issue when processing Xenium data (missing file)

[phoebehxf]

Hello, thanks very much for the great work!

I was processing the Xenium data following your instructions (preprocess/prep_xenium_fov.py) when I met this error: there is no such file as "cellseg_mask.npy" in the downloaded data from Xenium.

Could you please provide this file, or give some instructions on how to obtain it?

[maxpmx]

Hi,

you should find a file named cells.zarr.zip within the Xenium output folder. This Zarr archive contains the built-in segmentation output generated by the Xenium software.

To extract the cell masks from this archive, we used the following code from 10x tutorial:

# Import Python libraries
# This script was tested with zarr v2.13.6
import zarr
import numpy as np

# Function to open a Zarr file
def open_zarr(path: str) -> zarr.Group:
    store = (zarr.ZipStore(path, mode="r")
    if path.endswith(".zip")
    else zarr.DirectoryStore(path)
    )
    return zarr.group(store=store)

# For example, use the above function to open the cells Zarr file, which contains segmentation mask Zarr arrays
root = open_zarr("cells.zarr.zip")

# Look at group array info and structure
root.info
root.tree() # shows structure, array dimensions, data types

# Create cell and nucleus segmentation mask np array objects to read or modify
cellseg_mask = np.array(root["masks"][1])