how to add spatial transcriptomics to the h5ad file

[FADHLyemen]

• [ ] Additional function parameters / changed functionality / changed defaults?
• [ ] New analysis tool: A simple analysis tool you have been using and are missing in sc.tools?
• [ ] New plotting function: A kind of plot you would like to seein sc.pl?
• [ ] External tools: Do you know an existing package that should go into sc.external.*?
• [ ] Other?

...

Hi, If we have scrna-seq file and other spatial image, how to use scanpy to visualize them both I found visum example but I am interested in combining 10x scrna-seq and other image such as slideseq, mFISH? https://scanpy-tutorials.readthedocs.io/en/latest/spatial/basic-analysis.html

[Koncopd]

I suppose you need to check https://github.com/theislab/squidpy ping @giovp

[giovp]

hi @FADHLyemen ,

you can check out this tutorial on how to best do this: https://squidpy.readthedocs.io/en/latest/auto_tutorials/tutorial_read_spatial.html

let me know if you have a specific question re coordinates alignment or else

[giovp]

hi @FADHLyemen ,

you can check out this tutorial on how to best do this: https://squidpy.readthedocs.io/en/latest/auto_tutorials/tutorial_read_spatial.html

let me know if you have a specific question re coordinates alignment or else

[giovp]

hello @FADHLyemen was the suggested tutorial useful?