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SydneyBioX / BIDCell

Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
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suggestions for improving the README File #18

Open yulijia opened 2 months ago

yulijia commented 2 months ago
  1. It is better to include a complete step-by-step guide on how to run the example (the user needs to download the GitHub repository, not just install BidCell via pip).
  2. It is better to include the path of the example params_small_example.yaml; otherwise, I have to check each folder to find it. https://github.com/SydneyBioX/BIDCell/tree/main/bidcell/example_params
  3. If we can also provide a suggestion on how to run it on a specific GPU, it will benefit our group as well. CUDA_VISIBLE_DEVICES=3; python example_small.py

I will keep updating this list.

xhelenfu commented 1 month ago

Thanks for your suggestions! I've incorporated them into the latest README file.

yulijia commented 1 month ago
  1. I also need a clear explanation of the headers for the reference file and marker gene file.

what are the meaning of ct_idx,cell_type,atlas?

the ct_idx should start with 0 or 1?