ct3d 0.1 / at3d 0.1 – Cell Tracking Tools

ct3d 0.1 / at3d 0.1

:: DESCRIPTION

ct3d is a command-line tool for tracking cells in time series of 2D images or 3D image stacks. ct3d performs the basic cell tracking as a command line tool.

Visualization, exploration, and evalutation of the results can be done through the graphical user interface of at3d.

::DEVELOPER

Hang Xiao and Axel Mosig, THE RUB BIOINFORMATICS GROUP

:: SCREENSHOTS

at3d

:: REQUIREMENTS

:: DOWNLOAD

 ct3d / at3d

:: MORE INFORMATION

Citation

Ct3d: tracking microglia motility in 3D using a novel cosegmentation approach.
Xiao H, Li Y, Du J, Mosig A.
Bioinformatics. 2011 Feb 15;27(4):564-71. doi: 10.1093/bioinformatics/btq691. Epub 2010 Dec 24.

topaln 0.1 – Topological Alignments for Cell Tracking

topaln 0.1

:: DESCRIPTION

topaln implements an integer linear programming approach for topologically aligning two segmented images as the linking step in cell tracking.

::DEVELOPER

Hang Xiao and Axel Mosig, THE RUB BIOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • C++ Compiler

:: DOWNLOAD

topaln

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2009 Jul 16;4:10. doi: 10.1186/1748-7188-4-10.
Tracking cells in Life Cell Imaging videos using topological alignments.
Mosig A, Jäger S, Wang C, Nath S, Ersoy I, Palaniappan KP, Chen SS.

CellTrack – Cell Tracking and Motility Analysis

CellTrack

:: DESCRIPTION

CellTrack is a self-contained, extensible, and cross-platform software package for cell tracking and motility analysis.

::DEVELOPER

Sacan Bioinformatics Lab

:: SCREENSHOTS

CellTrack

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ COmpiler

:: DOWNLOAD

 CellTrack

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 15;24(14):1647-9. doi: 10.1093/bioinformatics/btn247. Epub 2008 May 29.
CellTrack: an open-source software for cell tracking and motility analysis.
Sacan A, Ferhatosmanoglu H, Coskun H.