Add Xenium tutorial using spatialdata

[LLehner]

An updated Xenium tutorial for analysis using Squidpy, but instead of only working with anndata, spatialdata is used.

@LucaMarconato please let me know if things should be added. So far I just reproduced the original Xenium tutorial with spatialdata.

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[LucaMarconato]

Extra thing: @giovp after the code that you wrote in the latest hackathon on graph support for squidpy, is there anything additional to add? If not needed, after the (quick) changes above, we can merge 😊

[giovp]

Extra thing: @giovp after the code that you wrote in the latest hackathon on graph support for squidpy, is there anything additional to add? If not needed, after the (quick) changes above, we can merge 😊

yes I think we could be using the new gr.spatial_neighbors that support directly spatialdata, but for that I think we'd first need to merge the PR/do release

[LucaMarconato]

Thanks for the fixes @LLehner! I think we are good to merge @giovp

[giovp]

super nice! I just reviewed it and there are few aesthetics that should be modified, for the rest it looks great! I would merge after the points in the review have been addressed

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giovp commented on 2024-08-23T15:38:30Z ----------------------------------------------------------------

Line above I would remove, it appears elsewhere in the nb

review-notebook-app[bot] commented 2 weeks ago

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giovp commented on 2024-08-23T15:38:30Z ----------------------------------------------------------------

also here and above

LLehner commented on 2024-08-27T08:07:22Z ----------------------------------------------------------------

Shouldn't some titles remain so people find certain sections more easily?

giovp commented on 2024-08-30T21:10:37Z ----------------------------------------------------------------

yeah but it doesn't look like they are rendered as title right? or you mean that the rendering here is incorrect with respect to how it will be render for in RTD? The lines are not about not having titles, but having titles rendered correctly, here I think the problem is that both --- and # are used. Does it make sense?

review-notebook-app[bot] commented 2 weeks ago

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giovp commented on 2024-08-23T15:38:31Z ----------------------------------------------------------------

would be nice maybe a screenshot to add here of the napari plugin open?

LLehner commented 1 week ago

Shouldn't some titles remain so people find certain sections more easily?

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giovp commented 1 week ago

yeah but it doesn't look like they are rendered as title right? or you mean that the rendering here is incorrect with respect to how it will be render for in RTD? The lines are not about not having titles, but having titles rendered correctly, here I think the problem is that both --- and # are used. Does it make sense?

---

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giovp commented 1 week ago

see the diffs here regarding the misunderstanding between lines and titles

or

please re-add the titles, but make sure that they are rendered correctly, before there was the title AND the --- which were extra

giovp commented 1 week ago

e.g. see what I mean here, the title is in both, and the text should stay, but there is the line --- which is unclear why is it there

giovp commented 1 week ago

in the current read the docs latest they are not present

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• Githubissues is a development platform for aggregating issues.

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giovp commented on 2024-08-23T15:38:30Z ----------------------------------------------------------------

also here and above

LLehner commented on 2024-08-27T08:07:22Z ----------------------------------------------------------------

Shouldn't some titles remain so people find certain sections more easily?

giovp commented on 2024-08-30T21:10:37Z ----------------------------------------------------------------

yeah but it doesn't look like they are rendered as title right? or you mean that the rendering here is incorrect with respect to how it will be render for in RTD? The lines are not about not having titles, but having titles rendered correctly, here I think the problem is that both --- and # are used. Does it make sense?

review-notebook-app[bot] commented 2 weeks ago

View / edit / reply to this conversation on ReviewNB

giovp commented on 2024-08-23T15:38:31Z ----------------------------------------------------------------

would be nice maybe a screenshot to add here of the napari plugin open?

LLehner commented 1 week ago

Shouldn't some titles remain so people find certain sections more easily?

---

View entire conversation on ReviewNB

giovp commented 1 week ago

yeah but it doesn't look like they are rendered as title right? or you mean that the rendering here is incorrect with respect to how it will be render for in RTD? The lines are not about not having titles, but having titles rendered correctly, here I think the problem is that both --- and # are used. Does it make sense?

---

View entire conversation on ReviewNB

giovp commented 1 week ago

see the diffs here regarding the misunderstanding between lines and titles

or

please re-add the titles, but make sure that they are rendered correctly, before there was the title AND the --- which were extra

giovp commented 1 week ago

e.g. see what I mean here, the title is in both, and the text should stay, but there is the line --- which is unclear why is it there

giovp commented 1 week ago

in the current read the docs latest they are not present

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[review-notebook-app[bot]]

View / edit / reply to this conversation on ReviewNB

giovp commented on 2024-08-23T15:38:31Z ----------------------------------------------------------------

would be nice maybe a screenshot to add here of the napari plugin open?

LLehner commented 1 week ago

Shouldn't some titles remain so people find certain sections more easily?

---

View entire conversation on ReviewNB

giovp commented 1 week ago

yeah but it doesn't look like they are rendered as title right? or you mean that the rendering here is incorrect with respect to how it will be render for in RTD? The lines are not about not having titles, but having titles rendered correctly, here I think the problem is that both --- and # are used. Does it make sense?

---

View entire conversation on ReviewNB

giovp commented 1 week ago

see the diffs here regarding the misunderstanding between lines and titles

or

please re-add the titles, but make sure that they are rendered correctly, before there was the title AND the --- which were extra

giovp commented 1 week ago

e.g. see what I mean here, the title is in both, and the text should stay, but there is the line --- which is unclear why is it there

giovp commented 1 week ago

in the current read the docs latest they are not present

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[LLehner]

Shouldn't some titles remain so people find certain sections more easily?

---

View entire conversation on ReviewNB

[giovp]

yeah but it doesn't look like they are rendered as title right? or you mean that the rendering here is incorrect with respect to how it will be render for in RTD? The lines are not about not having titles, but having titles rendered correctly, here I think the problem is that both --- and # are used. Does it make sense?

---

View entire conversation on ReviewNB

[giovp]

see the diffs here regarding the misunderstanding between lines and titles

or

please re-add the titles, but make sure that they are rendered correctly, before there was the title AND the --- which were extra

[giovp]

e.g. see what I mean here, the title is in both, and the text should stay, but there is the line --- which is unclear why is it there

[giovp]

in the current read the docs latest they are not present