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pixel coordinates from reading the 10X visium slide

Open YuanningEric opened this issue 2 years ago • 0 comments

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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?

YuanningEric avatar May 05 '22 22:05 YuanningEric