:warning: This is an old repository, you can find the latest version HERE :heavy_exclamation_mark:

Dissect : Segmentation and analysis of highly remodeled epithelial surfaces in 3D

Warning : tutorials and link to them are under construction.

Overview

Dissect library, for DisPerSE-based Segmentation and Exploration of Cells and Tissues, provide a way to segment and analyse apical 3D tissue. Using DiSperSE program to generate a skeleton, Dissect is able to segment apical surface of tissue on 2D and 3D (Figure 1 A) and provide geometric and signal quantifications. Dissect is also able to analyse meshwork signal and provide related analysis (Figure 1 B). Meshwork analysis can be crossed with geometric and/or signal quantification.
Dissect can be used with a graphical interface or with your own handmade script.

Figure 1 : Overview of differents types of skeleton that can be generated and analyse.
A. Segmentation of tissue on 2D (left) and 3D (right).
B. Analyse of meshwork signal. On right it is a zoom of a small part of the left tissue.

Generate a skeleton

Skeleton is generated by DisPerSE, a C++ program developed by Thierry Sousbie.
We provide a Docker images with DisPerSE already install that you can use on Docker. A tutorial of use can be found here.
You can install directly DisPerSE directly from the source code here.

Analyse a skeleton and/or meshwork

Analysis can be done with the graphical interface or with python script. At the end it provides tables with data, and can generate color-coded images.

Documentation

We provide some tutorial for install and use Dissect and DisPerSE :

• How install and use DisPerSE using docker : here.
• How use Dissect with the GUI : here.
• How use Dissect with python code : here.

Contact

For any questions or issues, you can open an issue here.

Authors

• Sophie Theis - @sophietheis
• Tatiana Merle - @TatiaM
• Emmanuel Martin
• Alain Kamgoué
• Florian Sarron
• Guillaume Gay - @glyg
• Magali Suzanne

Dependencies

• Python >= 3.6
• Numpy
• Scipy
• Matplotlib
• Pandas
• Jupyter
• Notebook
• exifread
• opencv
• tifffile >= 2021.8.3

Install

See INSTALL.md for a step by step install.

Licence

This project is distributed under the terms of the General Public Licence.

Versions 2.4 and earlier were distributed under the Mozilla Public Licence.

If GPL licencing is too restrictive for your intended usage, please contact the maintainer.