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theislab / ncem_benchmarks

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complete tutorial for MERFISH analysis #5

Open zhanglab2008 opened 1 year ago

zhanglab2008 commented 1 year ago

Hi team, Thanks for developing the tool. I think this tool will be super helpful to the community! However, I find that there is no a complete tutorial that can guide me from the raw MERFISH data to the final output. I search all scripts in this repo and can not find a complete one. I still have no idea how to analyze the merfish data with ncem. What I plan to do is that I use the brain MERFISH raw data from Zhang lab, run the NCEM pipeline and see if I can reproduce the same figures from your publication. However, I don't know how to proceed after I get the preprocessed_zhang.h5ad file. It would be really helpful if you could make a full tutorial that starts from the spatial files after segmentation (cell coordinates, counts, meta_data), then guide us how to do grid search, how to input the grid search results to generate the final figures. Really appreciate if you can do that. I find that you have made very excellent tutorials for scanpy and squidpy. Not sure it is possible to make a similar one for NCEM. This is not to criticize your beautiful work. I just really want to use NCEM to analyze my own MERFISH data. Thanks again to make the cell-cell communication analysis possible for MERFISH data! Sincerely, Zhang

AnnaChristina commented 1 year ago

Thanks for raising your comment. We are currently working on an extensive tutorial for all the ncem modules and how to run specific analysis steps for custom date.

Some functionalities of ncem require GPU access to run the ablation studies efficiently, hence the API differs significantly from out previous tools squidpy and scanpy. However the analysis functions from ncem will move to a new API that follows the main scverse structure. We will release it with ncem version 0.2, I can keep you posted on the new release.