superpixels

Setup

• Install conda
• Setup conda env:
  • conda env create -f environment.yml
  • conda activate superpixels
• Install copick: pip install git+https://github.com/copick/copick-utils.git
• Install cellcanvas_spp in editable mode:
  • pip install -e .
• Environment:
  • spp_segmentation requires COPICK_DATA to be set
    • e.g., export COPICK_DATA=COPICK_DATA="/Users/eraymond/Library/CloudStorage/[email protected]/My Drive/2024_CZHackathon_InteractiveImageEmbeddings"

Create a config for demo notebook

• USe an existing config OR
• Run setup notebook
  • Edit project_data_dir in setup