[Help wanted] --save-h5ad but missed transcript counts

[KunHHE]

Hi, @quentinblampey, Can I ask you if I run " sopa explorer write", the saved h5ad file only "AnnData object with n_obs × n_vars = 7589 × 315
obs: 'region', 'slide', 'cell_id', 'area', 'batch'
obsm: 'intensities', 'spatial'

But I did not see "transcripts count" under table-obs? So I cannot run AnnData, especially may be this is the reason why I run Tangram failed, because there are no common gene found.

Detailed codes using CLI:
sopa read C:/Users/hekun/Downloads/Slide1307/region_0 --technology merscope
sopa patchify image C:/Users/hekun/Downloads/Slide1307/region_0.zarr --patch-width-pixel 6000 --patch-overlap-pixel 150

sopa segmentation cellpose C:/Users/hekun/Downloads/Slide1307/region_0.zarr --diameter 60 --channels DAPI --channels Cellbound3 --flow-threshold 2 --cellprob-threshold -6 --pretrained-model C:/Users/hekun/.cellpose/models/CP_20241209_DRG --min-area 2000 --clip-limit 0.2 --gaussian-sigma 1

sopa resolve cellpose C:/Users/hekun/Downloads/Slide1307/region_0.zarr
sopa aggregate C:/Users/hekun/Downloads/Slide1307/region_0.zarr --gene-column gene --average-intensities --min-transcripts 5
sopa explorer write C:/Users/hekun/Downloads/Slide1307/region_0.zarr --gene-column gene

Thanks very much!

[KunHHE]

So I cannot processing the generated h5ad file. What I did is sdata1 = sd.read_zarr("C:/Users/hekun/Downloads/S3R1.zarr"); then read adata1 = sdata1.tables["table"], to pull out the Table data (AnnData). The h5ad file generation is not working, so the table is missed in the h5ad. Any ideas why?

[quentinblampey]

What do you mean by "The h5ad file generation is not working"? Could you provide error logs?