Part of the Oxford Instruments Group

Imaris 8.4 Release Notes

Welcome to the Imaris 8.4 release notes. Please have a look to the overview of Imaris Release notes for information about prior released features and fixed bugs.

Version Date: November 10, 2016

The main feature of Imaris 8.4 is manual filament tracing for large images. Both Autopath and Autodepth tracing are improved significantly in this version to enable filament tracing in large images. The following is a list of all the new features of the Imaris 8.4 release.


ImarisFileConverter is big data capable. It easily converts terabyte sized files from almost any microscopy format or from tiff-series to the high performance IMS format that allows immediate interactive visualization of terabyte sized images.

In version 8.4 we have made ImarisFileConverter more responsive with better progress updates and a more interactive user interface. Here is a screenshot of the new User Interface.

The top table of the user interface is the input area which allows users to set up the list of files to convert and to configure the settings of each file before they start the actual conversion process. When a conversion is started by pressing “Start All” files are moved to the bottom table which displays the progress on the running conversion.

New in ImarisFileConverter8.4:

Filament Drawing Autopath

Autopath filament drawing is big data capable.

Note: Be careful not to clip away parts of the filament that you are drawing because this can break the drawing.

Note: there is (unfortunately) no visual indication of the progress of the autopath calculation. The only way to find out is indirectly from moving the mouse pointer to different positions in the image. For those positions where the calculation has already arrived a tracing will be shown. For those positions where the calculation has not yet arrived no tracing is shown. Note also: Since it is very easy to trace a small piece and then continue the tracing from there users can work without interrupt.

Filament Drawing Autodepth

Autodepth filament drawing is big data capable.

Note: Because of autosnap it is important that the cursor size roughly matches the diameter of the filament that you draw.


The snapshot button in the main toolbar immediately produces a snapshot of the current view. By default, the snapshot is saved to a file in the source image directory and after creating the snapshot it is opened in the default image viewer to show the user what the snapshot looks like. The snapshot is by default also copied to the operating system clipboard for use in other applications. Users can modify the behaviour of the snapshot button by changing the snapshot preferences:

When the Scale value is set to 1 the snapshot button creates a snapshot with the size of the render-area. To create high resolution snapshots, the user can change the “Scale” preference to a value larger than one. If the Scale value is set to 2 the resulting snapshot will have 2x the width of the screen render area and 2x the height of the screen render area.

To help the user see the size of the screen render area Imaris displays this size in the top left hand corner of the render-area whenever the size is changed.

Also the view-menu now has the possibility to “Save Window State” and “Load Window State” which functions on a per viewer basis and saves and loads the size and visibility of all windows.

Note: Snapshots always have the same aspect ratio as the render-area of the current view. In previous versions of Imaris it was possible to create snapshots with aspect ratios differing from those of the current view.

New Navigation Control in Surpass-3D View

For those users who prefer the old behaviour of Imaris it is possible to change back to the old behaviour in the Preferences Display section.

Note: The functionality of “Set Center” in the 3D-view camera toolbar is affected by this new behaviour. While Set Center will reposition the camera to the same position as in previous versions the focus point around which the camera rotates is changed with the zoom of the camera (in order to allow to zoom through the dataset).

Graphics Memory Autodetection

The preference for Display::TextureCacheLimit is automatically determined from the available memory of the graphics board when Imaris is used for the first time.

Display Adjustment Improved Auto Function

The Auto setting of the display adjustment is improved.

The calculation now works as follows: The minimum value is set to the first mode (maximum) of the histogram. The maximum value is set to a value that is around the 99.8 percentile of the histogram which effectively disregards high intensity outliers.

Scalebar Position and Size

Scalebar Position and Size can be adjusted in the preferences:

Old Zoom Definition

100 per cent maps one voxel to one screen pixel in any of the views.

Parallel Spots Statistics Calculation

In Imaris8.4 the calculation of spots statistics is multithreaded and blockwise.

Renaming of Some Function in Cells Edit Tab

On the Cells edit tab the function “Merge” is renamed to “Fuse” and “Split” to “Fragment”.

Possible to Change Color of Vantage 1D Plot

Added a color wheel icon that allows changing color of each Vantage 1D object.

Statistics “Track Intensity Median” Definition Changed

To improve statistics calculation performance the definition of the “Track Intensity Median” Statistics is now:

Track Intensity Median = Average of all Intensity Medians of all objects at all time points in the track

In previous Imaris versions the Track Intensity Median had computed the median of all voxel intensities within all objects at all time points within the track. This operation required visiting image intensities. With the new definition it is possible to calculate the Track Intensity Median statistics from the already calculated Intensity Median voxel statistics for each object.

Exact Distance Transform

The distance transform calculation is an exact distance transform computed using the method of Meijster, Roerdink, Hesselink: “A general algorithm for computing distance transforms in linear time”in Mathematical Morphology and its Applications to Image and Signal Processing, Volume 18 of the series Computational Imaging and Vision pp 331-340.

The exact distance transform is used throughout Imaris8.4 wherever distance transform calculations are done. This leads to differences in statistics values like “vesicle distance to cell membrane”. Also the results of some of cells, surfaces, spots and filament detection may differ due to the changes in the distance transform.

The exact distance transform is also applied when distance transforms are run via ImarisXT.

New Filament Spine Statistics

Filament has 3 new statistics values:

Easier Access to some Functions on Filament Edit Tab

In previous versions Filament Edit Tab, there are three functions which need Source Channel Selection: Center, Diameter, and Join. Also, the function Diameter need other three input parameters: small diameter, large diameter, and threshold value. We streamlined the dialog in order to avoid the popup that was needed and integrated it directly in the edit tab.

New Reference Frame Manipulators

Reference Frames can now also be positioned using visible manipulators:

Also, as shown in this screenshot the reference frame axes have labels in the 3D scene.

Supported Operating Systems

Imaris8.4 is supported for Mac OS X 10.9 and higher. Imaris8.4 is supported for Windows 7 x64 and higher

Fixed Bugs

Fixed 99 Bugs (since Imaris 8.3)
9716Using the quality filter in membrane detection when no Cells are detected will cause a crash
9694Editing a Filament with loops causes the Save/Export to fail
9683Rebuild of Spines activates ROI
9651Incorrect opening of >2 gb Fused CZI tiled images
9648Crash on Filament Join...
9645Memory Limit Accepts Negative Values
9631Batch for Filaments fails on all datasets
9628Region Growing Slicer Position is Reset when changing threshold value
9621Truncated names in Arena when selecting objects for manual collections
9625Reference manual Missing description/diagram of Velocity Angle statistic
9608Disabling Interpolation has no effect
9602Batch fails on group of files for all the files
9586Cells wizard crashes when settings tab is open and you click into rendering area
9578Opening successive lsm files on mac will crash Imaris
9559Undo does not work for extract channel
9558Building Vantage Plot uses lots of RAM and takes virtually for ever
9555Cannot run successive XTensions on OS-X
9551Batch Queue is still enabled in file menu when the batch licence is not present but pressing it has no effect
9526Imaris crashes when free rotating a data set
9525Animation TIFF export jumps to first time frame in last keyframe
9524Filament statistics are doubled
9518Imaris crashes when opening a coloc data set and the license is not available
9509Clicking on the Cylinder track style crashed Imaris
9505ObjectIds of Tracked Cells change after store and load
9502Contour drawing mode 'Time' stops when new circle on same frame is started
9495The distance values in the 3D crop window should be closer to the corresponding pixel values
9489Reference Frame is listed as product Reference Frame instead of Imaris MeasurementPro
9483Extract Channel adds channel with improper dimensions
9481Data not saved when Arena is off and Imaris gets closed
9470Filter Dialog loses Filters after Duplicate Selection
9464Added Tags in Arena are lost/deleted if user moves/duplicates file to a new group
9458Visualization of objects in Vantage while only showing labelled objects differs between object rendering and center point
9457Order batch results by file name rather than by completion time
9456Cells Membrane Threshold entry for Creation Wizard missing from reference manual
9453Using Multiple filters is broken, in both Creation wizard and in regular filter set.(affects surfaces, cells, spots, filaments)
9443More sensible locations for file export and open dialogs to default
9438In version 8.3, upon Build Coloc Channel, No statistic is generated
9437Transparency of Shaded Volume Cells is too limited
9431About Dialog in Imaris Administrator should have its own window
9428Help for Programming Interface - Broken Link
9421Adding multiple Spot/Cell objects disables the Filter Dialog
9407Imaris crashes when I try to delete 16 segments in Filaments
9387Resample Image to align Reference Frames button should be inaccessible in single time point image
9383Imaris provides no indication of which axis is which while using Reference Frame
9378Imaris uses "Merge" and "Split" for two very different actions in Spots/Surfaces as compared to Cells
9351Switching between 'Create' tab and 'Settings' show more Seed Points than selected
9317Switching between manual filament and AutoPath or Auotdepth fails to remember postions
9316Filament classify spine statistics - Average stats only showing Stubby spines
9306Search tool in Annotation crashes Imaris
9304Add image folder throws warning for files which are associated with an image file
9243Datasets opened through Fiji/File/Open retain the file name of previously opened files
9242Manual Autopath can not trace filament in one go while wizard Autopath does
9181If Imaris can not reach the floating license server you get stuck in splash screen
9168Volume display is blank after deleting 1 or more timepoints from original ND2 file.
9130Frame number overlaps time values on the timebar for OS-X
9109Editing filaments removes all labels
9101Volume statistics get "lost" if time series is cropped
9095With 'Object' selection mode active in the track editor clicking on a track in the rendering area will highlight nothing
9093Cells object (without vesicles or nuclei) cannot be exported for plotting
9074Update text for 'Off Screen Rendering'
9064Dataset with millions of spots causes crashes in 'Edit Tracks' and 'Statistics'
9058Rebuilding Surfaces after editing a lineage track takes too long
9053Editing Lineage tracks then going to the Color Tab stalls during statistics calculations
8973Track Editor's bottom scroll bar behavior is different from right scroll bar behavior
8943BatchAgent doesn't clean up temp files from failed batch runs
8647filament should be displayed as line during rebuild process
8644Names for Surpass objects created in 7.6.5 do not display in Arena
8600Filament cylinder size set by default to 1000um in CZI files
8498Contour time drawing frequency not set
8310Default rendering style of Filaments from a batch run is line while from the wizard is cylinder
8189OME validation scripts generates errors for OME export
8089Coloc unstable when no dataset is loaded
8088Exporting annotation when no dataset is loaded crashes Imaris
8020You can not have the scale bar in the lower half of the gallery
8016Classify Spine XTension does not work for all datasets with recent Matlab versions
7979Adding manual Spots/Filaments with no volume data causes a crash
7925Rebuild filament leads to additional entries in the statistics which are zero
7895Coloc panel appears when Snapshot is activated from Surpass mode
7781Some ome-tiff files are not read in correctly
7774XT can access invalid data while background loading is active
7747Olympus Tiff saved by VS-ASW 2.5 (Build 9483) wrong XYZ calibration imported
7536Statistics Calculation for spots is slow compared to 7.6.5
7467Filament Rebuild All does not produce the same results like a fresh build
7301False/Misleading count display in "Selection - Average values" of the Statistics tab
7108Spine count varies between Imaris statistics and Matlab Plot if count=1
6904Snapshot output does not match preview of overlays (e.g. scale bar units)
6636Add workflow to automatically detect spines on manually traced filament
5969New OME files not properly read (reader and writer outdated)
4149Scalebar / Color bar label does not scale with snapshot size
3525Part of spines still visible when 'Show Spines' is off
3462Volume is not shown on load after surface or filament wizard started
3263Improve Duplicate Filtered Object Behavior
2417Snapshot of gallery mode is not properly imaging the preview
12 Feature Requests Implemented
1973Option to set behavior of default snapshot path
4016Imaris should support saving external objects as .WRL file type
4352FR:Autodepth Cursor Placement should be aware of clipping planes
6397No Crosshairs should be visible in a Snapshot of Section view
6564Snapshot widget forgets previously set filename
7675>2 gb Fused tile CZI image file does not open in Imaris (Imaris opens the fused tiles incorrectly)
8601Bring back the old Zoom value behavior
8803Cannot load (new) OME-XML files supplied by customer
9362Customer wants only "m:ss" time display in 3D View
9364Name of Statistic value not added to Excel export
9620Cannot change 1D vantage graph color
9633Default tab of 'Imaris Administrator' should be 'License' after installation

Imaris 8.4.1

Fixed 14 Bugs (since Imaris 8.4.0)
7249Artifact shown in Zeiss 3D+time LSM File
7420CZI file open in Imaris is not properly reading the defined channel colors
9763CZI file with 4 channels not opening with the proper color scheme
9774After first file, the consequetively name CZI SNAP files are not read by Imaris
7711Wrong palette when opening LSM file converted to CZI
9778Filament number statistic wrong!
9802Crash of Threshold Graph Compilation on larger dataset
9691Animations only contain a few frames on OS-X when viewed in quicktime
9811Imaris does not open .LSM file
9806LSM file fails to open in Imaris 8.4
9755Crash on delete of manual surface generated by time drawing mode
9794Zeiss .lsm file read correctly in 8.3.1 does not load correctly in 8.4.0
9772Torch View not working for 2D images
9818Contour loading is broken

Imaris 8.4.2

Fixed 1 Bug (since Imaris 8.4.1)
10005resource_type='bpFileDependenciesItem' can only be written to postgres 1000 times at which point Store becomes non-functional