BMDeep tutorial added

[DanielaSchacherer]

As discussed, I added the BMDeep tutorial. Happy for feedback! :)

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[DanielaSchacherer]

@fedorov did we already talk about this? If not, maybe we should briefly in the Slim meeting later today!

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[fedorov]

I admit I lost track of this PR...

[DanielaSchacherer]

no problem, me too :D

[fedorov]

@DanielaSchacherer I pushed some minor changes, and also left some suggestion in the comments here: https://colab.research.google.com/drive/1kD_mEbfi1ozhyyS0WK9zl3vyKYMJJJjA?usp=sharing

[DanielaSchacherer]

I took the feedback in and answered to your comments in the notebook linked above. I already changed the code to use ann_index, so let's not merge yet, but let me test as soon as ann_index is out :)

[DanielaSchacherer]

@fedorov do you have any additional feedback?

[fedorov]

You rely on "monolayer" in SeriesDescription in one of the queries, which is not a good pattern.

Why not use ann_group_index and search by Selected region?

Search by unstructured data is not desirable, especially when the query can be resolved using structured data.

client.fetch_index("ann_group_index")

# Select all annotation groups from ANN series whose SeriesDescription
# mentions "monolayer" in the bonemarrowwsi_pediatricleukemia collection
monolayer_ann_groups = client.sql_query("""
    SELECT
        ag.SeriesInstanceUID,
        ag.AnnotationGroupNumber,
        ag.AnnotationGroupUID,
        ag.AnnotationGroupLabel,
        ag.NumberOfAnnotations,
        ag.GraphicType,
        ag.AnnotationPropertyCategory_CodeMeaning,
        ag.AnnotationPropertyType_CodeMeaning,
        ai.referenced_SeriesInstanceUID
    FROM ann_group_index ag
    JOIN ann_index ai
      ON ag.SeriesInstanceUID = ai.SeriesInstanceUID
    JOIN index i
      ON ag.SeriesInstanceUID = i.SeriesInstanceUID
    WHERE i.collection_id = 'bonemarrowwsi_pediatricleukemia'
      AND ag.AnnotationPropertyType_CodeMeaning = 'Selected region'
    ORDER BY ag.SeriesInstanceUID, ag.AnnotationGroupNumber
""")

print(f"Found {len(monolayer_ann_groups)} annotation groups "
      f"across {monolayer_ann_groups['SeriesInstanceUID'].nunique()} ANN series")
display(monolayer_ann_groups)

[fedorov]

Also note that idc-index has been updated, and should allow fetching ann_group_index.

[fedorov]

I think similar comment applies further in the notebook where you deal with unlabeled cells.