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Imaris 9.1 Release Notes

Welcome to the Imaris 9.1 release notes. Please have a look to the overview of Imaris Release notes for information about prior released features and fixed bugs.

Version Date: December 19, 2017

Imaris Stitcher

Imaris Stitcher is a new standalone application that “stitches” multiple images with overlapping fields of view into one big image with one big field of view.

Imaris Stitcher initially positions images using stage coordinates stored by the microscope. If stage coordinates are available and correct the first display of multiple images in Imaris Stitcher will already have almost good positions for each image. The “Align” button in Imaris Stitcher allows to refine positions and align overlapping images precisely such that their content matches well. Here is a typical example:

If you have a file where stage coordinates are not available to ImarisStitcher you can use either a grid layout tool to position images on a grid or manually move images close to where they belong in relation to all other images. After having done that more or less well the “Align” button will take care of finding precise positions.

Imaris Stitcher requires IMS files as input. Imaris File Converter is the tool to produce IMS files. In this release Imaris File Converter functionality has been improved to produce input for ImarisStitcher. See section “File Series with Split” and “File Series Delimiters Configurable”.

Imaris 9.1 Multi-Image Functionality

In this version of Imaris it is possible to overlay two images with different extents and voxel sizes. It is possible to translate and rotate the images relative to each other to facilitate alignment. For example one may overlay a fluorescence microscopy image with an electron microscopy image of the same sample.

Most of Imaris functionality is available for each of the images when multiple images are loaded. A few exceptions apply: Volume rendering only allows for MIP rendering in the multi-image scenario. The Coloc module, the Easy3D viewer and the Gallery viewer are not available for multiple images. On the other hand it is possible to calculate spots or other objects from either image. And Imaris 9.1 will even calculate statistics of the other image when objects overlap with another image.

Frame Object Allows Image Positioning

In Imaris 9.1 the frame object in 3D View allows to position the image. In the case of multiple-images multiple frame objects appear and each one can be associated with one of the loaded images. When the position tab of the frame object is selected a little “tripod” appears in the 3D scene. When the tripod is moved or rotated by clicking on the center or the axes and manipulating their position the image follows along. This allows for efficient coarse positioning of one image relative to another in the multi-image setting. In order to do precise positioning it can be useful to use the buttons on the position tab of the frame object to make small changes.

Improved Reference Frame Manipulation

The reference frame object in Imaris is very useful to create measurements relative to a specific position or orientation within an image. To facilitate positioning of the reference frame it has a little “tripod” that one can click with the mouse and then reposition. The handling of mouse interactions with the “tripod” has been significantly improved in this version of Imaris to make positioning of the reference frame simpler than before. Also the size of tripod is now coupled to the screen rather than to the image voxel size. This enables very precise positioning at high zoom levels.

File Series With “Split”

The File Series Settings allow to choose “Split” in order to split a series into multiple IMS files. This allows to easily convert a series consisting of multiple fields of view into multiple IMS files. If the fields of view overlap these files can then easily be opened in ImarisStitcher9.1 to be stitched into one big field of view.

File Series Delimiters Configurable

The File Series Readers that are configurable automatically interpret parts of series file names as delimiters to indicate different indices of the X, Y, Z, C, T or F dimension. These delimiters can be configured in the Preferences of ImarisFileConverter or Imaris (on the Loading tab) as follows:

File Readers

ImarisXT Interface

Fixed Bugs

53 Bugs Fixed in 9.1
5504Image Proc --> Channel Shift fails for 2D
7152Contour tool can not create surface if voxel size is small
7428Unify surfaces crashes Imaris
7535Generation of transparency slow for Surfaces component with many objects
7590Intensity Statistics are not updated after Image Processing
7598IQ TIFF files split into channels not read correctly
7598IQ TIFF files split into channels not read correctly
7812Rebuild does not produce surface nor statistics on new dataset
8493Extreme variation of Zoom when rotating 3D View
8805Animation is "jumpy" during playback
9108Animation keyframes should be cleared upon loading a new dataset
9117Imaris does not read Olympus vsi dataset channel information properly
9124Export data as "Open microscopy enviroment tiff", info from different dimension is not splited completely
9321Arena is not displaying thumbnail of Stored files, Assay folder view is empty
9500Import Surface to Cells object is offset by ROI edge
9522Color coding for custom statistic 'ID' crashes
9695Multi image VSI file is not read properly
9810Top menu bar in Mac OSX 10.12.1 dissappears and is unretrievable
9918Running Batch on multi image CZI fails to show 3D objects&statistics
9942Filaments manual tracking solution (connect and disconnect inactive since 8.2)
10029Volume rendering brighter in 8.4.1 than 8.3.1
10073VSI File cannot be read by Imaris
10161XTension Vesicles outside Cell is reporting Distance to Cell as integer values
10178Colour palette 'Delete Selected' causes Imaris to hang
10180Initial rendering in Easy 3D can be blank
10209Contour surface mask starts one slice after first drawn contour
10213Timebar moves on pressing the Snapshot button
10256Slicer View grayed out
10263Imaris crashes hard when exporting a Cell to Surfaces
10264Tracked small spots crash when played back and forth
10276New .IMS Scene files do not import Surfaces or Cells correctly if using Add Components to Current Scene option
10281Crash when you try to save cells tracked and cropped time
10309Enabling Sub-Volume in Surface Wizard crashes Imaris hard when using "back" button
10339Imaris quits while starting when no license enabled
10348Warnings of bpManualBuilder are not visible in Report Email
10353Normal Shading rendering doesn't update if min and max are the same
10354Some Cells intensity related statistics will differ on the 6th significant figure
10355XT attenuation correct sometimes causing a crash
10367Tiles CZI files only load partially
10391Load another image during blend rendering crashes Imaris
10412OME tiff from Thorlab crashes Imaris
10414Check for updates window for 9.0.1 to 9.0.2 shows no release notes
10416FileConverter on the PC does not allow Unicode characters
10419Imaris Open command in HKEY_CLASSES_ROOT loses it's value after uninstall
10424Some zvi file not read correctly
10425Auto adjust all channels when no dataset is present will crash Imaris
10432Imaris hangs trying to calculate statistics for channel created in XT
10433Crash of Remove Disconnected Segments for time series
10440Imaris misreads the time interval for some .czi files
10442Adding Filaments using XT is too slow
10482Imaris crashes by Ctrl+C without loading dataset
10545Create colour coded region channel is broken
10546Deleting all slices crashes Imaris
10549Only one image of CZI File recognized

Imaris 9.1.1

Fixed 8 Bugs (since Imaris 9.1.0)
10259Adding a Reference Frame adds Ref Frame-based intensity statistics for surfaces
10587ImplExtend for some OME tiff files are showing a value of -0
10615Reference frame statistics are wrong (neglecting rotation)
10664CZI tiles open in stitcher with completely off stage coordinates
10666Reference Frame Play mode breaks camera, nothing is visible
10669Reference Frame > Planes set to visible results in Imaris crash
10681Imaris 9.1 opens LIF files very slow compared to 9.0.2
10696Channel colors are wrongly read for these Andor Multi-TIFF (Series) Files

Imaris 9.1.2

Fixed 1 Bug (since Imaris 9.1.1)
10715Imaris 9.1.1 hangs while zooming or panning on any dataset