GSoC - Coding Period Week 6

Work Done This Week (July 12th to July 19th)

• Swapped out the model for the Cell membrane segmentation with the upgraded model in DevoLearn’s repository, ran tests locally before pushing because Travis has been discontinued. (Link to commit)

• Renamed the embryo_segmentor package to cell_membrane_segmentor. The reason for this renaming is to avoid naming conflicts when new segmentation models are added. (Link to commit)

  • Old syntax - from devolearn import embryo_segmentor
  • New syntax - from devolearn import cell_membrane_segmentor

• Integrated the new nucleus segmentation model into the library (Link to commit)

  • Wrote the necessary functions to run inference, on CPU and GPU.
  • Made additions to the testing script to accomodate this additional model.
  • Steps for usage:
    1. from devolearn import cell_nucleus_segmentor
    2. segmentor = cell_nucleus_segmentor(device='cuda')
    3. pred = segmentor.predict(image_path = "input_image.png")
    4. plt.imshow(pred)

• Inference Examples:

  1. Input image with Varying Z axis -

  2. Inputs varying through time -

Planned:

• Build a GUI for all DevoLearn models and host them online.
• Look into ways of running bulk inference using the web-GUI.
• Move from Travis CI to Github Actions.