Imaris | Release Notes and Bug Fixes

Imaris 7.3.0 Release Notes

Welcome to the Imaris 7.3.0 release notes. Version Date: June 23, 2011. 
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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    New License Administrator

    • Properly handle User privileges (e.g. UAC under Windows)
    • Clean up GUI: preferences dialog, startup dialog
    • License installation is only required once per system. Imaris x86 and Imaris x64 use for all (future) versions and all users the same license setup.
    • System license installation requires Administrator user rights
    • Evaluation license requires normal User rights (not Administrator)
    • The new License Administrator resolves dozens of bugs (see list on the bottom)
  • When starting Imaris the first time after installation, you can either install an Imaris license, or start a 10 day SW evaluation.
  • Click the Key-Icon to start the License Administrator
  • If UAC is enabled (Windows Vista or Windows 7) the system will prompt for an admin password.
  • Initialliy no license is installed. Press "Add License Location" to continue the setup.
    • Download a Node-Locked License
    • Define a Floating License Server
    • Install License from existing File
  • You can install multiple license locations. E.g. Floating license and a Node-Locked license. In this case Imaris will search all the locations until it finds the license for the requested features.


  • If you requested Imaris for Evaluation you don't need a node-locked or a floating license. You should have received a Registration ID and a Passcode.
  • Evaluation can be activated either in Imaris' startup dialog (if no valid license was found), or from the menu "Help / License".
  • After entering the Registration ID and the Passcode into the according fields, switch on the light.

  • Movie Output with selectable Size
  • Link to Tutorial Movies (menu "help")
  • FileiIO
    • Reading Intelligent Imaging Slidebook Images (*.sld)
    • Olympus OIB for Mac (used to work for Win only)
    • Zeiss ZVI for Mac (used to work for Win only)
  • Stores layout and docking state of all windows and tool bars. See also MeasurementPro.
Surpass General
  • Creation Parameters
    Spots, Surfaces, Cells, and Filaments have an option to store and recall parameters for their creation wizard.

    • Press Remember Parameters on the bottom of the Create Tab
    • Stored parameter-sets will be selectable from the Creation Wizard's initial step
    • Organize, export, or import stored parameters under Edit / Preferences / Creation Parameters, or simply click the Preferencessymbol next to the new buttons



(Multiple Vesicle Types)

(Split Nuclei)

  • Cell detection based on Membranes

    Depending on the used cell staining techniques and sample preparation, you can select either Cell Body or Cell Membrane algorithm setting. Select the segmentation algorithm which is applicable:

    • for Cell-body stained images select Cell Body algorithm - (unchanged, "old" method)
    • for Cell Membrane stained images select Cell Membrane algorithm - (new method)

    The cell membrane algorithm set partition of a given image into two regions, one representing the objects to be detected and one representing the background. All background regions are considered as a single region. As initial region for the object of interest, the detected Nuclei objects are used. The algorithms first fits a close border around the nucleus object region creating the initial size of the cell. Then the algorithm is based on interactive boundary detection, where the border iteratively propagates until the optimal closed boundary is found by successively trying all possible positions in the object region. The membrane detection process is repeated until you are satisfied with the look of the segmented region by combining algorithms result and by using visual feedback.

    • Entirely smooth: This algorithm setting considers that the intensities are statistically homogeneous in each region assigned to the image. The intensity of each region is approximated by a value of mean intensity.
    • Piece Wise smooth: In practice, large objects usually have a heterogeneous intensity distribution. The PieceWise smooth algorithm setting takes into an account the presence of intensity variations. By using local region information, the algorithm divides the image region into sub regions with intensity matching the local mean properties.
    • Remove Tiny Regions: If this option is selected the small complex regions are removed.
    • Diameter: The value defended in the Diameter field defines the maximum size of the region considered to be removed.
    • Max diameter; The value defines the maximum diameter of the region border to be created. This parameter also affects the Maximum number of the algorithm iterations to be performed.
    • Accurate / Smooth: If the Shape slider is set to be more on one side the resulting border can be encouraged either to be smooth or more accurate with the original image characteristic.
    • Length / Curvature: The Curvature value constrains the shape of the resulting border. Setting the slider to be more on the Curvature side, results in a circularly shaped borderline.
    • Detect button: Press this button to perform the next the algorithm iteration. The result of the algorithm calculation is visible in the viewing area.
    • Reset Button: When this button is selected, all cell membrane computation is reset to initial state. Please note: Intermediate cell membrane computation result are not saved.
    • Detection iterations number: The value shows the number of the completed algorithm iterations

  • Multiple Vesicle Types
    To detect the additional vesicles types

    • Click on the drop-down list and select the Add new Group..option
    • Enter a Vesicle name in the Group name field
    • The new Vesicles type name appears in the list
    • Select the Source Channel
    • Define the Estimated Diameter
    • Decide on the Background Subtraction

    Alternatively to the creation wizard, Spots can be imported as Vesicle of a specified type. Available on Cells "edit" tab.
  • Split Nuclei
    Nuclei, which can't be separated by the basic thresholding are now separable by additional seed points. The Split Nucleus method for segmentation in Imaris starts with defined seed points. You use Nucleus as seed points for the Nucleus segmentation that is performed in the next steps. During the process around each seed point, the region grows until it reaches a border.
  • Statistics Output of Nuclei and Vesicles moving relative to Cell
  • Component Hierarchy for Statistics Export

  • Creation Wizard with Preview for all Time Points
  • Option to automatically extend Selection to attached Spines
  • "Create / Rebuild", and "Edit / Diameter" show a dialog which allows to select the according channel. Prior Imaris versions had no channel choice - they were using the first visible channel (from Display Adjustments).

Spots, Surfaces
    Quick Manual Tracking

  • Single-Click to add and track an Object (Spot or Surface)
  • The manual tracking option allows you to track objects with in a time-resolved data set by manually specifying the object location in each time point. Essentially, the manual tracking is done by clicking on the structure on the image, which serves as a visual reference (template).
  • The option can be activated by clicking in the Auto-connect to selected spot box
  • To start manual tracking, move the time slider to the first time point for the feature you want to track. Then use the pointer to Shift- left click on a feature in the dataset. After each mouse click, the time slider advances one frame, allowing you to see the subsequent image of the temporal stack. To continue manual tracking, keep clicking on the structure on the image. As you add more manual tracking points by clicking it within the viewing area, a track is created providing you an option to follow moving features, frame by frame from the point to the point, until you've build a complete motion path
  • Auto-connect to selected spot box
  • Select the option to add all selected or added objects to one track and advance to next time point when a new object is added or an existing is selected
  • The box on the drawing plane indicates the crated object diameter. The diameter of the object can be changed, during the manual tracking, by using the mouse wheel. Use the mouse wheel to increase/decrease the radius of the created object
Spots, Surfaces, Cells
    Fill Gaps with Life 

  • Option to detect Objects based on tracking information
  • Objects which have been curtly excluded at the Classification step will be reactivated in order to complete the track.
  • e.g. Object was detected for t=1 and t=3. It was not detected for t=2, because Object was very dim. The new Algorithm will try to find the Object at missing Time Point

  • Additional measurements have been added to ImarisCell.
  • New XTensions with statistics output have been developed for ImarisXT.
  • Imaris stores state and size of Surpass statistics window. Useful to place the Surpass tool bar on a second screen. See also Imaris
  • A lot of effort has been invested to improve the performance of the Statistics and the Edit Tabs. Especially statistics for long time series is calculated much faster.


  • Macintosh AND Windows
  • Better support for Java
  • New functions for Filament Tracking
  • New interface
    • Java based
    • The "old" COM-based interface for the Windows version of Imaris still works, but will not be further developed. Function set is freezed to the state of Imaris 7.2.
    • Migration Guide for XTensions from Imaris 7.2 to Imaris 7.3
  • Requires Matlab 2008 (for Imaris' uncompiled XTensions)
  • Requires Matlab Compiler Runtime (for Imaris' compiled XTensions)
    • Windows: MCR v7.10
    • Macintosh: MCR v7.11
  • Requires JRE 6
  • Example to setup pathes for Matlab under "Edit / Preferences / Custom Tools / Matlab" (required only for Macintosh):
    • Matlab Application: /Applications/MATLAB_R2007b/bin/matlab
    • Matlab runtime environment: /Applications/MATLAB/MATLAB_Compiler_Runtime/v711
    Similarity Statistics 

    The blue Objects have similar sphericity and volume like the two yellow (selected) reference Objects. The red Objects are very different. 

  • Available for Spots, Surfaces, Cells, and Filaments on Tools-Tab
  • Computes for all object a value of simiarity based on ...
    • ... one or more reference objects
    • ... one or more key properties (statistics)
  • Result can be used on Filter-, Statistics-, and Color-Tabs
  • Example: Find spherical Surfaces with similar Size
    • Create some Surfaces
    • Switch to Tools-Tab
    • Select some round Surfaces with the desired Size as Reference Objects
    • Click Add Similarity Statistics Value
    • Key-in a name for the new value (arbitrary)
    • Select Sphericity and Volume from the list (use ctrl-click)
    • Press OK => New Statistics Value is being added for all the Objects

    "Vesicles" outside Cells 

    Color is indicating the Spots'
    membership of to the Cell.
    Color is indicating the Spots'
    distance to the Cell.

  • Spot-like Objects outside of Cells can be related with the nearest Cell
  • The XTension adds two new measurements to the Spots
    • Distance to closest Cell
    • ID of closest Cell

  • Requires Batch Coordinator 1.1

Fixed 94 Bugs (since Imaris 7.2.3)
2321 Export/Load scene ignores channel visibility
2328 Export/Load scene does not preserve actual timepoint
2358 Preferences->License uncheck filereader has no effect
2382 Second marked tracking parameter can not be replaced
2809 floating licenses incorrectly denied for multi-ip client machine
3178 File converter should detect license configuration from Imaris
3339 License not found when in default place
3475 file converter: conversion speed per file decreases, when many files are in the list
3492 License not found when installed as Admin user with UAC on
3524 Path to old license server not deleted
3545 No notification to user in license dialog when license has expired
3646 ImarisBatch does not report if a module license is missing
3730 License dialog says "license valid but not checked out" even if there is no license at all
3951 FpBp does not find the license if there is only Imaris x64 installed
3965 Online activation fails to save license file with UAC enabled
4008 License dialog does not clearly report not available batch licenses
4092 2 channel Filament over time only 1st channel selected
4184 License disappears from 'Preferences - Licenses' if unchecked
4193 Batch jobs all give error "failed - license not available"
4240 Not well balanced progress on writing large datasets
4249 Changing time point with cursor keys (left/right) does not work after manually adding a surface (e.g. magic wand)
4296 ND2 file with ODD dimensions does not open properly.
4303 License path with Umlaute not accepted.
4358 Batch jobs error "failed - license not available" after upgrade
4381 Poor rendering performance (of surfaces) on Nividia chips
4389 Can not change base track color of a surface object tracked over time.
4419 Statistics Color Coding for Filament lost when saving Scene
4420 StatisticsTab not updated when enabling additional statistics
4421 Statistics lost after revert to file and not recoverable
4459 Non ISO Characters in license file path problems
4516 ProgressBar in Filament Tracking goes backwards
4522 Building statistics is very slow on ~1000 time point data set
4560 Large snapshot of large datasets shows different resolved blocks
4569 Multi-position .LSM files can not be opened in Imaris.
4571 Save does not store dataset after change of Display Adjustment or Orientation
4575 Time calibration on OME TIFF written by LaVision not imported
4612 Imaris keeps file lock on directory of loaded image
4621 Activation of satellite license fails with online method
4627 Clipping plane Distance value not updated when you switch between planes
4642 MINOR: Incorrect Example for HRESULT ISurfaces::GetVertices
4648 Manual Detection in time series uses the last starting point of other timepoint
4710 contour shortcut "a" (autocenter) can not be applied in sequence
4793 Typo: "Scholl" should be "Sholl"
4796 XTension "Split Branch Levels" does not correctly split
4820 Creation Recalculation - Multiple ROIs get lost
4929 Playback of animation very slow if time graph is active
4951 Olympus VSI reader can not open JPEG 2000 compressed images
4952 Filament creation with multiple beginning points in 7.2.0 is much slower than in 7.1.1
4962 Startup License Window corrupt when pressing Key
4965 Track Editor opens slow with big dataset
4981 Mouse scroll wheel changes Zoom and Diameter at Same time
4996 Color coded stats mode for multiple filaments is not working
5028 No description for Vesicle distance to closest nucleus center
5031 Track Displacement Description missing
5039 Definition of "Center of Homogenous Mass" is confusing to biologists.
5064 "Nothing to filter" if one or zero objects in first time point
5081 Adding a filter takes really long for Filaments
5119 imaris asks at startup if "usage data" should be collected, after license was reset
5125 Multi-selection of vesicles on timelapsed data does not work in 3D
5137 Nucleus base color not working after statistics color coding
5158 Unable to add spines in different channel for multiple filament start point
5161 Excel 2007 complains about "unreadable content" when opening exported cells statistics
5174 Vesicles outside of cell are not removed if cells are not filtered
5178 Filament Selection does not work in XT if more than one filament is present
5194 Statistics not updated after the second time 'mask channel'
5203 Animation made in orthogonal camera mode - major perspective artifacts upon reopening
5204 Formula for "Cell Area" and "Nucleus Area" wrong in Reference Manual
5231 Show Statistics after SplitSpots or SplitTracks freezes Imaris
5235 Added channels in Animation lead to crash
5239 Two Dendrite Filters can not be used for Filament
5242 Olympus VSI file reader crashes with Imaris OSX x64
5243 Description for Spine Diameter - Shortest Path wrong
5245 Imaris crashes when recording movie without dataset
5246 Statistics tab crashes for empty Spots
5247 Add Key Frame crashes if Undo is disabled
5250 saving animation to protected path causes crash
5275 FileConverter does not work with Specific folder as Output
5293 Imaris crashes during surface creation when loading another file
5294 Opening oib file crashes Imaris (new case)
5305 Imaris File Converter generates only .part files on a SMB share from Linux
5307 Crash by opening IPLab file
5308 object colors are ignored in animation
5314 Displacement ^2 description missing for Spots
5329 Save does not store dataset after editing a contour
5352 Mouse action is blocked if statistics coding is activated (color bar appears)
5356 Export Average Values for "Filament Loop" data crashes Imaris
5358 Imaris loads wrong LUT for iQ Files
5369 Olympus VSI file reader crashes with Imaris if the same named folder is not present
5371 Time lapse ZVI's take a long time to open in Imaris
5373 Input-Focus changes, when Progress-Bar appears (cursor keys in surpass tree stop working)
5383 Filament: "mouse selects point" switched to "mouse selects segment" after deleting the point and UI does not reflect this
5384 OME TIFF file open crash
5385 Calculate diameter dialog reappears for each filament
5390 Spots disappear from Edit tracks window after you undo a track connection


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

Last Modification: CL, 23-Jun-2011

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