Imaris | Release Notes and Bug Fixes

Imaris 6.4.0 Release Notes

Welcome to the Imaris 6.4.0 release notes. Version Date: Nov 02, 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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Imaris x64
for Macintosh
  • Imaris Scene Viewer

    • Load Imaris Scenes (all Formats)
    • Read Only (no option to modify and change image or scene data)
    • Snapshot
    • Animation Playback
    • Rotate, Pan, Zoom

  • Single File for Image Data and Surpass Scene
    • Extended Imaris 5.5 File Format
    • Fast "Save" (saves only if modified: image, metadata, or scene)
    • Compatible with old Imaris Versions (Imaris 5.5 ignores the scene data)
    • Option to export or import "old" IMX-Files

  • RGB Segmentation
    • Creates a new channel using a reference color and any number of input channels. The intensities of the new channel reflect the distance from the reference color. A high intensity in the new channel means that the color is very similar to the reference color.
    • Multithreaded (processing is performed on multiple CPUs)

  • Histogram Equalization
    • See Wikipedia
    • Multithreaded (processing is performed on multiple CPUs)

  • Accelerated "Normalize" (multithreaded)
  • Automated Crash Reports
  • Updated Manual with ALL the new features
  • Compact GUI for Lower and Upper Threshold
  • Recenter (moves manually set spots to the correct position)
  • Track Single Spot (very fast for large images, if only some spots are of interest)
  • New Statistics Values (see MeasurementPro)
  • Unify, Split (connects spacial separated objects)
  • Contours integrated into Edit-Tab (see MeasurementPro)
  • New Statistics Values (see MeasurementPro)

Creation Wizard

    Image above: A Neuron traced with the new Filament Creation Wizard. The Spines are colored using the Branch Level of the Dendrites. Red Spines are attached to low level branches (primary), and yellow Spines are attached to high level branches. Image courtesy of Kim Edward Light, Professor Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciencies
  • Separated Dendrites and Spines Detection:
    • Dendrites: Source Channel, Diameter for Beginning- and Seed-Points
    • Spines: Source Channel, Diameter for Seed-Points
  • Clean Unwanted Seed-Points near Beginning-Point
  • Interavtive Diameter Preview
  • Option to Calculate Diameter from Cross-Section (increases accuracy of volume measurements)
  • Accelerated Processing Speed for "Fast Marching Algorithm"
  • New Statistics Values (see MeasurementPro)

Measurement Pro
  • New Draw Modes: Circle, IsoLine, MagicWand
  • Autofit (Fitting manual contrours to image gradients using snakes)
  • Automatic / Manual Resolution for Surface Generation
  • Surface Generation requires less memory
  • Translate & Rotate Contour Lines
  • Many keyboard shortcuts for more efficient use
  • COM Interface (see ImarisXT)
  • Colored Tracks by Statistical Value (e.g. Speed):

  • Category Pre-Filter (Filter-Tab, Statistics-Tab):

  • Statistics Tab:
    • Icon for indicating a Statistics Value with Time Plot
    • New Time Plots:
      • Detailed / Average
      • Selection / Specific Value
      • Selection / Average Values
      • Selection / All Values
    • Export Plot Data
    • Statistics Tab on "Surpass Scene" Object (Group)

  • New Spots Statistics Values:
    • Acceleration
    • Track Position X Mean
    • Track Position Y Mean
    • Track Position Z Mean
    • Track Speed Min
    • Track Speed Max
    • Track Speed StdDev

  • New Surfaces Statistics Values:
    • Acceleration
    • Number of Disconnected Components
    • Number of Disconnected Components per Time Point
    • Total Number of Disconnected Components
    • Track Position X Mean
    • Track Position Y Mean
    • Track Position Z Mean
    • Track Speed Min
    • Track Speed Max
    • Track Speed StdDev

  • New Filament Statistics Values:
    • Spine Neck Volume
    • Spine Terminal Pt. Volume

  • Interface for Contour Polygon Coordinates
  • XTension to Track Spine Heads, Dendrite Terminal- and Branch-Points
  • Compiled Pre-XTensions (requires installation of Matlab Runtime)

72 Fixed Bugs (since Imaris 6.3.1)
ID Summary
3905 No respond when selecting a *.lei file in file loading dialog on Mac
3832 Save intensity profile crashes
3809 LIF Preview details are confusing/wrong.
3793 Loading Imaris scene file crashes in 50%
3775 Space activates Slice Viewer instead of activating draw mode
3774 Branch Level Statistics not available, even if beginning point is set
3735 Some Olympus OIB OIF files can not be loaded
3728 Crop3d crashes with specific input & output sizes
3703 Recorded Movie of the animation shows only frame without volume
3694 Save and reload a big image as ICS is corrupt
3692 need track speed minimum and maximum
3691 statistic does not update after deleting parts with DEL Key
3689 Spontan resampling of lif files in Imaris
3684 Typo in Leica Lif Reader Settings Dialog
3683 imarisApplication.fileOpen problems
3681 statistics don't update after setting dendrite beginning point
3673 Spine head volume and spine neck volume statistics
3670 request new statistic: shortest path to beginning point
3667 Add time points of multiple selected OIB files crashes Imaris
3666 Add Timepoints adds only 2 Timepoints regardless of the real amount of Add timepoints Commands
3654 ROI not used for All Time Points
3653 Drift Correction does not update statistics immediately
3643 Imaris cannot open newest multi-channel Prairie View Files (3.3.7)
3637 Merge Spots crashes after several datasets
3624 Objects show/hide animation not working
3621 cxd files not loaded correctly
3620 resampling open crashes with timepoints >2-x
3614 Imaris does not run successfully when compiled with Qt-4.5.2
3607 Delete Slices of LIF dataset crashes
3606 Contour surface calculation on 2d data set produces black screen
3602 Open Statistics tab of this scene crashes
3601 single contour can not be edited, if multiple contours are visible
3594 Diameter calc seems to crash imaris "randomly"
3593 Snapshot on the 2D histogram in coloc crashes
3592 Nested surface not generated
3584 RGB TIFF not read correctly (crash or image corruption)
3570 Font in Display Adjustment sometime to small
3561 Documentation of Filament's Edit Tab in wrong chapter
3560 Imaris launches very slowly if proxy server is not configured
3536 crash when cancelling a selection in the statistics view
3533 Channel Changes Erratically Stored in Animation
3530 Imaris may crash when statistics tab is clicked
3503 Large LSM time series are loaded corrupt
3495 Loading scene does not load data set if path contains Umlaute
3494 Saving a data set does not remove .part from file name if the path contains a Umlaut
3433 Some slices black on zoom 0.5 and higher
3423 Master slicer for multiple open contours
3422 Scenes are not saved if the path contains a Umlaut
3379 Re-Open Saved Filament Takes extremely long Time
3372 Need more shortcuts, especially for copy-paste with contour surface
3361 Virtual memory goes high, crash when exceeding 4GB
3348 Need option to directly navigate to slices which contain a contour line
3347 Lock slice position while drawing countour
3303 Statistics time track is equal for all channels of a (multichannel) image
3270 Complicated way from contour to mask
3249 Columns of statistics are often far to wide
3240 Surface Color Type Statistics Coded not remembered in scene file
3089 Merge selected surface objects
3074 Andor File Reader: Z size is incorrectly read, reading performance is poor
2981 use channel color as default color for spots, surfaces, and filament
2831 RGB/HSL segmentation
2749 Textures are defect, when Imaris is started the very first time after installation
2644 LUT of Leica LIF not imported
2448 Shift and rotate contour
2405 For single layer parts of a structure no contour surface is generated
1868 Files with asian character in path can not be read
1295 Create a new channel as blend of existing channels
1294 Active Contours
1258 make pasted contours repositionable
1222 Visualize Velocity
1220 Draw geometric objects circular - square contours.
932 Set parameters for contour surface calculation


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

Last Modification: CL, 02-NOV-2009

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