Imaris 9.3.0 Release Notes
Welcome to the Imaris 9.3.0 release notes.
Please have a look to the Overview of Imaris Release notes for information about prior released features and fixed bugs.
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Migration to Imaris9.3 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.
Bugs Fixed for Imaris 9.3
Imaris9.3 has 77 fixed bugs.
||Resetting Imaris will set the number of processors incorrectly in the "calculations" page
||Export of Coloc statistics does not remember the last path
||IQ Tiff Min Max Contrast settings not read
||“center” does not work properly for 3D+T filament
||Data set volume disappears on zooming after distance transformation
||Batch stops at some point and does not complete big batch jobs
||Importing Imod scene crashes Imaris
||Imaris crash when clicking "File name with Delimiter" in TIFF reader settings
||Display Adjustments not correctly interpolated in Keyframe Animation
||Color coding tracks with statistics doesn't work for Cells
||After 'Cut Surface' and 'Unify' 'Split' does not work
||Selecting one or multiple filament points, will not allow you to resize diameter in EDIT tab
||using path in filament does not select the terminal ending
||CZI FileReader does not correctly handle multi file datasets
||Imaris 9.0 incorrectly reads Z-step size from Prairie View OME tiff (version 5.3)
||Stage Positions not correctly read for some oif files
||CZI tiled image loading is failing in 9.02 and 9.1
||Timelapse Cell Vesicle name is wrong in statistics
||VSI Z Voxel size equals XY voxel size
||Imaris does not load metadata and datatype of this VSI image correctly
||Coloc button is available even though license is unchecked
||CZI file opening problem
||CZI file import creates vertical line in data set
||Number of Vertices statistic is not displayed for surfaces
||Cells Creation Tab - Rebuild - Tracking Nuclei and Vesicles' restarts the wizard
||oif file LUT table reading incorrect
||ROI handles are too big initially
||Micrometer character in file name blocks import of CZI
||Special characters in filename creates more strange characters
||When Interpolate is unchecked, image window still shows interpolated view
||CZI from Z1 imported with wrong voxel sizes
||Edit Surfaces step of creation wizard is non-functional
||Imaris 9 Drift Correction "correct volume and all objects" is failing for Surfaces
||Spots cannot be selected if track is under the pointer
||Only 100 tiles are read from CZI
||CZI file opens with some parts shifted
||2D Volume disappears when rotating it
||Cell to surface to mask to Filaments Threshold crashes
||Crash when going back in cells membrane wizard step 4/4
||Measurement points disappear after new channel added
||CZI file can't be opened in File Open dialog or by drag and drop
||GE Incell .xdce 'header file' causes problems up to crash when used for import
||Setting a specific color in XT for spots is not maintained when added to Imaris 9.2
||Filter tab content disappears after 'Duplicate Selection to new Surfaces/Spots' when the original Surfaces/Spots object was made with a manually set threshold
||Export data for plotting is grayed out if more than 50 objects are selected
||Distance Transform artifact on large 2D image
||CZI file can't be opened in 9.2.0
||Selecting custom statistics in Vantage crashes Imaris
||Time series object intensity plot is wrong
||Linear stretch -> channel arithmetics crashes Imaris
||Crash when exporting statistics of cells detected with ROI
||Surface unify deletes surfaces when multiple images are loaded and have adjusted viewing frames
||Measurement points 'delete' button doesn't work
||Export data for plotting should be grayed out for non-timelapse data
||Hard crash when pressing "Finish" button in Classify step of Surface Wizard
||Spots Wizard crashes hard after second step with customer data set
||Arena > Add an Image > Settings does not work
||Labels disappear after merge
||Opening Imaris file with 2640 filaments per time point (14 time points) is very slow to load
||Object Label doesn't work properly in duplicated objects
||Tracking Nuclei and Vesicle crashes Imaris if more than one vesicle type is imported
||Entering a value in channel shift crashes Imaris
||Hard crash when pressing "Delete" in Filter tab and no filter is in the list
||Multiple identical entries for same Spot in statistics
||Adding a Spot manually right before the tracking step will crash in Imaris
||Pair information for Measurement points not available anymore
||Some Statistics are duplicated for Threshold loop detected Filaments
||Manual track creation partially broken for Beginning Points of Threshold Filaments
||Spots with volume = 0 should be removed
||Time slider goes back to frame one in Animation
||ImarisCell membrane detection induces Imaris crash with no nucleus detected
||12GB file with Surfaces and Tracks takes 20+ Minutes to open
||Project to 2D XTension crashes Imaris with customer data set
||Excitation wavelength is not updated when changing it in the Image Preferences dialog
||Imaris could not finish making small surfaces
||Compressed filament draw and edit gui
||Imaris Batch Setup GUI does not read the stored "Batch Stores Processed Image" setting