Imaris | Release Notes and Bug Fixes

Imaris 7.5.0 Release Notes

Welcome to the Imaris 7.5.0 release notes. Version Date: June 13, 2012. 
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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Analysis of membrane stained cells
(no need for cytoplasmic labeling)

  • Brand new fully automated detection algorithm
    (additional and independent from iterative detection algorithm)

    3D embryo (cell membrane labeled). Original image curtesy of Katie McDole,
    Department of Biology, Johns Hopkins University, Baltimore

    2D cells (cell-cell marker). Image on the left from: google images.
    Center and right images are processed in Imaris (Cell).

  • Optimized usability of iterative detection algorithm

    Imaris 7.4.2
    Imaris 7.5.0
  • New measurements

    • Full range of cytoplasm-/cytosol-related parameters (e.g. cytoplasm volume and number of vesicles in cytoplasm)
    • Nucleus/Nuclei distance to cell membrane
    • Reporting on different types of vesicles (mean distance of type A vesicle to cell membrane reported separately from mean distance of type B vesicle to cell membrane
  • Variable vesicle diameter within each vesicle type

  • New and improved Cell preview and final result rendering

    Imaris 7.4.2 Imaris 7.5.0
    Cell preview is grey which allows to visualize the details of the fluorescent signal in a much clearer way than in 7.4.2 when the color or the related channel was used to create the preview of the cell.

    Final rendering is now done in blend mode (90% transparency for the cell, and 0% for the nucleus). The color of the source channel for each component (cell, nucleus and vesicle types) is used to drive the colors of the final rendering.

    This new rendering is particularly advantageous when multiple cells are clustered together. Using MIP only the borders of individual cells cannot be seen. In blend they can. This is even more obvious when moving the scene around in 3D.

  • Several statistics values have been added for ImarisCell.

  • Improved usability of XTensions to handle Super Resolution Data.
    Added Demo Image and User Guide.

    ... to Spots

    ... to Image

    Volume (detail/zoom)

    Volume + Spots
    The color (and size) of each rendered spot is related to the intensity at the related localization (data from super res. particle table)

  • New descriptive library (47 XTensions)

  • Ellipse in Z dimension
  • Mask using spots
  • Exclude when touching image border
  • Bounding box measurements object aligned or axis aligned (L.W.H)
  • Exclude when touching image border
  • Customizable / adjustable time stamp configuration and display
  • Color Maps
    • Automatic setting of elucidative default color map (i.e. spectrum)
    • Preview of different color maps
  • Combine multiple Imaris scenes
  • Improved usability for manual object tracking
  • File readers and data exchange
    • Zeiss CZI
    • Improved loading options for iQ users
    • Full metadata data exchange between AQ X3 and Imaris 7.5

Fixed 94 Bugs (since Imaris 7.4.2)
1930 Surpass 5.0.2 Measurment Point labels turn black on some Radeon systems
2948 Snapshot / Animation 6.1.0 Time Bar is corrupt (colour and text) when taking snapshots of tracks
3101 Documentation 6.1.3 Documentation of the XTensions
3426 Surpass 6.2.1 Snapshot messes up position of two colorBars
3429 Surpass 6.2.1 Two colorbars are wrongly rendered in snapshot
3676 Surpass 6.3.1 Rebuild Surfaces Region takes incorrect recreation path.
4223 Surpass Cells 7.0.0 Cells color cannot be changed after switching back from color coding
4320 Snapshot / Animation 7.0.0 Colorbar position not adjustable in snapshot mode with off screen rendering on 64 bit system
4378 Surpass Cells 7.0.0 Cells split by nuclei with nucleus background subtraction produces uneven cells
4450 Coloc 6.4.2 user interface heavily flickering, when playing time animation in coloc
4640 Surpass Surfaces 7.1.1 Key Frame Animation Properties should not overwrite common Object Properties (when loading from file)
4881 Surpass Spots 7.1.1 Automatic region threshold for spots with different sizes (region growing) is always 125
5024 Snapshot / Animation 7.2.0 Conversion Context error when saving a quicktime movie
5251 Surpass 7.2.3 Color of day in timestamp changes if time colorbar hidden
5252 Surpass 7.2.3 hide scalebar: can't move/resize Surpass timestamp anymore
5347 XT 6.3.1 Accessing deleted Spot element from XT crashes Imaris
5366 FileIO 7.2.3 Added channels are turned off in animation
5427 License 7.3.0 RLM license server crashes
5498 Snapshot / Animation 7.3.0 Can not write keyframe movies to folders with French characters
5542 _General 7.3.0 Check for Update does not report new version
5573 Surpass Cells 7.3.1 Long statistic name corrupts colour bar
5610 FileIO 7.1.1 Improper reading of the time data with ND2 files
5625 FileIO 6.1.5 TiffSeries reader crash
5628 FileIO 7.3.0 OpenLabLiff crashes
5642 _General 6.0.2 Resampling Open slice preview not rendering right on Radeon GPU
5707 Vantage 7.4.0 Bottom Part of some Letters in Main toolbar is missing (i.e. "Vantage" reads more like "Vantaqe")
5764 Surpass Surfaces 6.2.0 Edit buttons overlap vertically
5797 Vantage 7.3.0 Colorbar of Surpass stays when switching to Vantage
5820 Surpass Volume / Slice 7.3.1 Shadow causes color gradient on frame shading
5843 Surpass Cells 7.3.1 Vesicles Style Dialog missing, if name of vesicles contains the name "cell"
5854 Vantage 7.4.0 Vantage wizard fails, if some of the key statistics are switched off (e.g. "Position X")
5889 Documentation 7.4.0 Online documentation link for Surface Edit tab broken
5913 Surpass 7.3.1 Colorbar for invisible objects shown after loading
5914 Documentation 6.4.0 Formula for instantaneous Speed Calculation (Spot,Surfaces) wrong in the Reference Manual
5921 Surpass Filaments 7.4.0 For Rebuild Tracks it is not clear that all steps of the wizards will be repeated if 'Entire Image in All Time Points' is selected.
5923 Documentation 7.4.0 Evaluation license description wrong
5958 License 7.4.0 After changing the checked status of the license the table jumps to the top
5967 Surpass 7.4.0 Visibility state of objects not restored when IMS is loaded
5980 Surpass Filaments 7.4.0 Threshold based filaments algorithm does not split unconnected filaments
6008 Statistics 7.3.0 Detailed - Averages Values' statistics export generates corrupt file
6017 FileIO 7.4.0 ICS/IDS with �? character in filename can not be read
6020 XT 7.4.0 XTension Spots Split Into Surface Objects: mixed result for creation wizard status
6024 Surpass Volume / Slice 7.3.0 Using Volume->Draw on newly created channel --> Crash!
6025 Statistics 7.4.0 critically wrong statistic label: Displacement^2 [X Y Z]
6026 Time / Tracking 7.4.0 Time lapse playback gets stuck playing, only force quit can recover
6030 Surpass Filaments 7.3.1 Filament wizard does not show Filament tracking options if only one Filament identified
6034 Vantage 7.4.0 Crash when Nucleus Position Relative to Cell Position is selected for scatterplot
6045 Surpass Surfaces 7.4.0 Set default set vertex delay back to 300 ms
6046 XT 7.4.1 Fiji connection does not work after updating Fiji - Error: Could not create java virtual machine
6048 FileIO 7.4.0 OME Tiff written by Imspector (Lavision Biotech) not detected as OME
6049 XT 7.4.2 Line Profile XTension saves *.csv files with wrong (*.cvs) filename extension
6050 XT 7.4.0 "Licenses currently in use" dialog blocks usage of Imaris via ICE on OSX
6056 FileIO 7.4.0 Bad Metadata.txt (Micromanager format) causes instant crash
6065 Documentation 7.3.0 XT API Documentation: Dead link to ICE on first page
6066 Image Edit 7.3.0 "Apply" button for data-cache in preferences useless
6067 FileIO 7.3.0 Loading speed of OME tiff decreases dramatically while loading (time series)
6070 Surpass Surfaces 7.4.0 after masking surface multiple times, the channel dialog is ignored
6076 Surpass 7.4.0 Threshold setting follows mouse movement
6087 FileIO 7.4.2 OME XML (*.ome) reader loads corrupted voxel data
6088 FileIO 6.0.1 highlighting certain .txt files in Open dialog can crash Imaris
6090 Surpass Filaments 7.2.0 No statistics coded colors for tracks in color tab
6096 FileIO 7.3.1 Segmentation and rendering of large structures fails after the middle of a time series (image dimension: 1061 x 1061 x 10 x 60)
6099 XT 7.4.2 Spots Closest Distance XTension: Border mode fails
6109 Surpass Filaments 7.3.0 Dendrite Beginning Point is removed, if deleting some selection breaks one Filament into multiple unconnected parts
6110 Surpass Surfaces 7.4.0 Bug im Manual Contour: Channel visibility does not work in Surpass Surface
6111 XT 7.4.0 XTSuperResolutionSpotsToDataset missing as matlab runtime for mac
6120 XT 7.4.0 Image To Fiji losses the data for the second channel
6122 Surpass 7.4.2 Crash deleting component with annotation and vantage
6126 Surpass 7.4.2 Rebuilding color coded Spots/Surfaces causes instant Crash
6141 XT 7.4.0 Documentation error in Imaris::IDataItem::GetColorRGBA and SetColorRGBA
6155 Surpass Cells 7.4.2 Cells Settings Tab: Group-box "Vesicle Style / Quality" should not be visible under "Nuclei Tracks"
6156 Surpass Cells 7.4.2 Cells Color Tab: Vesicle tracks are listed by number and not by name
6160 Surpass Surfaces 7.4.2 Manual creation of surfaces crashes on big dataset
6161 XT 7.4.2 Multiresolution images are not recalculated when changing the image data
6164 Surpass Cells 7.2.3 Calculation of Distances to Cell incorrect
6165 _General 7.4.2 Zoom factor after starting Imaris set to -100%
6166 Image Edit 7.4.2 Add [channels/timepoints/slices] fails with multi-image (.SLD, .LIF, .kinetic, etc) files
6169 FileIO 7.4.2 File open failed on second time.
6176 License 7.4.2 In License Administrator the link to the reference manual doesn't work anymore
6184 Surpass Cells 7.3.0 Number of membrane detection iterations is not saved in the creation parameters
6187 Surpass 7.3.1 Crash when renaming component
6189 _General 7.4.2 Copyright year is out of date
6191 Surpass Spots 7.3.1 Using a statistically coded color map during the Spots creation wizard causes a crash
6192 XT 7.3.0 TrackTranslate
6196 FileIO 7.3.0 Ome Tiff load wrong data
6198 Vantage 7.4.2 Imaris crashes with spots/surfaces merge if Vantage object was created on scene object that is no longer present
6216 Surpass Filaments 7.4.2 Rebuild Threshold algorithm 'Keep Data' crash
6220 _General 7.4.2 Crash changing preferences or image origin after deleting Spots/Surfaces
6228 FileIO 6.4.2 Imaris crashes loading surface tracking scene file without dataset
6253 Surpass Cells 7.0.0 Overlapping Vesicles are not removed
6255 Surpass Cells 7.3.1 Crash on drift correction of cells
6258 Surpass Cells 7.4.2 Deleting vesicles does not remove all selected vesicles
6275 FileIO 7.4.2 Some Nikon ND2 version 3.0 files cannot be read
6296 FileIO 7.4.0 Save button does not save manually added surfaces

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

Last Modification: CL, 13-Jun-2012 

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