Tissue Analyzer

Description: Tissue Analyzer segments and tracks cells in 2D epithelia
© 2007-2017 Benoit Aigouy
Citations: If you use/like the tool please cite:

Segmentation and Quantitative Analysis of Epithelial Tissues.
Aigouy B, Umetsu D, Eaton S.
Methods Mol Biol. 2016;1478:227-239.
PMID: 27730585


Cell flow reorients the axis of planar polarity in the wing epithelium of Drosophila.
Aigouy B, Farhadifar R, Staple DB, Sagner A, Röper JC, Jülicher F, Eaton S.
Cell. 2010 Sep 3;142(5):773-86. doi: 10.1016/j.cell.2010.07.042.
PMID: 20813263
Author(s): Benoit Aigouy (tissue.analyser@gmail.com)
R. Farhadifar, D. Staple and M. Merkel made the stretch and polarity algorithms. M. Aliee made the boundary roughness algorithm.
Installation as a Fiji plugin:
  1. Download and install the latest FIJI (here)
  2. Launch FIJI
  3. Open the "help" menu
  4. Click on "Update..."
  5. Press "Manage update sites"
  6. Scroll down and tick "Tissue Analyzer"
  7. Press "Close"
  8. Press "Apply changes"
  9. Close FIJI
  10. Restart FIJI
  11. Open the "Plugins" menu and select "Tissue Analyzer"
Installation as a stand-alone: Download and unzip the appropriate file (see Downloads). Then double click on "launcher.jar"
Alternatively, you can run Tissue Analyzer directly from the command line type:
java -Xmx1024m -jar /path/to/TissueAnalyzer.jar
Installation as an ImageJ plugin: Extract the content of the Tissue Analyzer ImageJ Zip file, copy the whole TA containing folder to the ImageJ "plugins" directory.
Requirements: Requires java 1.6 or > or FIJI to be installed on your system
Tissue Analyzer works under Linux, Windows and MacOSX
Downloads: Tissue Analyzer (Standalone version around 11 Mb)
Tissue Analyzer (ImageJ version around 9 Mb)
Tissue Analyzer (FIJI version around 6 Mb)
Deprecated Tutorials: Segmentation/determine packing/cell stretch…
I want to track cells and bonds
I want to plot my data/please give me an excel file/I want to create a virtual clone
I want to create a video/I want to have a nice picture for my presentation
I want to correct a tracking error (lost cells/swapped cells)
How do I know if I have to rerun something/can I trust the data
I want to correct a mistake in cell divisions
Licenses: License Tissue Analyzer