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Generate Fluorescent Masks from Phase Cell Images

Downloading Pix2Pix repo:

  1. Git clone the Pix2Pix repo: 
    git clone https://github.com/junyanz/pytorch-CycleGAN-and-pix2pix
cd pytorch-CycleGAN-and-pix2pix
  2. Run the below command to install environment or follow installation instructions in the Pix2Pix repository. 
     pip install -r requirements.txt

Steps to generate the masks

  1. Convert all .tif images to .jpg using batch process option in Imagej as python does not convert .tif to .jpg or .png with these images as some particular factor is misisng and we get plain white or plain black images

  2. Create a folder with two subdirs A and B and then create a test dir in both of them copy the .jpg images to both of the test dirs.

  3. Ensure the name of the same image does not get changed and is maintained in the A and B folders

  4. Run rename_images.py to rename and add a suffix "_A" and "_B" to them. Update the path to folder A and B in lines 58-59 of rename_images.py. Look at the phase_to_cell_fluoro directory for an example.

  5. Then run the following command in the pix2pix codebase to create testing data

    python datasets/combine_A_and_B.py  --fold_A <path_to_A> --fold_B <path_to_B> --fold_AB <path_to_parent_A> --use_AB

  6. Run the following command from pix2pix codebase to generate fluorescent images

      python test.py --dataroot <path_to_parent_A>  \
  --name phase_fluoro \
  --model pix2pix --direction AtoB \
  --checkpoints_dir <path_to_checkpoints> \
  --results_dir <path_to_poutput_dir> \
  --num_test=<num_of_images> --preprocess scale_width --load_size 1024