Merge branch 'main' into 'main'

Updated doc and links to the plugins

See merge request !2

README.md

@@ -10,8 +10,28 @@ This study aims to understand the dynamics of muscle stem cells during regenerat
 In both systems, transgenic mice are used to fluorescently label muscle stem cells and muscle fibres, allowing for precise visualisation and analysis.
 
 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.
+- 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](https://github.com/gletort/ImageJFiles/tree/master/convertFiles)). 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.
 
-- 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.
+- The movie files generated from the _in vivo_ system are corrected for tissue deformation ([napari-3dtimereg plugin](https://gitlab.pasteur.fr/gletort/napari-3dtimereg)), and cells are tracked using the [TrackMate](https://imagej.net/plugins/trackmate/index) plugin in ImageJ software.
 
-- 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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+- 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.
+
+## Dataset
+
+You can find an example dataset to test all our plugins cited in this repository on Zenodo: [Dataset from Sarde et al; 2025](https://zenodo.org/records/15028169). 
+
+
+## Correcting for fiber motion
+
+In the _Ex vivo_ movies, the isolated muscle fiber are floating in suspension in the petri dish and can move a lot. To measure the cell displacement on the fiber, we registered the movie to have immobile fibers.
+To align these movies, we could not registered directly the movie as the petri dish would have influence the registration.
+Instead, we detected the fibers and used their motion to calculate the registration to perform.
+
+All these steps are possible with our Fiji plugin [cellsOnFiber](https://gitlab.pasteur.fr/gletort/cellsonfiber/-/blob/main/README.md) proposed open-source.
+Please refers to the [plugin cellsOnFiber repository](https://gitlab.pasteur.fr/gletort/cellsonfiber) for more informations, detailled usage steps and demo.
+
+## Registration of 3D movies
+
+To register _In vivo_ movies in 3D, which, due to experimental challenges, can move a lot and be deformed, we developed a customed Napari plugin based on elastix library. 
+
+Please refers to our [napari-3dtimereg plugin](https://gitlab.pasteur.fr/gletort/napari-3dtimereg) for more informations, detailled usage steps and demo.
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