Imaris 8.3 Release Notes

Welcome to the Imaris 8.3 release notes. Please have a look to the overview of Imaris Release notes for information about prior released features and fixed bugs.

Version Date: May 27, 2016

Membrane Based Cell Boundary Detection

Using Imaris’ Cell component it is now possible to detect cell boundaries based on a membrane signal even if no nucleus signal is available. The following screenshots show examples of this segmentation:

Algorithmically Imaris performs a multi-scale watershed with region merging to achieve this segmentation. Users can interactively adjust the merging thresholds to get an immediate visual effect of the threshold settings. In addition after running the membrane based cell boundary detection users can go to the edit tab of Cells and Merge or Split cells that were not segmented correctly.

Cells Visualization Improved

Improved visualization of Cells on 2D slicers facilitate easier validation of segmentation results. New features include:

Border rendering of cells as white lines

Region rendering of cells with original intensities overlayed by cell color

Cells Color Options

Cells can now be colored by ObjectID to facilitate discrimination of neighbouring cells.

Lineage Tracking Algorithm “Maximum Overlap” for Cells

To track cells that are segmented from a membrane signal the “maximum overlap” tracking algorithm was added to Imaris8.3. This algorithm can track dividing cells to produce lineages.

The algorithm works as follows: For each cell the algorithm searches a mother cell at the previous time point by calculating the spatial overlap with all cells of the previous time point and picking as the mother that cell with which it has the largest overlap. As a sanity check the link to the mother is created only if the overlap exceeds a minimum ratio which is 0.5 by default.

Reference Frame Component

A Reference Frame is Cartesian Coordinate System that can be positioned and oriented anywhere within an image.

Manual positioning:

• Select reference frame in surpass tree.
• Select Navigate mode
• Press Ctrl while doing 3D rotation or translation (as you would for 3D navigation) to move the reference frame.

Automatic positioning:

• Reference Frames can be created from tracks via the “Correct Drift” button on the track-editor tab of Spots, Surfaces, Cells or Filaments. They are then positioned in such a way that they “follow” the motion of the tracks.
• Reference Frames can be created from the Image Processing menu by choosing ImageAlignment->Set Reference Frames.

Reference Frames Affect Statistics Values

Statistics values of Spots, Cells, Surfaces, Filaments are reported both in the image coordinates and in reference frame coordinates (if the choice of coordinate system has an influence on the values).

For example “Spot Position X” will also be reported in reference frame coordinates as a new statistics value “Spot Position X Reference Frame” when a reference frame exists. The same happens for other positional values and for vectorial values like velocities and for speed values that also depend on the reference frame. 

Reference Frame Play Mode

When reference frames are used in time series it is possible to use the “Reference frame play mode” to play through the time series in such a way that the selected reference frame stays still while the time series plays.

If the reference frames are positioned to move with an object this play mode allows to play through the time series in such a way that the “tracked” object stays still.

Tracking in Reference Frame Coordinates

When a reference frame object exists it is possible to choose this reference frame as the coordinate system within which to perform tracking. This is useful when tracking vesicles that move inside a cell which moves itself.

Cells Split Option “One Nucleus per Cell”

Imaris8.3 has two options to perform the split “One Nucleus per Cell”:

Distance From Nucleus - Every pixel within the cells is assigned to the nucleus that it is closest to. All the pixels assigned to the same nucleus make up one cell. This method performs a robust split where borders end up “in the middle” between nuclei.

Cell Channel Intensity - Bright regions of the cell channel around a nucleus are assigned to that nucleus with the effect that the borders between cells end up at low intensity regions. This method tends to fail when two cells are not delimited by a low intensity region.

The “Distance from Nucleus” option is in many cases similar to the previous “Split one Nucleus per Cell” method.

New Statistics Values

Tracks have new statistics values for displacement in the scenario of lineages:

• Displacement Since Previous Division
• Displacement Since Previous Division^2
• Cell Cycle Displacement
• Time Since Track Start
• Velocity Angle X, Velocity Angle Y, Velocity Angle Z

Track Displacement definition for the lineage situation now is the maximum distance of the first position to any of the positions at the last time point of the track. This statistics was in 8.2 not well defined for tracks with multiple objects in the last time point.

Every object has a new statistics value - Distance From Origin.

Vantage 1D Statistical Tests

Vantage1D shows univariate distributions of statistics values for comparison between groups. In previous versions of Imaris it was possible to inspect visually whether distributions differ. Imaris now provides statistical tests to assess differences between distributions. The tests that are reported in the Statistical Tests tab in Vantage1D are the following:

Wilcoxon-Test Tests whether two samples come from continuous distributions with the same medians. F-Test Tests whether two samples come from normal distributions with the same variance.

T-Test Tests whether two samples come from normal distributions with the same means. Kolmogorov-Smirnov-Test Tests whether two samples come from the same populations.

It is possible for users to adjust the confidence level and whether the tests are performed left-tailed, right-tailed or two-tailed.

XT works with new Matlab Component Runtime (MCR) Versions

Imaris works with MCR v7.1 (Matlab R2009a/b) as before and additionally with MCR v8.4 (Matlab R2014b) and it is possible to configure XTensions to use other run Matlab Component Runtimes. Each XTension specifies which MCR it is compiled for in the xml file. The XTensions that are installed with Imaris8.3 are built for MCR v8.4.

Installation of the Matlab Component Runtimes is simplified by starting download directly from Imaris Preferences CustomTools section.

Imaris without Arena

Due to customer requests we decided to provide a version of Imaris that does not have Arena (and no batch processing capability either). This version is similar to pre-Imaris8 versions in that it can open and save one image at a time. To get this version users can choose to install Imaris without Arena during installation.

Speedups from Parallel Watershed Algorithm

The watershed algorithm in Imaris runs blockwise and parallel. This produces speedups (compared to previous Imaris versions) for the following steps:

• Surfaces - Split touching Objects (Region Growing)
• Spots - Different Spot Sizes (Region Growing)
• Cells - Split of Nuclei by Seed Points
• Cells - Split Touching Cells
• Cells - Detect Cell Boundary from Cell Membrane

Fixed Bugs