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

• New Dicom Reader
• New Leica .xlef and .lof Readers
• Updated Olympus VSI Reader
• OME Tiff Reader bug fixes

ImarisXT Interface

• 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

Fixed Bugs

Imaris 9.1.1