CompositIA - Automated computation of body composition scores from thoraco-abdominal CT scans.

It is open source and free for research purposes.
Try it online from your browser or download a portable version for Windows (works also on a USB-key without installation)
link: http://www.dp-lab.io/compositia
github: https://github.com/rcabini/compositIA

WId-U  Tracking unlabeled cancer cells imaged with low resolution in wide migration chambers via U-NET class-1 probability (pseudofluorescence) 

Struggling in segmenting/tracking cells using only transmitted light?
This tool creates a pseudofluorence (pink in the image below) that facilitates the task.It comes in three versions: FIJI plugin, FIJI macro, Imaris plugin.

code: https://github.com/pizzagalli-du/Wid-U/
paper: Antonello P et al, J. Bio. eng. (2023) https://doi.org/10.1186/s13036-022-00321-9

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.
This is a spin off from the IMMUNEMAP project.

• Imaris plugins or standalone program for Windows (doesn't need Imaris),  and Open Source code available here
• Please cite as Pizzagalli DU & Latino I et al., Frontiers in immunology (2019) https://www.frontiersin.org/articles/10.3389/fimmu.2019.02621/abstract

CANCOL - Computer assisted colocalization facilitates cell detection and tracking

Useful when cells emit in multipe acquisition channels or when they become dim.
Facilitates brushing guiding the user to annotate relevant parts of the image to get the best pixel classification results.
Ccreates an additional virtual imaging channel (magenta) specific for the cells of interest.
Enhances the automatic tracking.
This is a spin off from the IMMUNEMAP project.

The user just has to draw a few lines on the cells of interest and other lines on the background or other cells following the instructions provided by the interface.

• Imaris XTension and standalone version (download)
• Article at The Journal of Immunology https://doi.org/10.4049/jimmunol.2100811
• Preprint (with preliminary results using a different method, final paper is slightly different): https://www.biorxiv.org/content/10.1101/829838v2