scanpy
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pixel coordinates from reading the 10X visium slide
...
Hi,
I noticed that when scanpy reads the spatial information from the "tisslue_position_list.csv" file of the 10X visium data, the (x,y) coordinate for pixels is flipped:
positions.columns = [
'barcode',
'in_tissue',
'array_row',
'array_col',
'pxl_col_in_fullres',
'pxl_row_in_fullres',
]
However, from here: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/output/images, the pxl_row is supposed to be ahead of pxl_col .
Is there any explanation for this?