Unverified Commit dbf73bdf authored by Jean-Yves TINEVEZ's avatar Jean-Yves TINEVEZ Committed by GitHub
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Add proper TOC to README.md

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DeProj is a MATLAB app made to yield accurate morphological measurements on cells in epithelia or tissues.
**Table of Contents**
* [DeProj.](#deproj)
* [What is DeProj useful for.](#what-is-deproj-useful-for)
* [Measuring cell morphologies on 2D projections.](#measuring-cell-morphologies-on-2d-projections)
* [Projection artefacts.](#projection-artefacts)
* [How to use DeProj.](#how-to-use-deproj)
* [Requirements.](#requirements)
* [Installation.](#installation)
* [Running the example.](#running-the-example)
* [Running DeProj from MATLAB prompt.](#running-deproj-from-matlab-prompt)
* [From a segmentation mask and a height-map.](#from-a-segmentation-mask-and-a-height-map)
* [The segmentation mask.](#the-segmentation-mask)
* [The height-map.](#the-height-map)
* [Running the analysis.](#running-the-analysis)
* [More documentation.](#more-documentation)
* [Appendix.](#appendix)
* [Projection tools that yields the height-map.](#projection-tools-that-yields-the-height-map)
* [Segmentation tools for the projection.](#segmentation-tools-for-the-projection)
## What is DeProj useful for.
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- [EpiTools](https://github.com/epitools) is a toolbox with MATLAB and [Icy](http://icy.bioimageanalysis.org/) components built to study the dynamics of drosophila imaginal discs. Its segmentation algorithm relies on region growing from seeds determined automatically and merged based on region areas.
- [SEGGA](https://github.com/ZallenLab/SEGGA) is standalone applications written with MATLAB proposed for the investigation of drosophila embryo germband epithelium.
- TissueAnalyzer is a tissue segmentation tool, distributed along [TissueMiner](https://github.com/mpicbg-scicomp/tissue_miner).
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- TissueAnalyzer is a tissue segmentation tool, distributed along [TissueMiner](https://github.com/mpicbg-scicomp/tissue_miner).
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