Myosoft-IMCF
IMCF-adaptation of Myosoft, a Fiji script that identifies muscle fibers in images of sections.
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
- Will identify all fibers based on the membrane staining using 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 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.
- Can be run in batch.
2a_identify_MHC_positive_fibers.py
- Allows to manual re-run the MHC positive fiber detection. Useful in case you would like to re-run detection with a manual threshold for an image.
2b_central_nuclei_counter.py
- Will identify centralized nuclei given a ROI-zip together with its corresponding image.
- Identification is based on the same logic as before incorporating the information of a MHC staining channel.
- The ROI color code is annotated in the results table.
2c_fibertyping.py
- Identifies positive fibers in up to 3 channels given a ROI-zip together with its corresponding image.
- Includes identification of double and triple positive combinations.
- The ROI color code is annotated in the results table.
3_manual_rerun.py
- Requires an already open image with an already populated ROI manager.
- Allows to manually select measurement parameters and the measurement channel.
- Extracts the ROI color code and stores it in the result table.
All scripts store resulting ROI-zips, logs, result tables and overview PNGs.
A potential workflow could look like this:
- Run script 1) over night in batch mode on as many images as desired.
- You can potentially manually curate the resulting ROIs now, or directly move on to the next step.
- Run either script 2b) or 2c), depending on the assay.
- With the results open, manually edit the ROIs and run script 3) for the final result.