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zcang / COMMOT

MIT License
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Questions about dis_thr #15

Open ysbioinfo opened 1 year ago

ysbioinfo commented 1 year ago

Hi COMMOT developers, Thanks for providing such an awesome tool for us. I am now using COMMOT on my Visium data and having some questions about the distance threshold:

  1. The default unit in adata.obsm['spatial'] is pixel but not μm, so the value you used in the tutorial is 200 pixel, but not 200μm, am I right?
  2. I noted that you used 1000 μm for Visium data in the NM paper. How did you tranform the pixel to μm? What scale factor should be used?
  3. Is there any general guidance on selecting this threshold? Or some recommended value?

Thanks in advance.

Yang