@@ -11,9 +11,10 @@ Original code: <https://github.com/Hyojung-Choo/Myosoft/tree/Myosoft-hub>
## [`1_identify_fibers.py`](1_identify_fibers.py)
- Will identify all fibers based on the membrane staining using [Cellpose](https://github.com/MouseLand/cellpose) segmentation, filter them according to the morphometric gates and save the
corresponding ROIs.
- Need to be installed ont the machine where the script is run. Follow [this guide](https://wiki.biozentrum.unibas.ch/display/IMCF/Cellpose+python+environment) to create the environment.
- Will identify all fibers based on the membrane staining using [Cellpose](https://github.com/MouseLand/cellpose)
segmentation, filter them according to the morphometric gates and save the corresponding ROIs.
- Need to be installed on the machine where the script is run. Follow
[this guide](https://wiki.biozentrum.unibas.ch/display/IMCF/Cellpose+python+environment) to create the environment. Please don't recreate the environment if it already exists!
- Will now also save the Cellpose segmentation as a binary so it can be edited
manually. If you do so, you need to run the "extended particle analyzer"
manually as well to choose & apply the morphometric gates.
