Thank you for developing such an excellent software tool!
I'm currently using stlearn for CCI analysis on Visium HD data, and I'm only interested in a subset of specific cell types.
I have a question about the optimal workflow: Should I filter the AnnData object to retain only my cell types of interest before performing CCI analysis (note that these cell types may not be spatially contiguous), or should I follow the Xenium tutorial approach by performing CCI analysis on all cells after gridding, and then filter for my cell types of interest only during the visualization/plotting stage?
I would greatly appreciate your guidance on the recommended best practice for this scenario.
Thank you in advance for your time and help!
Thank you for developing such an excellent software tool!
I'm currently using stlearn for CCI analysis on Visium HD data, and I'm only interested in a subset of specific cell types.
I have a question about the optimal workflow: Should I filter the AnnData object to retain only my cell types of interest before performing CCI analysis (note that these cell types may not be spatially contiguous), or should I follow the Xenium tutorial approach by performing CCI analysis on all cells after gridding, and then filter for my cell types of interest only during the visualization/plotting stage?
I would greatly appreciate your guidance on the recommended best practice for this scenario.
Thank you in advance for your time and help!