EpiTools logo by Lorenzo Gatti

Welcome to Epitools

Here we present a new software toolkit to extract the membrane signal from epithelial tissues and analyze it with the aid of computer vision. The development of EpiTools was inspired by the challenges in analyzing time-lapses of growing Drosophila imaginal discs. The folded morphology, the very small apical cell surfaces and the long time series required a new automated cell recognition to accurately study growth dynamics.

EpiTools is composed of two main software projects to allow extended modularity

First an image processing application for MATLAB to extract the membrane outlines from the experimental data, featuring:

Second a plugin collection for the bioimaging platform icy to interactively analyze the skeleton files, featuring:

Our projects are pulished with Open source licenses. Follow us on BitBucket!

EpiTools was published in Developmental Cell (January 2016), freely available at http://dx.doi.org/10.1016/j.devcel.2015.12.012


2018-11-06 GUI-Independent EpiTools MATLAB modules
* added projection module at github.com/epitools/module_projection
* added segmentation module at github.com/epitools/module_segmentation

2018-07-26 EpiTools Icy Plugins v0.9.1
* IMPORTANT Bugfix for EDGE_COLOR_TAG, the length measure in the CSV export was reported incorrectly
* new CELL_CLONE overlay (see CellClone page under Icy plugins) to interactively detect clones
* new CELL_INTENSITY overlay to measure the junction intensity for all cells
* more details in the github release page

2018-07-10 EpiTools Project moved to Github!
* new website address: epitools.github.io
* new repository: github.com/epitools
* download sections are now pointing to the release tab of each repository
* example datasets can be found in the epitools-samples repository

View older news here.


MATLAB Application ICY Plugins
Epitools for Matlab v2 Epitools for Icy
MATLAB source code Plugins surce code

For best compatability we reccomend using Matlab 2014a

visit our F.A.Q. section for more details on the topic.

EpiTools is licensed under GPLv3 you can find the details here.

Video Tutorials

EpiTools v2 Video Tutorials

Icy Plugin Tutorials (with audio!)

Make sure to download them to enjoy the HD quality (click on the dots in the lower right corner and click download).

Who built EpiTools?

  • Davide Heller (1)
  • Alexander Tournier (5)
  • Andreas Hoppe (2)
  • Simon Restrepo (1)
  • Lorenzo Gatti (1,3,4)
  • Nicolas Tapon (5)
  • Konrad Basler (1)
  • Yanlan Mao (6)
  1. Institute of Molecular Life Sciences, University of Zurich, Switzerland
  2. Digital Imaging Research Centre, Faculty of Science, Engineering and Computing, Kingston University, Kingston-upon-Thames, KT1 2EE, United Kingdom.
  3. Institute of Applied Simulations, Zürich University of Applied Sciences, Einsiedlerstrasse 31a, 8820 Wädenswil, Switzerland
  4. SIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne, Switzerland
  5. Apoptosis and Proliferation Control Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London, WC2A 3LY, United Kingdom.
  6. MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom

How to cite EpiTools

Davide Heller, Andreas Hoppe, Simon Restrepo, Lorenzo Gatti, Alexander L. Tournier, Nicolas Tapon, Konrad Basler, and Yanlan Mao (2016). EpiTools: An Open-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics. Developmental Cell 36 (1) (January): 103–116. doi:10.1016/j.devcel.2015.12.012


Matlab Application v2

Matlab Stable V2

Icy Plugins

Icy Plugins V1


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This page was written by Lorenzo Gatti and Davide Heller on 26.08.14@16:57