Imaris | Release Notes and Bug Fixes

Imaris 7.1.0 Release Notes

Welcome to the Imaris 7.1.0 release notes. Version Date: June 14, 2010. 
Please have a look to the Overview of Imaris Release notes for information about prior released features and fixed bugs.

[Fixed Bugs
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  • Accelerated Save and Load of IMS files with large Surpass Scene
    • Spots, Surfaces, Cells, and Filaments
    • Scene data is now written in binary format (loading up to 20 times faster, saving up to 2 times faster)
    • Imaris 7.1 reads all data from "old" 7.0 files
    • Imaris 7.0 ignores the scene data from the new files. In order to transfer scene data from 7.1 to 7.0 use "Export Scene" from Imaris' "File" menu.
  • Read Scene Data from IMOD files (image, points, contours, and surfaces)
  • Andor iQ image reader (reads all 5D images from iQ image disk, i.e. it can not read images with more dimensions - like "confocality")
  • Free Rotations (from Image Processing menu)
    • Allows arbitrary rotation axis / angle
    • Use Surpass View to setup the rotation angle
    • (In the 3D alignment example below for illustrating rotational drift correction, the free rotation was used to generate the red image)
  • Fixed brightnes changes when zooming in and out
  • Fixed many issues related with multithreading
Brightness changes:

Imaris 7.0 above: Brightness differences of neighbouring images blocks with different resolutions (zoom levels) are clearly visible.

Imaris 7.1 above: Brightness differences are mostly suppressed.

 Track Editor

  • New interactive tool for manual track editing
    • Available as new tab for Spots, Surfaces, Cells, and Filaments
    • Interactions:
      • Mouse wheel zooms the view
      • Right mouse button pans the view
      • Left-mouse-click onto a vertex to select it
      • Left-mouse-click onto the beginning of a line to select entire track
      • <ctrl> + left-mouse-click to toggle the selection
      • <shift> + left-mouse-click onto an edge to delete a connection
      • <shift> + left-mouse-click onto a vertex, and drag to create a connection
    • Show selection: Option to reduce displayed tracks to a smaller working set
    • Moved "Mouse Selection" from "Edit" tab to "Track-Edit" tab
    • Moved "Connect" and "Disconnect" from "Edit" tab to "Track-Edit" tab
    • Moved "Drift Correction" from "Edit" tab to "Track-Edit" tab
Drift Correction

(Earlier Imaris versions supported only 
Translational Drift Correction)
  • Available for Spots and Surfaces
  • Select one ore more tracks to correct drift:
    • 0 Tracks selected: Imaris acts as if all tracks were selected
    • 1 Track selected: Imaris does the same as for pure translational drift correction
    • 2 Tracks selected: Imaris compensates rotational and translational drift in 2D images (for 3D images it is recommended to select at least 3 tracksd)
    • 3 Tracks or more selected: Imaris compensates rotational and translational drift in 3D
  • Result Image:
    • Crop largest common region: can lead to a really small image (old feature)
    • New size equal to current size: moderate / predictable image size (new in Imaris 7.1)
    • Include entire result: can lead to a really huge image (old feature)
Example: 3D image alignment

Two unaligned images (unaligned red image was artificially created with Imaris' "Free Rotate")

Key points time 1

Key points time 2

The image above shows the result after rotational drift correction using all the 3 tracks. (The key points were manually set and tracked. For this reason the location of the key points is not perfect, and the result seems not accurate. Nevertheless this perfectly illustrates the behavior of the new feature)


    Tracked Spines using Imaris' FilamentTracer: the image above shows the filaments, the trajectories of the Spine heads together with a volume rendering. Image Courtesy of Dr. Anne McKinney, McGill University, Montreal, Canada
  • Automatic and manual Tracking of Dendrites and Spines
  • Analyze Spine-Lenght, Spine-Volume, etc. over time
  • Uses Autoregressive Motion Model for
    • Dendrite Branch Points
    • Dendrite Terminal Points
    • Spine Attachment Points
    • Spine Branch Points
    • Spine Terminal Points
  • Requires a License for FilamentTracer and ImarisTrack

The time plot above is showing the length of the three selected Spines

Close-up view of the shrinking Spine (red line in time plot)

 Statistics Annotations

  • Annotations with Object Statistics
  • Available for Spots, Surfaces, and Cells
  • Requires a License for InPress and MeasurementPro
  • In order to add a Statistics Annotation, switch to statistics tab, select an object and a value, and press the Annotation Icon on the bottom of the dialog.
  • Color, Font, additional Text, or additional Statistics Values can be adjusted using the InPress-Tab

Fixed 63 Bugs (since Imaris 7.0.0)
1045 Free rotation
1881 Compensation for rotation
2074 Textures blocks change brightness
2997 First Snapshot 'Size from image' 100% zoom has wrong scale
3098 Selection of selfpainted spots, selects also first spot
3114 3D drift correction; rotation defined by a 3-point plane
3301 split surfaces on time series crashes (system config dependent)
3343 tracking of 2D time series crashes
3369 Spot generation 3D time series with background subtraction crashes on XP x64, OS X and Vista X64
3413 Generation of 8 million triangles crashes on XP x32
3481 Crash at 77% Calculating surfaces/watersheed/copying
3594 Diameter calc seems to crash imaris "randomly"
3618 Filament "autodepth" drawing does not make connections, if filament contains a spine
3652 Surface calculation with split touching objects and big dataset crashes
3675 Crash during Filament diameter calculation (step 4)
3699 Surface with split touching objects crashes on osx
3733 certain image sizes and/or Resample3D result in Surfaces crash
3786 Surfaces wizard crashes when frequently stepping backward & forward
3815 canceling a Save As operation deletes IMS dataset file
3822 crash during dendrite diameter calculation
3880 Quit greyed out after opening an image
3893 Store number of frames and playback speed with keycrame animation
3909 Snapshot crashes with blend for volume and Shading and Shadow for frame
3923 Spots detection crashes at diameter / Gaussian stage
4012 Exceptions can not be caught on Mac
4018 bypass load dataset dialog
4053 Missing unit in Orthoslicer Slice Position
4126 Export components in binary format
4163 LIF subseries name is not read properly.
4206 switch to Color tab during Cell creation wizard -> crash
4207 Crash when view area smaller than snap shot w/ no off screen rendering
4220 Cells Export for Plotting does not write any file
4221 Enforce one nucleus per cell applied too early
4232 saved ims files in AutoDeblur: crashes Imaris File converter
4233 saved ims file in AutoDeblur cannot be opened in Imaris
4235 Matlab 2009a/b crashes with when changing into folders with .ims or .imx files.
4236 vesicles remain in view when using back button in wizard
4244 Import fails from Volocity 5.3.1 export of ICS/IDS, LIFF, openlabraw
4250 The threshold value in step Threshold of the surface wizard shows the unit
4263 bad performance in the Shadow projection in Imaris 7 compared to Imaris 5.72
4274 Preview line not shown when contour visibility is switched
4281 Crop to fill does not crop
4284 Fit to selection crashes if there is no selection
4286 Filament Additional regions sometimes loses initial region if stepping back in wizard
4288 black blocks in lower resoltion levels
4289 The threshold value in step Threshold of the spots wizard shows the unit
4291 "do you want to save dataset?" "yes" response is ignored
4301 Scholl statistics disappeared
4305 multiple selection of statistics values does not work
4310 Vesicles still visible if user goes from back one step
4311 Cells-LUT/Stats coded coloring is applied differently.
4314 C++ Runtime Error 6034
4322 Matlab command not executed
4323 Correct drift crashes imaris if dataset has less time points than spots
4324 Time calibration not read for Zeiss ZVI files
4328 Last 4 slices of a tiff series with 311 files seem not to be loaded (they are rendered black)
4333 Center function for filament moves the line off center
4338 Coloc crashes when opened with 32 bit float dataset
4345 Resample Open - Resample Time fails
4380 error message appears, when saving a file as "Tiff"
4393 PlayBack State panel missing scroll bar
4403 additional SimplePCI file reader problems CXD file incompatible
4410 Repositioning surfaces scissor during cut crashes Imaris


Any feedback on the installation, and the usage of Imaris and its features are welcome. Please send your comments to

Last Modification: CL, 15-Jun-2010

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