This is more of a question than an issue. Thank you for the package, and I appreciate if you have the opportunity to clarify this.
How does commot calculates distance in visium data? Is it read from the spaceranger json file? I tried looking into the anndata object, but couldn't find the spatial scale stored. I suppose it could be estimated from the spots positions, knowing they should be 100 microns apart. Is this how it is done? If it is stored in the anndata, how could I access it to crosscheck with the json file?
Hello,
This is more of a question than an issue. Thank you for the package, and I appreciate if you have the opportunity to clarify this.
How does commot calculates distance in visium data? Is it read from the spaceranger json file? I tried looking into the anndata object, but couldn't find the spatial scale stored. I suppose it could be estimated from the spots positions, knowing they should be 100 microns apart. Is this how it is done? If it is stored in the anndata, how could I access it to crosscheck with the json file?
Thank you!