@@ -18,4 +18,20 @@ Here is the rationale behind the folders in this repository:
...
@@ -18,4 +18,20 @@ Here is the rationale behind the folders in this repository:
## Dataset
## 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).
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).
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## 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.
