@@ -32,7 +32,7 @@ Or you can clone this repository and build the plugin from the source files.
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@@ -32,7 +32,7 @@ Or you can clone this repository and build the plugin from the source files.
The plugin can be launch from `Plugins>DSCB>CellsOnFiber
The plugin can be launch from `Plugins>DSCB>CellsOnFiber
The plugin depends on:
The plugin depends on:
- Fiji plugin `TrackMate` (installed by default in Fiji) to read cell tracking.
- Fiji plugin [`TrackMate`](https://imagej.net/plugins/trackmate/) (installed by default in Fiji) to read cell tracking.
- Fiji plugin `CSBDeep` to run a neural network and it should be installed before. See here for [installation instructions](https://github.com/CSBDeep/CSBDeep_website/wiki/CSBDeep-in-Fiji-%E2%80%93-Installation)
- Fiji plugin `CSBDeep` to run a neural network and it should be installed before. See here for [installation instructions](https://github.com/CSBDeep/CSBDeep_website/wiki/CSBDeep-in-Fiji-%E2%80%93-Installation)
- Fiji plugin `TurboReg` to calculate/apply the transformation of the segmented fiber movie. You can get it [here](http://bigwww.epfl.ch/thevenaz/turboreg/).
- Fiji plugin `TurboReg` to calculate/apply the transformation of the segmented fiber movie. You can get it [here](http://bigwww.epfl.ch/thevenaz/turboreg/).
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@@ -117,4 +117,5 @@ You can see what you can obtain with our [demo dataset](./data/demo_output).
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@@ -117,4 +117,5 @@ You can see what you can obtain with our [demo dataset](./data/demo_output).
# License/Reference
# License/Reference
Our plugin and trained neural networks are availabel freely and open-source under the BDS3-license.
Our plugin and trained neural networks are availabel freely and open-source under the BDS3-license.
If you use it, please cite our paper [Sarde et al.](https://www.biorxiv.org/content/10.1101/2025.03.13.643016v1).
If you use it, please cite our paper [Sarde et al.](https://www.biorxiv.org/content/10.1101/2025.03.13.643016v1).
