Xenium cell segmentation mask export requires coordinate flipping among y-axis

[matt-sd-watson]

I have a script that pulls the cell segmentation mask from a spatialdata io object from Xenium and exports it as a tiff for our visualization software. The data are taken from this publicly available breast dataset:

sdata = sd.read_zarr(zarr_path)

cells = sdata.shapes['cell_boundaries']

x_min, y_min = np.min((adata.obsm['spatial']), axis=0)
x_max, y_max = np.max((adata.obsm['spatial']), axis=0)


transform = rasterio.transform.from_bounds(x_min, y_min, x_max,
                                           y_max, int(x_max - x_min), int(y_max - y_min))

shapes = [(geom, idx) for idx, geom in enumerate(cells.geometry)]

mask = rasterize(shapes=shapes, out_shape=(int(y_max - y_min), int(x_max - x_min)),
                 transform=transform, dtype='int32')

tiff.imwrite(f"mask.tiff", mask)

However, upon exporting the mask to tiff format, the coordinates in the y-axis are flipped:

If I flip the mask array among the y-axis prior to export, the mask now aligns with the expression results:

tiff.imwrite(f"mask.tiff", np.flip(mask, axis=0))