Add support for Space Ranger cell segmentation data

[asmlgkj]

What kind of feature would you like to request?
Additional function parameters / changed functionality / changed defaults?

Please describe your wishes
will scanpy add support for this
thanks a lot.
because sc.pl.spatial will throw error
-> 1311 return spatial_data["scalefactors"]["spot_diameter_fullres"]
1312 else:
1313 return spot_size

KeyError: 'spot_diameter_fullres'

a typical scalefactor_json.json file (that I used to analyze) as follows:
{
"microns_per_pixel": 0.2637383875630947,
"tissue_lowres_scalef": 0.011981168,
"fiducial_diameter_fullres": 1206.530590494683,
"tissue_hires_scalef": 0.11981167,
"regist_target_img_scalef": 0.11981167
}
thanks a lot

[selmanozleyen]

sorry I don't get it. Which data do you use? And could you provide with a minimal reproducable example?

[asmlgkj]

thanks a lot , I am using the visium hd cell segmentataion outputs, which do not have spot_diameter_fullres parameter n the json file.

import trackcell as tk
sample = 'test'
adata = tk.io.read_hd_cellseg(datapath="./", sample=sample)
adata.var_names_make_unique()
adata

it will fail when using sq.pl.spatial_scatter(adata, color="cluster") , give the error like above

the data download as following

Core output files

wget https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Zebrafish_Head/Visium_HD_3prime_Zebrafish_Head_barcode_mappings.parquet
wget https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Zebrafish_Head/Visium_HD_3prime_Zebrafish_Head_binned_outputs.tar.gz
wget https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Zebrafish_Head/Visium_HD_3prime_Zebrafish_Head_cloupe_008um.cloupe
wget https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Zebrafish_Head/Visium_HD_3prime_Zebrafish_Head_cloupe_cell.cloupe
wget https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Zebrafish_Head/Visium_HD_3prime_Zebrafish_Head_feature_slice.h5
wget https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Zebrafish_Head/Visium_HD_3prime_Zebrafish_Head_metrics_summary.csv
wget https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Zebrafish_Head/Visium_HD_3prime_Zebrafish_Head_molecule_info.h5
wget https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Zebrafish_Head/Visium_HD_3prime_Zebrafish_Head_segmented_outputs.tar.gz
wget https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Zebrafish_Head/Visium_HD_3prime_Zebrafish_Head_spatial.tar.gz
wget https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Zebrafish_Head/Visium_HD_3prime_Zebrafish_Head_web_summary.html

echo "Download complete!"
echo "Extracting archive files..."

Extract binned outputs (contains 8um and 16um resolution data)

tar -xzf Visium_HD_3prime_Zebrafish_Head_binned_outputs.tar.gz

Extract segmented outputs (contains cell segmentation data from Spaceranger 4.0+)

tar -xzf Visium_HD_3prime_Zebrafish_Head_segmented_outputs.tar.gz

Extract spatial data (contains images and spatial coordinates)

tar -xzf Visium_HD_3prime_Zebrafish_Head_spatial.tar.gz