Imaris | Release Notes and Bug Fixes

Imaris 6.3.0 Release Notes

Welcome to the Imaris 6.3.0 release notes. Version Date: May 04, 2009. 
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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 Huge images Imaris 6.3 allows faster (and smoother) zoom and pan. This works with ALL viewers: Slice, Section, Gallery, Surpass Volume, Surpass Ortho Slice, Surpass Oblique Slice, Surpass Surface Preview, Coloc

While panning (or zooming): Low resolution textures are used as long as there are no high resolution textures loaded.

Finished panning (or zooming): High resolution textures are loaded asynchronous (like google maps).


  • The "Fit" button in Surpass now fits the bounding box of the scene to the border of the Surpass window. The illustration below shows the behavior of the "old fit" and the "new fit":
  • A preview shows the expected result.
  • "100% Snapshot" adjusts the width and the height of the snapshot. The resulting image will have a zoom factor of 1 (one pixel per voxel).
  • Example: export an xy-slice from the slice-view in original resolution without a border:
    • From "Predefined Dimensions" select "... x ... Dataset".
    • Make sure that "Crop to fill whole snapshot area" is checked.
    • Press "Fit" from the Imaris status bar.
    • Press "..." to select an output file name.
    • Hit "Do Snapshot"
New File Readers
  • Compix: SimplePCI
  • Gatan Digital Micrograph
  • Prairie Technologies
  • Compressed Openlab LIFF

  • Image Prrocessing Performance
    • Overall 15% faster
    • Resample 3D is 5 times faster
  • Improved Performance of Crop3D
  • Collect Usage Data (user is asked to agree during the initial setup of Imaris)

Statistics Filtering

  • Objects can now be filtered by TWO thresholds
    • If the lower threshold is checked, all objects above the threshold are selected.
    • If the upper threshold is checked, all objects below the threshold are selected.
    • If the lower and the upper threshold are checked, all the objects in between the thresholds are selected. If the value of the lower threshold is higher than the value of the upper threshold, all the objects outside are selected.
    • If no thresholds are checked, all the objects are selected.
  • If only one of the Thresholds is et to "automatic", a two means algorithm is used to calculate the threshod value
  • If both thresholds are set to "automatic", a three means algorithm is used to compute the threshold values.
  • The threshold mode is set to "manual" as soon as the user clicks into the histogram.
  • Click with the left mouse button into the histogram changes the lower threshold.
  • Click with the right mouse button into the histogram changes the upper threshold.
  • The updated filter dialog is available for the creation wizards of Surfaces and Spots, and as filter tab for Surfaces, Spots and Filament.

Color Coding

  • The statistical values of dendrites and spines can be mapped as color to the according filament segments (similar to Surfaces and Spots). 

  • A real branch level is introduced. In earlier Imaris versions there were already statistics values named "Level", but it was not the same as the level from the biological point of view - it was the tree depth from the graph theory. Therefore we renamed the old "Level" into "Depth"
    • Dendrite Branch Level
    • Dendrite Branch Depth
    • Spine Branch Level
    • Spine Branch Depth

  • Filaments for all time points within one surpass object:
    • Easy Export of Statistics
    • Common Filtering
    • Common Color handling
    • (tracking not yet implemented)

44 Fixed Bugs (since Imaris 6.2.1)
ID Summary
3503 Large LSM time series are loaded corrupt
3488 inconsistency between the parameter values in the screenshots and in the written text
3471 Incomplete Imageprocessing with Multiple CPU's enabled..
3444 The name "level" is missleading (wrong) - rename it into "depth"
3443 need branch level statistics
3440 floating license des not work in combination with nodelocked license
3437 "Error signature" when starting Imaris
3435 LEI Thumbail requires refresh to display all files.
3430 Imaris Batch crops allways to one time point
3424 only subset of STK is loaded in 6.1.x-->6.2.x
3421 Add Channels dimensions test gives wrong result after Resampling Open
3415 Additional volume statistics needed
3411 Creating a surface with no dataSet loaded crashes Imaris
3393 Resampling Open: Crop plus Resample corrupts image pyramid
3388 Crop 3D crashes (with 850 MB image)
3376 Crash at about 75% loading a specific scene on OSX
3375 Olympus Fluoview 2.0 OIB OIF can not be loaded
3368 Add Channel Fails on Large XYZT data sets.
3363 Resampling Open: Min Limit for Cropping does not work
3332 Surfaces - Edit - Duplicate to All Time Points - non-functional
3276 crop3d on huge image: black xy MIP (or crashes)
3247 Units missing for Y axis of statistics graph (time plots)
3244 SplitBranchHiearchy.m --> Integrate into Imaris
3216 License file selector appears behind Imaris
3187 installer error: FpBp.ocx failed to register
3157 ImarisServer can not be registrered
3149 missing units for frame axis labels
3148 Missing units in status bar of slice and section view
3125 Need statistics coded coloring for FilamentTracer
3086 Output file name should include Leica .lei sub filename
3024 Contour Surface: changing the draw mode has no effect unless moving to a new slice
2990 documentation for track statistics unclear
2942 crop 3d is very slow even for a small image (retina.ims)
2929 Export Filament statistics off all time points to one file
2765 Time animation of Slice viewer gives corrupt result
2402 Shadow Projection slow and to bright if Frame Shadow is activated
2381 Olympus OIF OIB LUT not loaded
2345 Export of Spot statistics to Excel crashes Imaris
2274 Read LSM file larger 2 GB
1968 Coordinate Axis do not have X Y Z labels
1527 Surpass Color Tab: there is no material palette
1357 Group with global editing possibilities
1345 Keyboard shortcuts to change selection mode...
862 Statistics tabs units are always um


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

Last Modification: CL, 04-MAY-2009

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