Quentin Blampey

Regarding the fully integrated section: We want to add small demos of tools that are using SpatialData as a backend: bento (@ckmah), Sopa, squidpy, ...

Hello @asmitaL99, sorry for the delay! Since you have Xenium data, can you try using the ome_tif reader, i.e. `sopa.io.ome_tif("Xenium_V1_hPancreas_Cancer_Add_on_FFPE_he_image.ome.tif")`? Also, what would you like to do with this H&E...

Hi @asmitaL99, is your issue concerning (i) package installation or (ii) reading a WSI slide image (as this feed suggests)? If it's because of package installation, could you send be...

So nothing appears at all? In that case, I think the issue is not related to Sopa, but related to the setup of your machine/computing ressources. Some questions that could...

In the new version of sopa, `sopa.io.xenium` should load all the images, including the H&E image. This issue should be resolved now, please let me know!

Awesome @stergioc! I'll have a look and try to run more tests. We'll need many tests to ensure this doesn't create regression. I think we could add this in `sopa==2.1.0`...

Hi @stergioc, I had a look to your updates, it looks very good. I added a script in the tests to check how different the new implementation is from the...

Another question @stergioc, I saw in the docs of `skimage` that they use very often a [disk](https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.disk) for the opening/closing kernel, see example [here](https://scikit-image.org/docs/stable/auto_examples/applications/plot_morphology.html#sphx-glr-auto-examples-applications-plot-morphology-py), instead of matrices of ones. What...

Thanks for having a look @stergioc! Actually, when trying your code on the shape below, I loose the square in the middle: ```python import numpy as np mask = np.zeros((100,...

I have the same result using `min_size=0` in `remove_small_objects` (if this is what you suggested). Indeed, since `_vectorize_mask` doesn't account for holes, then `holes = _vectorize_mask(holes_no_small)` will create a square...