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Hi, thanks for reporting. I have tried running the notebook on macOS using spatialdata==0.2.2 and spatialdata-plot==0.2.4 and I could not reproduce the bug. I also tried using the latest dev version and I could not reproduce.
My guesses:
It could be a OS problem but I don't think this is the case because before release we tested that notebook on a linux machine.
As a double check, I would try to visualize the data using napari-spatialdata with the following code
If you can reproduce with napari, it could be a problem with the data. I'd try to regenerate the sdata object by running the lightweight scripts download.py and to_zarr.py for here: https://github.com/giovp/spatialdata-sandbox/tree/main/merfish. If this fixes the issue it could be that there has been a problem with the pipeline we use to regenerate the data.
Describe the bug
Hi there, I'm running the public MERFISH tutorial using spatialdata
0.2.2
and spatialdata_plot0.2.4
(https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/technology_merfish.html) and when I execute the final cell containingI get
To Reproduce
Run the public MERFISH tutorial
Desktop (optional):
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