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Imaris 8.3 Release Notes

Welcome to the Imaris 8.3 release notes. Please have a look to the overview of Imaris Release notes for information about prior released features and fixed bugs.

Version Date: May 27, 2016

Membrane Based Cell Boundary Detection

Using Imaris’ Cell component it is now possible to detect cell boundaries based on a membrane signal even if no nucleus signal is available. The following screenshots show examples of this segmentation:

Algorithmically Imaris performs a multi-scale watershed with region merging to achieve this segmentation. Users can interactively adjust the merging thresholds to get an immediate visual effect of the threshold settings. In addition after running the membrane based cell boundary detection users can go to the edit tab of Cells and Merge or Split cells that were not segmented correctly.

Cells Visualization Improved

Improved visualization of Cells on 2D slicers facilitate easier validation of segmentation results. New features include:

Border rendering of cells as white lines

Region rendering of cells with original intensities overlayed by cell color

Cells Color Options

Cells can now be colored by ObjectID to facilitate discrimination of neighbouring cells.

Lineage Tracking Algorithm “Maximum Overlap” for Cells

To track cells that are segmented from a membrane signal the “maximum overlap” tracking algorithm was added to Imaris8.3. This algorithm can track dividing cells to produce lineages.

The algorithm works as follows: For each cell the algorithm searches a mother cell at the previous time point by calculating the spatial overlap with all cells of the previous time point and picking as the mother that cell with which it has the largest overlap. As a sanity check the link to the mother is created only if the overlap exceeds a minimum ratio which is 0.5 by default.

Reference Frame Component

A Reference Frame is Cartesian Coordinate System that can be positioned and oriented anywhere within an image.

Manual positioning:

Automatic positioning:

Reference Frames Affect Statistics Values

Statistics values of Spots, Cells, Surfaces, Filaments are reported both in the image coordinates and in reference frame coordinates (if the choice of coordinate system has an influence on the values).

For example “Spot Position X” will also be reported in reference frame coordinates as a new statistics value “Spot Position X Reference Frame” when a reference frame exists. The same happens for other positional values and for vectorial values like velocities and for speed values that also depend on the reference frame. 

Reference Frame Play Mode

When reference frames are used in time series it is possible to use the “Reference frame play mode” to play through the time series in such a way that the selected reference frame stays still while the time series plays.

If the reference frames are positioned to move with an object this play mode allows to play through the time series in such a way that the “tracked” object stays still.

Tracking in Reference Frame Coordinates

When a reference frame object exists it is possible to choose this reference frame as the coordinate system within which to perform tracking. This is useful when tracking vesicles that move inside a cell which moves itself.

Cells Split Option “One Nucleus per Cell”

Imaris8.3 has two options to perform the split “One Nucleus per Cell”:

Distance From Nucleus - Every pixel within the cells is assigned to the nucleus that it is closest to. All the pixels assigned to the same nucleus make up one cell. This method performs a robust split where borders end up “in the middle” between nuclei.

Cell Channel Intensity - Bright regions of the cell channel around a nucleus are assigned to that nucleus with the effect that the borders between cells end up at low intensity regions. This method tends to fail when two cells are not delimited by a low intensity region.

The “Distance from Nucleus” option is in many cases similar to the previous “Split one Nucleus per Cell” method.

New Statistics Values

Tracks have new statistics values for displacement in the scenario of lineages:

Track Displacement definition for the lineage situation now is the maximum distance of the first position to any of the positions at the last time point of the track. This statistics was in 8.2 not well defined for tracks with multiple objects in the last time point.

Every object has a new statistics value - Distance From Origin.

Vantage 1D Statistical Tests

Vantage1D shows univariate distributions of statistics values for comparison between groups. In previous versions of Imaris it was possible to inspect visually whether distributions differ. Imaris now provides statistical tests to assess differences between distributions. The tests that are reported in the Statistical Tests tab in Vantage1D are the following:

Wilcoxon-Test Tests whether two samples come from continuous distributions with the same medians. F-Test Tests whether two samples come from normal distributions with the same variance.

T-Test Tests whether two samples come from normal distributions with the same means. Kolmogorov-Smirnov-Test Tests whether two samples come from the same populations.

It is possible for users to adjust the confidence level and whether the tests are performed left-tailed, right-tailed or two-tailed.

XT works with new Matlab Component Runtime (MCR) Versions

Imaris works with MCR v7.1 (Matlab R2009a/b) as before and additionally with MCR v8.4 (Matlab R2014b) and it is possible to configure XTensions to use other run Matlab Component Runtimes. Each XTension specifies which MCR it is compiled for in the xml file. The XTensions that are installed with Imaris8.3 are built for MCR v8.4.

Installation of the Matlab Component Runtimes is simplified by starting download directly from Imaris Preferences CustomTools section.

Imaris without Arena

Due to customer requests we decided to provide a version of Imaris that does not have Arena (and no batch processing capability either). This version is similar to pre-Imaris8 versions in that it can open and save one image at a time. To get this version users can choose to install Imaris without Arena during installation.

Speedups from Parallel Watershed Algorithm

The watershed algorithm in Imaris runs blockwise and parallel. This produces speedups (compared to previous Imaris versions) for the following steps:

Fixed Bugs

Fixed 99 Bugs (since Imaris 8.2)
9399 Drift Correction wrong
9381 Using an ROI of one time point with Cell and selecting a cell object crashes Imaris
9355 Possibility to select which MATLAB version to use together with Imaris
9344 Region Growing Threshold display is not visible if cells rendered on a slicer XY
9338 Incorrect coloring of track segments and connections in track lineage editor after connecting two objects.
9332 Imaris shuts down when user deletes a contour surface object
9328 When RecordingDate value for Leica files is not present Imaris uses '-4713-11-24 00:00:00.000'
9326 File converter 8.2 crash with OME tif files
9324 License issues with Imaris 8.2.0 Track vs. LineageTrack
9315 Track lineage editor in native theme uses white branch connections against a white background
9312 Wrong formula for velocity in reference manual
9310 Imaris holds at 'finishing up' on the flash screen when Arena is active
9308 Opening an OME image causes DrawVolume call to freeze
9305 Filament No. Dendrites Branches illustration not clear.
9299 Enabling Nucleus visibility slows Display Adjustment responsiveness
9294 'Filaments points tracks' XTension crashes when trying to create the spots object
9292 Filament branch hierarchy XT does not work in Imaris 8.3 with matlab 2014b
9290 Automatic threshold for Cell segmentation does not work in batch processing
9280 Vesicle outside Cell XTension has "1" based CellID (Imaris is zero based)
9258 Arena Data storage location unable to be moved - file not found error
9244 File with lots of manually edited objects can't be opened again
9233 importing IMX file with contour lines crashes Imaris when surface is generated
9231 Documentation link for Spots Edit Dialog in Spots Wizard wrong
9223 Automatic caching of image data if data set fits completely into the assigned RAM
9219 Imaris not using .IMS color table when default colors are selected in Preferences
9208 Document for the Cell module what negative Vesicle To Nucleus distances mean
9197 Show Help does not work in Track Editor
9180 Filament IDs change on editing - causing problems with labels
9174 Corrupt Statistics display after deleting one channel
9173 if image is opened in Surpass and file not read completely, deleting the image from Arena will not delete the file on disk
9163 Description of 'Imaris Administrator - Data Management' is missing
9154 Imaris quit and will never load .nd2 files (Nikon SIM)
9150 No channel check boxes are selected in all the Image Processing operations
9142 Measurement Points Center to Selection does not work if one point is selected
9140 Deleting multiple assays which contain image data in quick succession will cause Imaris to crash
9138 Radiobuttons for "Add / Delete (Cursor intersects with):" are truncated in Edit Spots
9137 CTRL-S does not store dataset
9129 Correcting Drift then CTRL + Z and clicking in the Track Editor causes a crash
9118 Annotate area can be activated even when licence is disabled
9115 Voxel Calibration of TIFF exported by ImageJ 1.47b (Fiji) not read
9105 Track Editor numbering doesn't match the frame number when analysing a subset of data
9103 3D cursor should disappear when loading new image
9086 Merging Spots objects then rebuilding tracks stalls Imaris
9085 Changing the displayed statistics while in the Colour tab will lead to multiple instances of Points and Tracks displaying
9073 3D View flickers at some zoom levels with files
9013 Vesical histogram disappear after swithing tabs
8994 ZVI file crashes Imaris with 'Out of Memory' Message
8993 Cannot read compressed ZVI files
8991 Imaris is really slow if Arena has many batch runs
8961 Show Help from the context menu for labels leads to a page that does not exist
8952 Missing labels columns in statistics tab after adding more statistics type through preferences
8940 Cells parameters are altered in duplicate
8933 Colour Type in the material editor should revert to 'Base' on rebuild
8916 Explain the Arena Preference options when moving the database in detail
8896 Spines are branched even though that function was unchecked, during the creation of the filament.
8886 Link Vesicle Track-ID's with Cell Track-ID's
8860 Selecting specific statistics for Filament is still showing all filament stats
8846 Filename in Fiji is not the filesystem name
8797 The time column in Export Data For Plotting is incorrect
8783 Timestamps from LIF files not read correctly (from new LAX software)
8780 File series detection limited to "999" files
8762 Launch of AutoQuant from 'Image Processing - AutoQuant' fails
8718 PlotNumbersArea Doubleclick to open original image does not work for Collections of 1 item
8701 Mac does not support credentials that require a workgroup
8696 ROI in Surfaces is very small and not in the center anymore
8694 Various Missing links
8680 Imaris incorrectly warns the user after opening the file using "image only" even after using store as
8652 Cannot access 'Edit Spots' options (stylesheet)
8620 Coloc parameter naming for ROI usage is inconsistent
8550 All Spine Part Length(s) Incorrect (many negative and zero values)
8466 Auto-path won't add dendrites even signals are strong
8370 Crash when stored creation parameters are used
8295 Not all z slices are read in for an tiff file
8028 Imaris does not read Nikon Elements ND2 Time interval (or reads incorrect time)
7850 Filters in Wizard "ignored" delivering false results
7796 Missing texture blocks after Resampling Open (.lif)
7681 Nucleus transparency has no effect
7633 Import Spots and Surfaces to Cells does not work with mismatching times
7613 Imaris keeps file read locks on some loaded tiff images
7530 Free rotate does not allow normal editing of Axis values
7528 Disabling the currently selected statistics colour coding type can cause Imaris to swap to a different surpass object
7449 Edit single time point calibration
7423 Big Tiff files loading only first frame - not entire image.
7189 Volume statistics tab not updated when switching from Surface object
7183 Cellbody segmentation - split by seed points does not split as expected
7152 contour tool can not create surface if voxel size is small
7114 Update compiled Xtensions to newest Matlab version
7090 Imaris fail to open .cxd file if data contain z information
6889 Multiscale Watershed
5979 Duplicate Selection should also duplicate the creation parameters
5868 Make it apparent to the user if he is using normal matlab or runtime
5692 split cells by seed point gives fewer cells than seed points
5330 ImarisCell continues to miss these cells that are in close proximity but clearly different cells.
5281 Find location of installed Matlab and Matlab runtime on MAC
5046 Camera Drift Correction (without resampling the image)
4641 Changes to image composition (i.e. adding or deleting channels), all channels become visible
4508 statistics channels not updated after delete channels
4030 ND2 file reader problem: timelapse with multiple XY positions not opened properly
2740 ImageJ Tiff can not be read

Imaris 8.3.1

Fixed 7 Bugs (since Imaris 8.3.0)
9453 Using Multiple filters is broken, in both Creation wizard and in regular filter set.(affects surfaces, cells, spots, filaments)
9451 Filament Autopath is broken if the starting point size is set too large - Imaris 8.3
9446 Cell Cycle Displacement (X,Y,Z) and Displacement Length are incorrectly calculated
9445 Cell Cycle Duration values are incorrect
9438 In version 8.3, upon Build Coloc Channel, No statistic is generated
9427 Imaris 8.3.0 cannot open 12GB tif dataset, while 8.2.1 can
9385 Confusion concerning Reference Frame statistics