Software

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Cell segmentation/tracking software

The table below lists freely available software in the field of image segmentation and cell tracking.

Software Segmentation methods Tracking methods Aimed at Operation System Website Notes
Braincells manually manually following cell and axon movements Windows Braincells half English - half Hungerian; not further improved since 2001
CellTrack Threshold, Edge Detection Feature Matching, Mean-Shifts, Optical Flow, Active Contours tracking cell motility (of eukaryotic cells), measuring cell movement speed, taking into account cell deformation Cross-platform CellTrack intuitive user interface, general image processing operations; PubMed: Sacan et al. 2008
CellTracker Threshold, Level Sets, Active Contours Edge Detection, Active Contours tracking nuclear and cytoplasmic fluorescence intensities (of eukaryotic cells) Windows CellTracker intuitive user interface, segmentation needs manual seeding; PubMed: Shen et al. 2006, Du et al. 2010
ImageJ (+ Mtrack2 plugin) Threshold, Edge Detection, Watersheds Feature Matching no particular aim Cross-platform ImageJ, Mtrack2 plugin Abramoff et al. 2004, no pre-defined workflows
Schnitzcells Edge Detection point-matching (thin plate spline), custom developed process analysis of phase contrast and fluorescence time-lapse movies/image sequences (of prokaryotic cells) Windows (should run on Linux, Mac OS) Schnitzcells package of single Matlab-scripts (usage is well documentated), segmentation method changes has to be done directly in the Matlab code; PubMed: Young et al. 2011
TLM-Tracker Threshold, Watersheds, Level Set/Active Contours, Edge Detection Overlapping regions/boxes combinatorial analysis of brightfield and fluorescence time-lapse movies/image sequences (of prokaryotic cells) Cross-platform TLM-Tracker intuitive user interface with pre-defined methods and workflows, sophisticated image processing operations, easily adaptable segmentation procedures, lineage tree presentation (with fluorescence data), cell pole aging analysis, cell growth analysis
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