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