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STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.
MIT License
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More samples within the same slice #176

Closed MariaRosariaNucera closed 6 months ago

MariaRosariaNucera commented 11 months ago

Hi, thank you for the beautiful tool! I have one question, from the tutorial I can see the option on how to analyse one single sample and slice, or multiple slices. I am not sure how to deal with the case of multiple samples on the same slice. What should I do in this case, is there a way to separate them?

Thank you Maria

UglyRay7 commented 11 months ago

I don't know if I got you correctly. It's like several slices have been integrated into one slice? So you just have one data file now? If your data is in AnnData h5ad format, you could use the AnnData library to separate them.

Ray

MariaRosariaNucera commented 11 months ago

I don't know if I got you correctly. It's like several slices have been integrated into one slice? So you just have one data file now? If your data is in AnnData h5ad format, you could use the AnnData library to separate them.

Ray

It's not like several slices have been integrated into one slice, there was no integration, the tissues are physically located in the same slide.

I have the coordinates and the anndata, but I don't understand why I am not able to capture them using the function data.plt.interact_spatial_scatter(), I can select the area but I am not able to store it in any way.

Zhenbin24 commented 6 months ago

Sorry for replying so late,. You can refer to this information to deal with it.

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