README.md

README.md

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 This repository contains the material used to perform the statistical analysis of the data presented in:
 
 Liza Sarde, Gaëlle Letort, Hugo Varet, Vincent Laville, Julien Fernandes, Shahragim Tajbakhsh and Brendan Evano. *Impaired stem cell migration and divisions in Duchenne Muscular Dystrophy revealed by live imaging*. BioRxiv 2025. [https://doi.org/10.1101/2025.03.13.643016](https://doi.org/10.1101/2025.03.13.643016)
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+This study aims to understand the dynamics of muscle stem cells during regeneration in Duchenne Muscular Dystrophy, a muscle wasting disease. Two biological models are used:
+1) _Ex vivo_ – Muscle fibres and their associated stem cells are isolated, cultured in suspension, and filmed for three days. Successive divisions of muscle stem cells are manually tracked throughout the movie.
+2) _In vivo_ – Regenerating muscle is imaged through intravital imaging in anesthetised mice.
+In both systems, transgenic mice are used to fluorescently label muscle stem cells and muscle fibres, allowing for precise visualisation and analysis.
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+Here is the rationale behind the folders in this repository:
+- The movie files generated from the _ex vivo_ system produce .czi files, which are then converted to 8-bit TIFF format using a macro (see convertCZIto8bTiff.ijm). Muscle stem cells are tracked using the TrackMate plugin in ImageJ software. The movement of the muscle fibre is then corrected (CellonFiber repository), allowing the tracking of cells to be adjusted relative to a fixed reference frame.
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+- The movie files generated from the _in vivo_ system are corrected for tissue deformation (napari-3dtimereg repository), and cells are tracked using the TrackMate plugin in ImageJ software.
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+- All generated data are stored in the "data" folder and follow the order of the figures in the paper Sarde_et_al_2025. The code for the statistical analyses associated with these data is in the RMD file and is visually presented in the HTML file.
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