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Colocalization Module for MountainsMap
Combine surface data from different instrument types
- carry out correlative studies
For 3D optical profilers & AFM, STM, SEM, fluorescence, Raman, IR & other microscopes
Colocalization of images from different microscopes
Colocalization of microscope images with 3D topography
Overlay of microscope and spectrometer images on 3D surface topography
Stupendous 3D images at any zoom level and angle
Conversion of color or grayscale images into 3D colored pseudo-surfaces
Image and surface data correction, horizontal distance & angle measurement
Basic metrological filters and studies for surfaces
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Colocalization Module for MountainsMap®
The Colocalization module for MountainsMap provides tools for colocalizing images from different
instrument types and for overlaying microscope and spectrometer images on 3D surface topography. It
facilitates correlative studies.
Broad range of applications.
Applications span the physical and life sciences, nanotechnology and
biotechnology. For example, they include studies of nanowire morphology, cell morphology, and carbon storage
in bacteria that are a potential source of bio-fuel.
Colocalization correlates surface data from different instruments
The Colocalization module is used to colocalize:
Microscope and spectrometer images with surface
topography.
•
Two or more microscope and/or spectrometer images.
Colocalization of STM topography &
SEM images
Images courtesy of IEMN, Lille, France.
•
For example SEM, fluorescence or density map images
can be colocalized with surface topography obtained by
3D optical and scanning profilometers, SPM (AFM, STM,
etc.) and other 3D capable instruments.
The flexible set of colocalization tools includes:
•
Automatic colocalization
recognition algorithms.
using
advanced
pattern
•
Interactive colocalization including shift, rotate and
transparency.
Sawtooth faceted sidewalls revealed by
colocalization of STM topography with a SEM
image of an Si nanowire.
Images courtesy of LNE
(French National Metrology Institute).
Colocalization of AFM topography &
SEM images
AFM – nanostructure topography with
highlighted zone.
Colocalization of zone topography and SEM image.
SEM image of zone.
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Colocalization Module for MountainsMap®
Images courtesy of Agilent Technologies
Colocalization of simultaneous AFM topography
& fluorescence images
AFM – cell topography.
Colocalization of topography and fluorescence image.
Fluroescence image
Images courtesy of IEMN, Lille, France
Colocalization of SEM
SE & BSE images
SEM secondary electron (SE) image.
Composite image obtained by colocalising the SE
and BSE images (following conversion and coloring
of the BSE image).
SEM back-scattered electron (BSE) image
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Colocalization Module for MountainsMap®
Images of courtesy of Carl Zeiss
Colocalization of SEM image and
color optical microscope image
SEM image
Colocalization of cropped SEM image
and color optical microscope image.
Optical microscope color image
Image overlays on 3D surface topography
After colocalization it is easy to overlay SEM,
fluorescence, density map and other images on 3D
surface topography.
3D visualization includes fast zooms as well as
translation and rotation of all axes, making observation
of surface features easy.
Overlays facilitate the study of correlations between
features in the images and topographical features.
Superb 3D rendering can be achieved by adjusting the
transparency of the overlaid image.
Images courtesy of LNE
(French National Metrology Institute).
SEM image overlay on AFM 3D topography
Overlay of SEM image on AFM topography.
Colocalized AFM topography and SEM image.
www.digitalsurf.com
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Colocalization Module for MountainsMap®
Images courtesy of Agilent Technologies
Simultaneous fluorescence image overlay on AFM 3D topography
Colocalized AFM topography & fluorescence image.
Overlay of fluorescence image on 3D topography provides
insights into cell morphology.
AFM topography
Overlay of color-coded IR absorption image
on AFM 3D topography highlights fat
pockets stored in a bacterium.
IR absorption image
Images courtesy of A. Dazzi & A. Deniset-Besseau,
Laboratoire de Chimie Physique, Université de Paris-Sud
IR absorption image overlay on AFM 3D topography
Additional features and tools
Other features include the ability to convert a color or
intensity image into 3D colored pseudo-surfaces (with z
axis in intensity units). Following colocalization it is
possible to overlay another image on a pseudo-3D
surface.
www.digitalsurf.com
Additional tools for working with images and surfaces are
listed on the back page of this document.
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Colocalization Module for MountainsMap®
Colocalization module for MountainsMap®
Colocalization
• Colocalize images of the same surface obtained by different instruments or
dectectors, for example:- colocalize (1) topography and other images obtained by
SPM (AFM, STM, etc.), a 3D optical profiler or a 3D scanning profilometer with (2)
images obtained by SEM, fluorescence, IR, Raman and other microscopes and
spectrometers - colocalize (a) a SEM secondary electron image with (b) a
backscattered electron image.
3D overlays
• Overlay microscope or spectrometer images on 3D surface topography obtained
by any microscope or profiler.
• Convert any color or intensity image into a 3D colored pseudo-surface (with z axis
in intensity units), overlay microscope or spectrometer images on 3D pseudosurfaces.
Tools for images and
surfaces
• Axis units and scale editor.
• Flip.
• Rotate.
• Smoothing filters.
• Measure horizontal distances and angles.
Tools for images
• Select one of ten laser wavelengths for fluorescence images.
Tools for surfaces
• Real time 3D view at any zoom level and angle.
• Leveling.
• Basic metrological roughness/waviness filters.
• Abbott-Firestone (bearing ratio) curve and depth distribution histogram for
surfaces.
• 2D profile extraction and visualization of profile curve (x,z).
Compatibility
• Works with surface data and images loaded by the MountainsMap product to
which module is added.
• Inputs and works with images in standard file formats.
Doc Revision: 20160627
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Digital Surf, 16 rue Lavoisier,
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Tel +33 3 81 50 48 00
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