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Imaris 9.5.0 Release Notes

Welcome to the Imaris 9.5.0 release notes. Please have a look to the Overview of Imaris Release notes for information about prior released features and fixed bugs.

[Fixed Bugs]

Native Distance Statistics for Surfaces and Spots

The Surfaces and Spots component of Imaris9.5 natively compute shortest distances to any other Surfaces or Spots. The computation is fast and capable of running on large images. It is now very easy to find the spots that are close to Surfaces by just adding a Spots filter for the ShortestDistanceToSurfaces statistics value.

imaris 9.5 release notes

The ShortestDistance Statistics makes several applications very simple:

  • Color code Spots or Surfaces by Distance from Surfaces.
  • Filter Spots inside or outside of Surfaces.
  • Filter Spots in a specific distance band outside or inside Surfaces.
  • Filter tracks of objects that “go inside” Surfaces.

The Spots have two new statistics:

  • ShortestDistanceToSpots: computes the shortest distance from the center of each spot of “this” Spots to the centers of all spots from the other Spots.
  • ShortestDistanceToSurfaces: computes the shortest distance from the center of each spot of “this” Spots to the border of all surfaces from the Surfaces. Distances are positive for spots outside of the Surfaces, and negative for spots inside of the Surfaces.

The Surfaces have two new statistics:

  • ShortestDistanceToSpots: computes the shortest distance from the border of each surface of “this” Surfaces to the center of all spots from the Spots.
  • ShortestDistanceToSurfaces: computes the shortest distance from the border of each surface of “this” Surfaces to the border of all surfaces from the other Surfaces. Distances are positive for surfaces that are entirely outside the other Surfaces. Distances are negative for surfaces that are entirely inside the other Surfaces. Distances are zero for surfaces that intersect the other Surfaces.

For performance reasons the Shortest Distance Statistics calculations can be turned on/off on a per object basis. To do so the creation wizards of Spots and Surfaces have a checkbox “Shortest Distance Calculation” on the first creation tab and on the edit tab (so that the setting can be changed after creation too). Note that shortest distances are calculated only between components that have the setting turned on, meaning that “Shortest Distance Calculation” must be turned on in at least two components to get such statistics. Note also that the first four Spots or Surfaces components created will have “Shortest Distance Calculation” set to “on” by default and further components are “off” by default.

Native Distance Statistics in Batch Processing

Shortest distance statistics between components produce an interdependence of components. As a consequence in Step 2 of Batch Setup where objects are created each object in the BatchPipeline has shortest distance statistics only to objects that are above the respective object in the list of objects. In the example below the “Spots 1” have “Shortest Distance to Surfaces 1” but not vica versa.

imaris 9.5 release notes

As another consequence of the interdependence of objects the following scenario can occur. Suppose you have set up the Spots in the above example to be filtered by Shortest Distance to Surfaces. If subsequently you rebuild the Surfaces component with different parameters the Spots component should be rebuilt too. Imaris warns you of this interdependence with a dialog as follows:

imaris 9.5 release notes

This dialog only pops up when it is necessary. If Spots1 had not been filtered by Shortest Distance to Surfaces then the interdependence would not exist and the warning upon rebuild of Surfaces would not appear.

Insightful Rendering of Surfaces

Imaris9.5 Surfaces have new rendering options.

imaris 9.5 release notes

All Surfaces are rendered with a “Material” that can be chosen from a list of “Material Preset”. Many of the new “Material Preset” choices have “bright edges” highlighting regions where the surface normal is perpendicular to the line of sight. Some of the “Material Preset” choices have some texture added to the surface. This texture is a rendering effect and does not come from the original image data. We hope that this is obvious to the user.

New Color Tabs

All surpass objects have a new color tab designed in alignment with the new Surfaces color tab. Some material choices are available only for Surfaces because only the Surfaces renderer has been implemented with this capability so far. The label color options on the color tab have been made a subsection of the base color mode. This allows better access to base color changes than in previous Imaris versions.

Visually lossless Resolution Changes in Volume Rendering

Large data volume rendering uses a multi-resolution image to choose the optimal sufficient resolution for all the image intensities to be rendered to a pixel on the screen. In the rendering the volume is sub-divided into blocks and each block is sampled and rendered on slices that are orthogonal to the camera direction. In versions prior to Imaris9.4 the slices in each block were rendered in one of the discrete resolutions available in the pyramid. In Imaris9.5 each slice is rendered as a mixture of two resolution levels and this mixture changes with the distance from the camera. The two approaches are sketched in the following figure.

imaris 9.5 release notes

The effect of interpolating resolution on a slice by slice basis is that discrete switches of resolution when the image is rotated or zoomed become almost invisible.

High Performance Slice Rendering

The performance of Imaris’ slice renderers, OrthoSlicer, ObliqueSlicer, Extended Section View has been significantly improved for version 9.5.

WYSIWYG Animation

The Animation View user interface lets users configure the output video size and automatically adapts the render area to have the same aspect ratio as the output video size such that users see on screen a realistic preview of what will end up in the movie.

imaris 9.5 release notes

High Quality Video Output

Imaris9.5 produces higher quality h264 video than previous versions of Imaris.

Histogram Improvements

In the filter dialogs the sliders for min and max thresholds have been improved for ease of use and for reproducibility in batch processing. When a slider is dragged to the end of the histogram, i.e. the min slider to the left or the max slider to the right the respective threshold for the filter is automatically deactivated.

Updated ICS File Reader

The ICS reader has been updated to use version 1.6.4 of libics which is capable of reading ICS version 2.0 format.

ImarisXT supports Python3

The ImarisXT python interface now supports Python 3.7 in addition to Python 2.7.

MSD XTension

A new XTension “MSD Plot” on the XTensions tab of Spots and Surfaces creates a “Mean Squared Displacement Plot” from Tracks. This plot is useful to understand if the observed motion is consistent with Brownian motion or not.

Gallery View and Easy3D View discontinued

The Gallery View and Easy3D View are no longer available in Imaris. We learnt from usage data analysis that both were not very popular and decided to let go of these in order to simplify the application.

86 Bugs Fixed for Imaris9.5

2064 Add support for ICS2
7351 Original Manders Coefficient does not take the ROI
7545 Make formulas in the reference manual visually more appealing
9877 Spots not detected in the timepoint that has been deleted
10177 Crash when opening Settings tab of Surfaces if using Intel Graphics
10252 Extended Section on Ortho Slicers causes very slow rendering
10733 Reference Manual Definition of Filaments - Spine Part Length Ground/Neck/Head not correct
10759 Imaris stitcher 9.1.2 opens file in Imaris 9.0.2
10918 The window 'Edit Image Properties' should be called 'Image Properties'
10990 'RIGHT-Mouse Show Help' on slider of Slice viewer links to Time Bar help
11022 Graphic performance loss during OrthoSlicer view in 3D View in Imaris9.1 and later
11023 GE InCell 512 pixel dataset loaded as 2048 pixel dataset
11036 Consistently use the same filament terminology
11038 Provide definition of 'Branch'
11040 Description Filaments Pt Distance wrong
11041 Filaments Filament No. Dendrites Branches revise description and Figure 8
11048 Add definition of 'Vertex' to the Filaments Statistic reference manual
11080 Add support for Huygens .ics "2.0" format
11081 Imaris File Converter does not preserve stage positions of LaVision OME tiff file
11128 Vesicles not rendered in Vantage
11312 Huygens ICS/IDS flipped along Z
11320 Description of 'Distance from Origin' missing
11339 Surface duplication makes 'live clone' after 'Rebuild'
11343 List of supported File Formats in Reference Manual is not up to date
11382 Reference frame drift correction places reference frame outside volume
11448 lsm file with multi position converts incorrectly
11452 Spots Region Growing ignores "automatic" threshold when batch processing
11473 This tiff series cannot be split properly
11496 Clicking "Cancel" during creation wizard for Spots and Surfaces Crashes Imaris
11533 Scale bar jumping around when making movie by animation
11551 Metadata listed in Imaris LIF file after conversion to IMS seems to be missing
11564 Invalid installer EULA
11565 Remove readme files from installers
11577 Vantage plot crash
11599 Imaris will crash if you "Save" an image with an added coloc channel
11619 Crash at start of Imaris cured by registry reset
11622 Batch Processes Ignore Statistical Selections
11627 Scale bar doesn't update when zooming in Section view
11633 Batch "Revert to Original Image" fails if a Batch Vantage plot is made
11637 For Surfaces, Imaris does not just display the preference-enabled statistics
11647 Crash if ROI in creation parameters defined for not existing time points
11650 Missing help link for normal folders in Arena
11653 VSI-File not read correctly empty slices are added between
11665 Installer for ImarisStitcher 9.3.1 removes the ImarisStitcher 9.3.0 application
11677 Camera rotation changes drastically when Reference frame planes are set visible
11679 Not able to read Leica Files properly in Imaris 9.3.1
11692 Preferences crash with deactivated Arena and wiped Current User Registry
11696 Order of Surpass Objects in Surpass Tree is not saved after changing it
11697 Title of Observe Folder dialog should be changed
11703 Export data for plotting is broken in Imaris9.3 for stat that have 3 parts
11706 Change the naming of the exported csv files back to the Imaris9.2.1 style
11708 Split Spots into Surface objects is failing on this 2D dataset
11709 2D ND2 image files is opening with extremely small X Y voxel scaling values
11714 FileConverter readme must be adjusted
11728 Invalid icsx file is shown with the old Creation Parameters Icon in Imaris Arena
11733 Imaris does not choose the correct graphics card
11749 Blurred Image in Fusion on last two z slices after 9.3 Upgrade
11752 Imaris crashes when Normalize Layers uses cache
11756 File dimension detection does not work if non of the preset prefixes is found
11765 File dimension detection does not work if non of the preset prefixes is found
11770 Filament automatic creation is failing to draw Filaments properly
11779 CZI pixel scaling from dual-side fusion light sheet is off by a factor of 1000
11780 CZI image from dual side fusion light sheet are converted as individual Z-slice
11782 Imaris crashes when creating plot of these two folders with batch runs
11784 TIFF images do not generate a IMS after conversion
11786 Vantage does not show objects for all selected folders
11787 Vantage plot contains many cells which do not have any content - correlated to FilamentStats?
11788 Save does not work for almost all surpass objects added to the 3D Menu, except the four main components
11795 Channel shift will change voxel size
11801 Imaris crashes when saving this file
11805 Light Source And Frame Color Tab should not have "Object ID" and "Track ID" enabled
11807 Create new folder in Arena fails when the same name already exists and has been removed
11810 Multi-dimensional TIFF with metadata not converting correctly
11820 Batch result is omitted if same objects is stored in data
11823 Imaris installer has Arena disabled by default
11843 Stitcher fails to save when sample closest is selected resample method
11850 File names with higher unicode characters can become corrupt or cannot reload
11860 Corrupted registry prevents Imaris from starting up
11873 Imaris 9.3.1 node-locked license not starting Imaris 9.3.1 - solved by reset registry
11874 Imaris does not configure voxel size or channel meta data properly when reading
11875 Description Displacement ^2 wrong
11890 Normalize Layer(s) documentation is not correct
11895 GPU Load unusually high for Cells Rendering
11922 Imaris File converter correctly converts these mrc files but shows an error
11931 Surfaces with missing Intensity statistics
11937 Cell Intensity Statistic Not Calculated or Display when manual input surface in a 2D image

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