V0.3 qp workflow

[pwalczysko]

In preparation of the Turku workshop, adding new features to the guide.

Ready for review.

cc @jburel

[pwalczysko]

Ready for review cc @melvingelbard

[melvingelbard]

Looks good to me!
Maybe it could directly link to the right section of the QuPath docs to refer back to it to avoid confusion (e.g.
https://qupath.readthedocs.io/en/latest/docs/advanced/omero.html#browsing-an-omero-server & https://qupath.readthedocs.io/en/latest/docs/advanced/omero.html#send-objects-back-to-your-omero-server).

I was a bit confused at the bit where it refers to Detections as 'derived Annotations'. Annotation and Detection objects are very similar in some ways but quite different in the way they are processed in QuPath. But I'm not sure this is very important in this case :)

It's very nice to see tutorials on this. Looking forward to working more on the extension and listening to more feedback for improvement!

[will-moore]

typo "necessritates"

[will-moore]

and "whcih"

[pwalczysko]

fixed in 00853dd

[will-moore]

Looks good (at https://omero-guides--6.org.readthedocs.build/projects/qupath/en/6/qupath.html 👍 ).
Few minor comments. NB: I haven't tried running the steps myself.

[pwalczysko]

fixes pushed e7fc3cc, 7e49f72 cc @melvingelbard - Re the derived Annotations formulation - I have removed this formulation replacing it with derrived ROIs. I have left at another place the Annotation ROIs though - let me know if this is acceptable. The problem we are having here in terms of terminology is:

In OMERO, all ROIs are a subtype of annotaion, other annotations might be e.g. key-value pairs, or Tags etc.
In QuPath, afaik, the Annotations are what we would call in OMERO (for the lack of better terms) "special large ROIs". I would like to avoid this explanation in the workflow, as it is bound to be confusing.

[pwalczysko]

@will-moore fix pushed 00853dd

[will-moore]

Looks great, thanks.

[pwalczysko]

@will-moore thank you. @jburel can we merge please so that we are ready for next week's outreach ?

[jburel]

@pwalczysko I have adjusted the permissions on that repo, so that next time you can merge

[pwalczysko]

@pwalczysko I have adjusted the permissions on that repo, so that next time you can merge

@jburel thank you