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


2016-07-22 EpiTools Icy Plugins v0.9.0
* Fixed uncontrolled plugin shape due to new features in the EzPlug library
* Updated descriptions for some plugins

2016-04-22 EpiTools Icy Plugins v0.8.9
* Added layer option panel for CellEditor with buttons to confirm or undo modifications
* Added the possibility to Convert icy ROIs like rectangles&squares to CellColorTag
* Added an import functionality for CellColorTag to use previous tags
* Fixed missing labeling of excel sheets in EdgeColorTag

2016-02-09 EpiTools Matlab: Parallel Computing Support
* Due to a software regression the parallel computing capabilities are currently broken.
  As consequence, please do not increase the number of processors in the input GUI.
  We hope to re-add the support in the next release!
* We added an FAQ section to the wiki [Support > Faq] for reported problems

2015-12-15 EpiTools Icy Plugins v0.8.8
* Fixed excel sheet export on EDGE_INTENSITY overlay (for single time points output file would be empty)
* Fixed relative intensity option in EDGE_INTENSITY overlay (error on icy >= 1.7)

View older news here.


MATLAB Application
Epitools for Matlab v2

For best compatability we reccomend using Matlab 2014a

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

ICY Plugins
Epitools for Icy

The source code can be downloaded from our Bitbucket repository

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?

  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

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