@@ -11,9 +11,10 @@ Original code: <https://github.com/Hyojung-Choo/Myosoft/tree/Myosoft-hub>
...
@@ -11,9 +11,10 @@ Original code: <https://github.com/Hyojung-Choo/Myosoft/tree/Myosoft-hub>
## [`1_identify_fibers.py`](1_identify_fibers.py)
## [`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
- Will identify all fibers based on the membrane staining using [Cellpose](https://github.com/MouseLand/cellpose)
corresponding ROIs.
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.
- 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
- 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. If you do so, you need to run the "extended particle analyzer"
manually as well to choose & apply the morphometric gates.
manually as well to choose & apply the morphometric gates.
