fibrotug-improc

DSP Image Processing

Installation using VScode

1. using the terminal, navigate to the location where you want to have the code and do git clone https://github.com/javijv4/fibrotug-improc.git . This will create a subfolder fibrotug-improc/
2. Open VScode, go to File → Open… → and select the fibrotug-improc/ folder.
3. Do cmd+shift+P and type Python. Select Python: Create Environment…. Select Venv. It might ask you for the Python interpreter, select any that is > 3.9.
4. Do cmd+shift+P and type terminal. Select Terminal: Create New Terminal.
5. Check that the Python interpreter is correct by typing which python. It should show you path_to_fibrotug-improc/.venv/bin/python
6. In the terminal, run python -m pip install -e . .This will install all the codes and required packages.
7. That’s it. It should be ready to run. You can test that everything works running the register_pre_to_post.py file that, as default, points to a test case that is downloaded when you clone the repository (test_data/ folder)

Processing images

WAIT! Before start, check that the post and pre files are in the same orientation (they can be flipped in 180)

1. Generate tissue masks:
   1. generate_tissue_masks.py → fibrotug_mask_init.tif It works for both fibers and actinin
      • pre images: use actinin
      • post images: use fibers
   2. use itksnap to fixed up the mask.→ fibrotug_mask.tif
2. Register pre-to-post:
   1. register_pre_to_post.py → fibrotug_mask_init.tif
   2. open pre_mask.tif in itksnap and get rid of the posts →pre_tissue_mask.tif
3. Process Actin Images
   1. actin_processing.py → improc_”which”_actin.npz
      • improc_”which”_actin.npz contains the image angles and smooth angles.
   2. Visualization can be done with visualize_actin.py
4. Process Fiber Images