From f23b00009ac20fa264d633b86b48f278dcb03dab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ga=C3=ABlle=20=20LETORT?= <gaelle.letort@pasteur.fr> Date: Tue, 25 Mar 2025 11:00:01 +0100 Subject: [PATCH] update doc and links --- README.md | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 69b4a1b..6e3d5ac 100644 --- a/README.md +++ b/README.md @@ -18,4 +18,20 @@ Here is the rationale behind the folders in this repository: ## 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). \ No newline at end of file +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. \ No newline at end of file -- GitLab