Data fomr new spatial transcriptomics from 10x

dear all,
I am working with very new data formats from 10x visium (from the Cystassist).

  • I had first to change the name “tissue_positions.csv” in “tissue_positions_list.csv” in the spatial folder in order to read the data (sc.read_visium function)

  • but I didnt" manage to plot the data (function I got the error:

Thanks !!


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HI @sophieRAIBAUD ,

can you use read_visium and plotting from squidpy instead of scanpy? Think they should work,

Let me know!

thanks !
but I get the same kind of error

when I use, color = [“total_counts”], vmin = 300, vmax = 20000)

You can find data from Cystassist new device:
Did you already test it ?
Many thanks !!

hello again,
in the data generated with the cytassist, the image.tif does not contains the fiducials.
So a supplementary step is needed to align the image corresponding to the spatial data and the image scanned before.
did you already test this ?
Many thanks !!

Dear all,
I finally figured out how to use squidpy with data generated using the Cytassist from 10x:

  • you need to change the name of the file with tissue positions in the spatial folder: tissue_positions.csv → tissue_positions_list.csv

  • you need to change the format of spatial position from string to integer: adata.obsm[‘spatial’] = adata.obsm[‘spatial’].astype(

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