Data fomr new spatial transcriptomics from 10x

Help squidpy
1

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 sc.pl.spatial). I got the error:

    image
    image945×164 45.6 KB

Thanks !!

Sophie

1 Like
2

HI @sophieRAIBAUD ,

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

Let me know!

3

thanks !
but I get the same kind of error

image
image2588×675 135 KB

when I use sq.pl.spatial_scatter(adata, color = [“total_counts”], vmin = 300, vmax = 20000)
Sophie

4

@giovp
hello,
You can find data from Cystassist new device:
https://www.10xgenomics.com/resources/datasets/fresh-frozen-visium-on-cytassist-human-breast-cancer-probe-based-whole-transcriptome-profiling-2-standard
Did you already test it ?
Many thanks !!
Sophie

5

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 !!

image
image2994×678 223 KB

6

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(np.int)
    Sophie

1 Like