[LucaMarconato]

@timtreis @Sonja-Stockhaus there seems to be a bug in the spatial query notebook around a spatialdata-plot call, could you please have a look? Thanks

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[Sonja-Stockhaus]

@LucaMarconato when downloading the data set from the link in the notebook (https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zip) I think I get different data than the one used in the notebook. Bc the coordinate systems are named ST8059048 and ST8059049 and in the original notebook it's ST8059050 and ST8059051. The plots also look slightly different.

It doesn't matter for the bugfix but I just thought I'd let you know bc I also didn't find the correct dataset

[timtreis]

Same for me, I think those changed at one point.

[LucaMarconato]

Thanks for pointing this out, I will track this in a issue. I will re-enable the script uploading the data in S3, I think the notebook is correct and the data in S3 has not been updated.

[LucaMarconato]

I have temporarily replaced the static plots with napari plots in #55 so that the users can reproduce the visualzations, I will put them back with this PR when it's ready. Thanks for your help.

[timtreis]

Hey @LucaMarconato, fixed the notebook. Can you confirm?

There is one final napari screenshot that I didn't delete because it was there before, shall I delete and then merge?

[LucaMarconato]

Thanks @timtreis, which branch of spatialdata-plot shall I use to reproduce?

[timtreis]

Ah sorry, the transformations refactoring branch.

[LucaMarconato]

Looks great thank you!
Please add also these lines of code in the last plot

cropped_sdata.pl.render_images().pl.show(ax=ax)
cropped_sdata2.pl.render_images().pl.show(ax=ax)

and make the plot a bit larger.

Then the screenshot Jupyter cell (and the corresponding file in attachments) can be removed.

[LucaMarconato]

Please leave the commented napari code since I will reenable napari in the tests in a follow up PR.

[timtreis]

@LucaMarconato, managed to fix the CI error, you just need to figure out which exact data name should be used (48/49/50?), then it's good to merge 👍

[LucaMarconato]

I've just verified, it's 50. Gonna update the notebook and merge. Thanks for the fix!

[LucaMarconato]

@timtreis @Sonja-Stockhaus, please redownload the visium.zarr data, the correct one should have the FOVs 50, 52. Tomorrow, unless the nightly upload job fails, you should be able to see the correct data.

Also, please rename the file to visium_brain.zarr. Other notebooks use the Visium breast cancer dataset and it is also called visium.zarr in the notebook, so let's use visium_brain.zarr here to distinguish them.