Tools

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General motility measures (track based and step based)

This tool reads Imaris exported xls files, as well as TrackMate xml files and computes basic motility patterns  useful in intravital imaging studies including:
track length, speed, directionality, displacement, arrest coefficient, density. Moroever, it creates plots of track with common origin.

Standalone program for Windows (download coming soon)
MATLAB source code (download coming soon)

Motility heatmap

This tool reads Imaris files (ims) and creates a motility heatmap based on Optical Flow as described in Pizzagalli et al. Frontiers in Immunology (2019)
It is useful to identify hotspots with high motility, or to analyze cell motility without requiring tracking.

Standalone program for Windows (download coming soon)
MATLAB source code (download coming soon)

Cell action recognition (track-based)

This tool to detects and count actions of neutrophils as described in Pizzagalli et al. Frontiers in Immunology (2019)
https://www.frontiersin.org/articles/10.3389/fimmu.2019.02621/abstract
Like a FACS gating, but for motility patterns.

Semi-supervised Colocalization

This tool creates an additional imaging channel, specific for the cells of interest.

The user can draw a few lines on the cells of interest and other lines on the background.
The program will automatically separate them into 2 classes.

Useful when cells appear in more than one acquisition channel.