No experiment.xenium file after running `sopa explorer write`

[NJNataren]

I have just run sopa explorer write /media/nnataren/Nat_NATAREN_SSD/PhD_Backup/_Xenium_ICI_melanoma/combined_runs/GR_lung_non-res.zarr --gene-column feature_name

for my sample on the CLI version of Sopa and get all of the expected outputs ( analysis.zarr.zip, cell_feature_matrix.zarr.zip, cells.zarr.zip, transcripts.zarr.zip, morphology.ome.tiff).

Is this command meant to also produce the experiment.xenium file as well to view everything in Xenium Explorer? Is this my mistake or something that is being addressed with the new version of Sopa?

Below is the output when I run the code on command line (Linux 24.04.1 LTS, conda environement with python=3.10). Thanks!

/home/nnataren/miniforge3/envs/sopa/lib/python3.10/site-packages/numba/core/decorators.py:246: RuntimeWarning: nopython is set for njit and is ignored warnings.warn('nopython is set for njit and is ignored', RuntimeWarning) /home/nnataren/miniforge3/envs/sopa/lib/python3.10/site-packages/zarr/creation.py:614: UserWarning: ignoring keyword argument 'read_only' compressor, fill_value = _kwargs_compat(compressor, fill_value, kwargs) /home/nnataren/miniforge3/envs/sopa/lib/python3.10/site-packages/zarr/creation.py:614: UserWarning: ignoring keyword argument 'read_only' compressor, fill_value = _kwargs_compat(compressor, fill_value, kwargs) /home/nnataren/miniforge3/envs/sopa/lib/python3.10/site-packages/zarr/creation.py:614: UserWarning: ignoring keyword argument 'read_only' compressor, fill_value = _kwargs_compat(compressor, fill_value, kwargs) /home/nnataren/miniforge3/envs/sopa/lib/python3.10/site-packages/zarr/creation.py:614: UserWarning: ignoring keyword argument 'read_only' compressor, fill_value = _kwargs_compat(compressor, fill_value, kwargs) /home/nnataren/miniforge3/envs/sopa/lib/python3.10/site-packages/zarr/creation.py:614: UserWarning: ignoring keyword argument 'read_only' compressor, fill_value = _kwargs_compat(compressor, fill_value, kwargs) [INFO] (sopa.io.explorer.table) Writing table with 541 columns [INFO] (sopa.io.explorer.table) Writing 2 cell categories: region, slide [INFO] (sopa.io.explorer.shapes) Writing 4265 cell polygons [INFO] (sopa.io.explorer.points) Writing 7512350 transcripts [INFO] (sopa.io.explorer.points) > Level 0: 7512350 transcripts [INFO] (sopa.io.explorer.points) > Level 1: 1878087 transcripts [INFO] (sopa.io.explorer.points) > Level 2: 469521 transcripts [INFO] (sopa.io.explorer.points) > Level 3: 117380 transcripts [INFO] (sopa.io.explorer.points) > Level 4: 29345 transcripts [INFO] (sopa.io.explorer.points) > Level 5: 7336 transcripts [INFO] (sopa.io.explorer.points) > Level 6: 1834 transcripts [INFO] (sopa.io.explorer.images) Writing multiscale image with procedure=semi-lazy (load in memory when possible) Writing tiles: 0%| | 0/2730 [00:00<?, ?it/s][INFO] (sopa.io.explorer.images) > Image of shape (5, 13699, 39750) Writing tiles: 100%|████████████████████████████████████████████████████████████████▉| 2729/2730 [02:25<00:00, 18.75it/s] [INFO] (sopa.io.explorer.images) (Loading image of shape (5, 6849, 19875)) in memory Killed

[NJNataren]

Please disregard, this issue was due to my system killing the task!