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Additional function parameters / changed functionality / changed defaults?
Please describe your wishes
Hey
VisiumHD will now be the main data type for 10X technology on spatial data, and due to the higher number of barcodes used, we can't use a normal .csv file anymore due to row limitations. Instead, they're now using .parquet files, but on scanpy when using the read_visium method, there doesn't seem to have support for that.
Rafael-Silva-Oliveira
changed the title
Supporting VisiumHD tissue_position.parquet files
Suggestion to support VisiumHD tissue_position_list files (using parquet files)
Apr 7, 2024
Hello, I'd like to ask which version of scanpy you're using? The code you provided doesn't match the latest version, which is causing errors when I try to use it.
What kind of feature would you like to request?
Additional function parameters / changed functionality / changed defaults?
Please describe your wishes
Hey
VisiumHD will now be the main data type for 10X technology on spatial data, and due to the higher number of barcodes used, we can't use a normal .csv file anymore due to row limitations. Instead, they're now using .parquet files, but on scanpy when using the
read_visium
method, there doesn't seem to have support for that.Lines of code:
I would suggest something like this to check if there's a csv file or parquet file:
This way we can use
read_visium
if the tissue location file is .parquet instead:Using scanpy 1.9.6
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