Publication | Spatial Single Cell Mapping

Delighted to say that our manuscript “Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography” is now published in Communications Biology and thus out there for everyone to read in its final form. This is the paper that describes the theoretical underpinnings for stereoscope, which allows you to spatial map cell types found in single cell data onto spatial transcriptomics data. There is also a nice bit of discussion as to whether spatial transcriptomics data (ST/Visium) can be properly modeled using a negative binomial distribution (which we use) found in the supplementary (spoiler, it seems like it). Have a look at it if you are interested!

• manuscript link : HERE
• stereoscope link : HERE

P.S: I’m also planning to update the code base in the future, providing an API for scanpy, but also add some features like subsampling and gene selection to the standard modules; but that is for later.