
 The opening of Points Of Interest (POI) metrics was optimized to run faster for the case of a large
number of POIs.
o
Analysis Jobs, Processing Definition and Image Collections
Features
 An Image Collection can now be re-assigned to a different Analysis Job type during the “Save
Copy” and “Save as” operations.
 New fluorescence intensity metrics are available for the Neurotrack nucleus channel.
 Importing and updating Processing Definitions created with older versions of the software is now
supported.
 When an attempt is made to delete an Image Collection that was used for phase training in one or
more Processing Definitions, the user is now presented with a grid that shows where the
collection is being used. An option for deleting the associated Processing Definitions is offered in
order to allow the Image Collection deletion to proceed.
 A new column in the Image Collections grid aids the search for those collections that consist of
Regions Of Interest extracted from larger, whole-well images.
Fixes
 The mask used for phase training from a 96-well Whole-Well image collection is now consistent
with the mask used during the running of the analysis.
 A Processing Definition that had once been used in the scan scheduler can now be deleted
successfully. Only the deletion of Processing Definitions found in the current scan schedule
should be blocked.
 The handling of corrupt Analysis Job databases and missing jobs folders is now handled more
robustly on the controller and in the GUI. This eliminates the need for intervention by Essen
engineers to remove the offending jobs and allow the processing of new jobs.
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o
Schedule Scans and Scanning
Features
 Two periodic scan intervals were added to the list of options: 20 minutes and 8 hours.
 The cursor is now placed in the Find search text editor when the Add Vessel window is opened.
 The device control software now tracks exposure-time cases where fluorescence signal levels vary
from expected values and limits the number of retries generated as a result of this condition.
 When the objective magnification is changed through the GUI, the device control software now
attempts to confirm that the correct objective has been physically placed in the instrument. The
confirmation takes place at the beginning of the next scan, and a warning is issued in the GUI log
if a mismatch is discovered.
 For robustness, the device control software now avoids simultaneously saving image data and
acquiring fluorescence images. In addition, certain activities associated with operating the
camera are not conducted while the RAID storage is queried for status.
 Support for a future 6th Tray ID bit has been added.
 The “Next Scan” field on the controller LCD panel now shows the duration of the upcoming scan.
Fixes
 A Scan On Demand that is started while the device is in “Self Test” mode no longer terminates on
error when the Self Test incorrectly resumes shortly after the scan starts.
 The “Self Test” status no longer blocks a request to reconfigure the optics.
 Because they are used for spheroid assays, the 96-well Corning Round Bottom ULA microplate
scan-time estimates are now longer.
 The Dilution Cloning scan time estimate was lengthened to account for autofocus retries.
 If image stitching fails during stitched-image scanning (Whole Well, Dilution Cloning, Wide-Mode
Scratch Wound, Tiled FOV, etc), a best attempt at stitching is now made to avoid the No Image
Found condition.
 The following issue was fixed: if the controller booted up less than 1 minute before the next scan,
there was a window of opportunity for that scan to be missed as well as all subsequent scans
(until the next schedule is set).
 More time is now allotted for terminating a warm-up prior to an upcoming scan.
 An issue was fixed that was the result of using the Vessel Delay feature in Vessel Scheduling for
scans of ImageLock microplates. In cases where searches for the lock fiducials were required,
only the microplates in the very first scan block were searched. Lock-fiducial searches for
microplates found in other scan blocks were incorrectly skipped.
o
Plate Map Editor Features
 Dilutions of cell seeding densities can now be created.
 Custom units can now be used with compounds.
 A “Save as…” button was added to the toolbar at the top.
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o
Vessels Database
Features
 Added support for over a dozen new vessels.
 The speed of the Update Vessels Database procedure was improved significantly, and there is no
longer a need to unzip the vessel update files to a folder prior to the update.
 Vessel Database updates are now included as part of controller updates, eliminating a step in the
overall upgrade process.
Fix
 The IBIDI Microslide VI is now available for scans at 20x and 4x magnifications.
o
Miscellaneous
Features
 A new “Grid Groups” convenience tool presents a grid view that groups rows by User or Creator.
 The user account management tool now allows a user with Administrator credentials to change
another user's Permission Level.
 A warning is now issued when the GUI is run using a font size other than the target size of 96 DPI.
 An email client is now opened automatically when the GUI contains an error that should be
mailed to Essen BioScience support.
 Reboot and Shutdown requests made via the GUI, the controller LCD panel, or the device control
software are all rejected if the RAID is rebuilding.
 The connection to the device is now closed automatically when a controller update is run.
 As an aid before shutting down or restarting the controller, an “Archiving” warning status is now
visible on the controller LCD panel.
Fixes
 The “Disk Nearly Full” and “Disk Full” device status states are now displayed correctly in the GUI
status. Prior to this, the status was only shown on the LCD panel. However, the controller itself
was blocking activity once the “Disk Full” limit was reached.
 Grid columns that contain integer numerical data are now correctly sorted by the value, not
alphabetically.
 The Help | Supported Vessels menu no longer crashes when it is selected and there is no device
connection (for instance, when you are connected to an archive).
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Service/Support
Features
 The “Confirm” portion of spatial calibrations can now be disabled when using the “Run All Tests”
option from the LCD panel.
 A new “Support” button found on the Administer tab gathers together a set of typically-requested
support files in a single archive: GUI Logs, Device Setup Files, and Windows Events.
 All controller update logs are now retrieved via the Export Setup Files tool.
 A fixed-width font is now used in various device log and device test views.
 Action is now taken by the device control software if either the C: or D: partitions are marked as
“Dirty”.
Fixes
 When changing the magnification manually via the Firmware User Interface, the device control
software no longer loses synch with the magnification stored in the database.
 If the device control software is not restarted as it should be after running a drawer leveling
procedure, there is no longer a logging “leak”.
 When running a calibration via the Firmware User Interface, the illegal combination of calibrating
all tray positions without also selecting a spatial calibration (or confirmation) is now disallowed.
2015A Software Revisions
2015A GUI Revision 1 / Controller Revision 1 -- 04 May 2015 [Chemotaxis Release]
GUI
Controller
Firmware
Motion Controller
20151.2.5599.16xxx
20151.2.5599.16xxx
20151.2.4.0
20151.1.1
GUI Fixes and Improvements
o
o
o
New Feature: 96-well Chemotaxis scans and migration analysis
 Introduction of Essen BioScience ClearView 96-well plate with an 8 x 12 regular grid of pores
 Phase and Color imaging of both the top and the bottom of the membrane separating the upper
chamber from the lower chamber
 Both Top-Only and Top/Bottom migration analysis in both phase and color
Users are messaged when trying to add a vessel to the schedule for which they don’t have a license.
In the 2015A base release, an automatic email message was always sent to Essen BioScience support
in the event of a GUI fault. Users are now given a choice about sending this email.
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ZOOM® Software Release Notes
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Improvements and Fixes
o The Plate Map editor was improved as follows:
 The cell dilution option for subtracting a fixed number of cells was improved by replacing the
numeric up/down control with a text box. The numeric up/down control had an upper limit of
100, making it impossible to use the tool for subtractive dilution of large cell counts.
 The divide-by dilution control permitted the use of divisors < 1.0, leading to a math overflow
exception if a small enough divisor was selected. Given that the purpose of dilution is to reduce
concentrations, the divisor is no longer allowed to be < 1.0.
o A top-hat background subtraction bug that was introduced in the 2015A base release was corrected:
 Due a programming error, a jagged ring of uncorrected signal along the outermost edge of the
keepout mask was not subtracted off.
o The Export Single Image tool in the Vessel View no longer incorrectly exports images in JPEG format
when a different format (TIFF, PNG, etc.) is selected.
o A number of metric export problems were addressed:
 Grouping by replicates with a Plate Map attached would lead to large negative-valued metrics if
the metric data contained any NaN values (e.g., as created by divide-by-zero normalization).
 Dragging Raw Data to Document from a graph did not handle missing data properly. This, in turn,
led to incorrect shifts of metrics, thereby assigning these metrics to the incorrect well/sector.
o Numerical data in a number of grids were being treated as strings, leading incorrectly to string-based
sorting rather than numerical sorting when the built-in column-sorting grid functions were used.
o A new feature in 2015A added the Time Zone string to the controller details reported via the Help |
About menu. This exposed the opportunity for a GUI to push a Time Zone with non-English
characters onto the controller (which uses English culture and locale settings). This, in turn, led to
illegal characters in the controller details, which blocked the GUI from displaying this information or
attaching controller details to GUI log exports. Only valid ASCII characters are now reported for the
Time Zone information.
Controller Fixes and Improvements
o
o
o
The incomplete cleanup of scan data and Analysis Job files and folders on the controllers was
addressed as follows:
 The long-operation web service timeout was increased from its value of 7 minutes, 20 seconds.
We observed cases where it takes longer than this to delete vessels with larger amounts of scan
data and Analysis Job data. In those cases, the file/folder deletion was terminated by the web
service after the timeout was reached, leaving behind “orphaned” file system artifacts.
 The device control process now uses idle time to seek out these “orphaned” file system artifacts
and to remove them.
Added stitched-image diagnostic files (.ssf and .spf file extensions) to the list of valid web-service files
in order to suppress errors that are generated when trying to archive these files.
The objective magnification check that was introduced in the 2015A base release was improved,
making it more robust to strong glints near open tray ID bits.
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After reviewing a customer scan log, a minor improvement was made to wide-mode Scratch Wound
scans: the same exposure time is used for every tile in the final stitched image. This improvement
helps the scans adapt to illumination problems encountered in the first tile. Illumination issues in tiles
other than the first continue to be an issue, since exposure-time retries have always been suppressed
for these tiles (and continue to be so).
Page | 36