@@ -9,22 +9,22 @@ Original publication: <https://doi.org/10.1371/journal.pone.0229041>
Original code: <https://github.com/Hyojung-Choo/Myosoft/tree/Myosoft-hub>
## `1_identify_fibers.py`
## [`1_identify_fibers.py`](1_identify_fibers.py)
- Will identify all fibers based on the membrane staining using WEKA pixel
classification, 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) segmentation, filter them according to the morphometric gates and save the
corresponding ROIs.
- Will now also save the WEKA segmentation as a binary so it can be edited
- 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 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.