Imaris 9.1.0 Release Notes
Welcome to the Imaris 9.1.0 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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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:
- New Dicom Reader
- New Leica .xlef and .lof Readers
- Updated Olympus VSI Reader
- OME Tiff Reader bug fixes
- New functions to Get/Set Transform of images and objects.
- New functions to Get/Set any image in multi-image situation.
- New functions to Get/Set Labels of objects
53 Bugs Fixed in 9.1
||Image Proc --> Channel Shift fails for 2D
||Contour tool can not create surface if voxel size is small
||Unify surfaces crashes Imaris
||Generation of transparency slow for Surfaces component with many objects
||Intensity Statistics are not updated after Image Processing
||IQ TIFF files split into channels not read correctly
||IQ TIFF files split into channels not read correctly
||Rebuild does not produce surface nor statistics on new dataset
||Extreme variation of Zoom when rotating 3D View
||Animation is "jumpy" during playback
||Animation keyframes should be cleared upon loading a new dataset
||Imaris does not read Olympus vsi dataset channel information properly
||Export data as "Open microscopy enviroment tiff", info from different dimension is not splited completely
||Arena is not displaying thumbnail of Stored files, Assay folder view is empty
||Import Surface to Cells object is offset by ROI edge
||Color coding for custom statistic 'ID' crashes
||Multi image VSI file is not read properly
||Top menu bar in Mac OSX 10.12.1 dissappears and is unretrievable
||Running Batch on multi image CZI fails to show 3D objects&statistics
||Filaments manual tracking solution (connect and disconnect inactive since 8.2)
||Volume rendering brighter in 8.4.1 than 8.3.1
||VSI File cannot be read by Imaris
||XTension Vesicles outside Cell is reporting Distance to Cell as integer values
||Colour palette 'Delete Selected' causes Imaris to hang
||Initial rendering in Easy 3D can be blank
||Contour surface mask starts one slice after first drawn contour
||Timebar moves on pressing the Snapshot button
||Slicer View grayed out
||Imaris crashes hard when exporting a Cell to Surfaces
||Tracked small spots crash when played back and forth
||New .IMS Scene files do not import Surfaces or Cells correctly if using Add Components to Current Scene option
||Crash when you try to save cells tracked and cropped time
||Enabling Sub-Volume in Surface Wizard crashes Imaris hard when using "back" button
||Imaris quits while starting when no license enabled
||Warnings of bpManualBuilder are not visible in Report Email
||Normal Shading rendering doesn't update if min and max are the same
||Some Cells intensity related statistics will differ on the 6th significant figure
||XT attenuation correct sometimes causing a crash
||Tiles CZI files only load partially
||Load another image during blend rendering crashes Imaris
||OME tiff from Thorlab crashes Imaris
||Check for updates window for 9.0.1 to 9.0.2 shows no release notes
||FileConverter on the PC does not allow Unicode characters
||Imaris Open command in HKEY_CLASSES_ROOT loses it's value after uninstall
||Some zvi file not read correctly
||Auto adjust all channels when no dataset is present will crash Imaris
||Imaris hangs trying to calculate statistics for channel created in XT
||Crash of Remove Disconnected Segments for time series
||Imaris misreads the time interval for some .czi files
||Adding Filaments using XT is too slow
||Imaris crashes by Ctrl+C without loading dataset
||Create colour coded region channel is broken
||Deleting all slices crashes Imaris
||Only one image of CZI File recognized