Open rocketeer1998 opened 2 years ago
Hi, thanks so much for asking! 1.The position of the centroid represents the 'center'/density peak of each cell. It's neither determined by DAPI image nor equal to the DAPI position of a cell. The function of DAPI image is to help cell segmentation in the tissue of high cell density and variable nuclear/cytosolic distribution of RNAs.
Thanks for your reply!
Hello @heihaizhengdong , I’m very interested in ClusterMap. I’d like to ask several questions which are crucial to improving ClusterMap
Questions
xy_radius
andz_radius
? μm? How can one know the area of an individual cell? Can I extract this information from theAnnData
produced by ClusterMap pipeline?thresh
and decreasemin_spot_per_cell
.Enhancements
model.cell_adata
so users can easily interoperate it with other tool, like scanpy. In addition, there is an error when I try to export ClusterMap AnnData.h5ad file usingadata.write
which saysTypeError: 0 of type <class 'int'> is an invalid key. Should be str. Above error raised while writing key 'var' of <class 'h5py._hl.files.File'> from /.
. I try to resolve this byadata = ad.AnnData(model.cell_adata.X, obs=model.cell_adata.obs,var=model.cell_adata.var)
but it is still not working. Any recommendation?In a word, ClusterMap is well performed in analyzing spatial transcriptomics data. Thanks again for your excellent work. And I would appreciate it if we can discuss more details about ClusterMap.