Performance on Xenium/Merfish(Vizgen) - Single cell integration about tangram HOT 2 OPEN

Hi, I believe using count based data for training is more acceptable, that is because 1. Since there are missing genes in the spatial data, we cannot directly normalize the raw count spatial data. 2. Tangram does not have specific distribution modeling for input data.

But I think Xenium has large-scale spots and it is hard for me to place tangram in my gpu node. Do you use the cpu version to train your model? Thanks.

from tangram.

Hi @mortunco , one restriction of Tangram is that the cell type compositions between the scRNA-seq and spatial need to be similar. For Q2, how does the cell type composition compare between the sc and spatial? And another question is that how does the gene prediction behavior looks like overall? Can you help to plot the cos_sim vs sparsity of the gene as in the tutorial.

from tangram.