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Imaris 9.3 Release Notes

Welcome to the Imaris 9.3 release notes. Please have a look to the overview of Imaris Release notes for information about prior released features and fixed bugs.

Version Date: April 9, 2019

Migration to Imaris 9.3 Arena

If you have used Arena in Imaris9.2 or prior you will want to migrate data to the new Imaris9.3 Arena. The ImarisArenaMigrator guides you through the migration. During migration the tool copies images from the previous Arena location to the new location and the tool does not delete any images from their previous location.

New Arena: A File Browser for Microscopists

Imaris9.3 has a new Arena Image File Browser that shows thumbnails of microscopy images on your file system. Irrespective of whether images are stored in multi-file tiff series or multi-image czi files Arena is a file browser that “understands” microscopy images and shows one thumbnail for each image. Arena lets you easily browse vast numbers of images on local or remote file systems. It is important to note that this new version of Arena is a file system browser in the sense that it automatically displays the content of a file system folder and when the file system folder is changed Arena displays the content accordingly. Also when files are copied to a folder within Arena the files are copied to the corresponding folder on the file system.

Conversion to IMS format within Arena

Beyond file browsing Arena facilitates the conversion of original microscopy format images to Imaris’ native IMS format. When you double-click a thumbnail of an image that is not yet in IMS format Arena will suggest to start the conversion of this image to IMS. The conversion progress is displayed in the FileConversionQueue in the lower right hand corner of the Arena Window.

Once an image is available in the IMS format it can be opened for visualization and processing in Imaris and this opening is very fast even for large images due to the multi-resolution IMS file format.

Batch Setup Wizard with Image Processing and Pipelines

Another major purpose of the Arena view is Batch Processing (available with the appropriate license). You can easily set up batch processing for images within a folder by starting the “New Batch” wizard from the main toolbar. The wizard guides you through the batch processing setup and it allows to create batch pipelines consisting of multiple image processing steps followed by detection of spots, surfaces, cells or filaments. With this feature it is possible for example to first invert a channel and then compute spots on that inverted channel.

Batch Results: It’s all in the File

The output from batch processing is always a “complete” IMS file. When a batch run modifies the image data the result is stored in a new IMS file. When a batch run “only” produces spots, surfaces, cells or filaments the result is added to the existing IMS file (unless that is the original file, in which case a copy is created and the objects are added to the copy).

When new files are created as a result of running batch processing, the old versions remain on the file system as “restore points”. All restore points are visible in the “Restore Points” tab of each image. In this tab it is possible to “undo processing”.

Image Processing with Preview

Imaris 9.3 has a new image processing dialog with a side-by-side view of original and processed. The side-by-side view shows the original and the processed image data from both a top view along the z-axis and a side-view along either the x- or the y-axis of the image.  It can be used in “Volume” or “Slice”-view to show either a volume rendering of the image data or a slice rendering for more detailed inspection.

The image processing dialog with Preview provides all those “image processing” methods which do not change the dimensionality of the image such as Gaussian Filter, Threshold, and Background Subtraction. Those methods that change the image dimensionality such as “Swap Time and Z” are still located in the image processing menu.

Deconvolution and Batch Deconvolution

New in Imaris9.3 is Deconvolution. If you have a license for Deconvolution it appears in the list of Image Processing commands in the image processing dialog. Deconvolution in Imaris can run on the GPU to provide optimal performance. To see if GPU-deconvolution is supported on your system open the Imaris Preferences and check the information on the “System” tab. 

Deconvolution is also available for batch processing. It can be setup in the batch setup wizard to be run either alone or in combination with the other available batch processing commands.

Arena Storage and Backup: It’s all in the Folder

A design principle of Arena is that all the information pertaining to a folder is stored within the folder. This has some very convenient consequences:
a) Running Arena on different computers working on the same network folder automatically shares all information, images, subfolders, batch results, batch parameters.
b) Once a thumbnail cache is created for a folder it is available to all computers accessing that folder.
c) To create a backup of an Arena folder all you have to do is to create a backup of the the corresponding file system.

Arena creates a hidden folder named .imaris_cache in each directory and stores in it a cache of image thumbnails and metadata for all images within the parent folder. This cache facilitates fast loading of thumbnails and metadata when Arena displays the content of a directory. Upon first creation of a cache Arena puts individual jpg files and metadata files into the .imaris_cache directory. Once these individual cache files have been built Arena will create a faster cache by combining many thumbnails and many metadata into fewer files for faster loading

Fixed Bugs

Bugs Fixed in Imaris 9.3
6115 Resetting Imaris will set the number of processors incorrectly in the "calculations" page
7207 Export of Coloc statistics does not remember the last path
7217 IQ Tiff Min Max Contrast settings not read
7320 “center” does not work properly for 3D+T filament
7674 Data set volume disappears on zooming after distance transformation
8623 Batch stops at some point and does not complete big batch jobs
8876 Importing Imod scene crashes Imaris
9931 Imaris crash when clicking "File name with Delimiter" in TIFF reader settings
10262 Display Adjustments not correctly interpolated in Keyframe Animation
10397 Color coding tracks with statistics doesn't work for Cells
10478 After 'Cut Surface' and 'Unify' 'Split' does not work
10504 Selecting one or multiple filament points, will not allow you to resize diameter in EDIT tab
10506 using path in filament does not select the terminal ending
10519 CZI FileReader does not correctly handle multi file datasets
10538 Imaris 9.0 incorrectly reads Z-step size from Prairie View OME tiff (version 5.3)
10591 Stage Positions not correctly read for some oif files
10644 CZI tiled image loading is failing in 9.02 and 9.1
10712 Timelapse Cell Vesicle name is wrong in statistics
10716 VSI Z Voxel size equals XY voxel size
10722 Imaris does not load metadata and datatype of this VSI image correctly
10747 Coloc button is available even though license is unchecked
10764 CZI file opening problem
10765 CZI file import creates vertical line in data set
10789 Number of Vertices statistic is not displayed for surfaces
10804 Cells Creation Tab - Rebuild - Tracking Nuclei and Vesicles' restarts the wizard
10808 oif file LUT table reading incorrect
10814 ROI handles are too big initially
10818 Micrometer character in file name blocks import of CZI
10819 Special characters in filename creates more strange characters
10830 When Interpolate is unchecked, image window still shows interpolated view
10845 CZI from Z1 imported with wrong voxel sizes
10846 Edit Surfaces step of creation wizard is non-functional
10892 Imaris 9 Drift Correction "correct volume and all objects" is failing for Surfaces
10906 Spots cannot be selected if track is under the pointer
10920 Only 100 tiles are read from CZI
10942 CZI file opens with some parts shifted
10950 2D Volume disappears when rotating it
10969 Cell to surface to mask to Filaments Threshold crashes
10976 Crash when going back in cells membrane wizard step 4/4
11001 Measurement points disappear after new channel added
11002 CZI file can't be opened in File Open dialog or by drag and drop
11007 GE Incell .xdce 'header file' causes problems up to crash when used for import
11010 Setting a specific color in XT for spots is not maintained when added to Imaris 9.2
11015 Filter tab content disappears after 'Duplicate Selection to new Surfaces/Spots' when the original Surfaces/Spots object was made with a manually set threshold
11021 Export data for plotting is grayed out if more than 50 objects are selected
11025 Distance Transform artifact on large 2D image
11026 CZI file can't be opened in 9.2.0
11030 Selecting custom statistics in Vantage crashes Imaris
11047 Time series object intensity plot is wrong
11052 Linear stretch -> channel arithmetics crashes Imaris
11057 Crash when exporting statistics of cells detected with ROI
11058 Surface unify deletes surfaces when multiple images are loaded and have adjusted viewing frames
11062 Measurement points 'delete' button doesn't work
11069 Export data for plotting should be grayed out for non-timelapse data
11070 Hard crash when pressing "Finish" button in Classify step of Surface Wizard
11071 Spots Wizard crashes hard after second step with customer data set
11076 Arena > Add an Image > Settings does not work
11133 Labels disappear after merge
11134 Opening Imaris file with 2640 filaments per time point (14 time points) is very slow to load
11135 Object Label doesn't work properly in duplicated objects
11175 Tracking Nuclei and Vesicle crashes Imaris if more than one vesicle type is imported
11247 Entering a value in channel shift crashes Imaris
11250 Hard crash when pressing "Delete" in Filter tab and no filter is in the list
11257 Multiple identical entries for same Spot in statistics
11264 Adding a Spot manually right before the tracking step will crash in Imaris
11270 Pair information for Measurement points not available anymore
11296 Some Statistics are duplicated for Threshold loop detected Filaments
11313 Manual track creation partially broken for Beginning Points of Threshold Filaments
11332 Spots with volume = 0 should be removed
11347 Time slider goes back to frame one in Animation
11360 ImarisCell membrane detection induces Imaris crash with no nucleus detected
11368 12GB file with Surfaces and Tracks takes 20+ Minutes to open
11393 Project to 2D XTension crashes Imaris with customer data set
11411 Excitation wavelength is not updated when changing it in the Image Preferences dialog
11457 Imaris could not finish making small surfaces
11518 Compressed filament draw and edit gui
11530 Imaris Batch Setup GUI does not read the stored "Batch Stores Processed Image" setting

Imaris 9.3.1

Fixed 18 Bugs (since Imaris 9.3.0)
11018 Show Help on some parts in Stitcher do not work
11441 For this CZI file, Imaris 9.3 detects 64 individual images while 9.2.1 loads one single image
11506 Manual missing for Preferences/Batch and Preferences/Arena
11536 Deconvolution Copy function copies emission wavelength
11552 Filament selection centering and diameter results in Crash Imaris 9.3.0
11560 Imaris crashes when observing a folder that contains a scene file
11568 Making new channel in XT Distance transform or Channel Arithmetics breaks the Save button
11574 Imaris crashes when started with an unsupported file from command line
11575 Export of Open Microscopy Environment XML and TIFF not working with 9.3 libraries
11578 Missing Arena documentation
11586 Surface drift correction is wrong
11589 Imaris Batches fail if "&" character is anywhere in path to file
11593 ESC does not work in batch creation wizard
11596 Stitcher does not resample with weighted mean
11599 Imaris will crash if you "Save" an image with an added coloc channel
11605 ImarisCell batch run data export fails for .csv (default format)
11652 Preferences/Arena manual needs update
11666 Image Extents have wrongly been multiplied by a factor of 10^6 for these 2 CZI files