Skip to content

BMDeep tutorial added #95

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
DanielaSchacherer wants to merge 34 commits into
base: master
Choose a base branch
from
Open

BMDeep tutorial added #95

Show file tree
Hide file tree
Changes from 14 commits
Commits
Show all changes
34 commits
Select commit Hold shift + click to select a range
393795d
Created using Colab
DanielaSchacherer Oct 27, 2025
f9772b4
Add files via upload
DanielaSchacherer Oct 27, 2025
5cb6e38
moved bmdeep tutorial and image
DanielaSchacherer Oct 27, 2025
2a49ff1
renamed notebook
DanielaSchacherer Oct 27, 2025
80d4e0a
Merge branch 'ImagingDataCommons:master' into bmdeep_tutorial
DanielaSchacherer Nov 19, 2025
d3a7cd4
Add files via upload
DanielaSchacherer Nov 19, 2025
9bd740f
updates with test against idc-etl-dev
DanielaSchacherer Nov 19, 2025
bed62d5
Delete notebooks/collections_demos/bonemarrowwsi-pediatricleukemia.ipynb
DanielaSchacherer Nov 25, 2025
f0c39d3
cleared and tested notebook with idc-index-data v23
DanielaSchacherer Nov 25, 2025
e47f184
added more text and reorganized code a little
DanielaSchacherer Nov 27, 2025
c24c840
introduced demo mode for quicker overview
DanielaSchacherer Nov 27, 2025
b9559f8
Moved text cells above code cells
DanielaSchacherer Nov 27, 2025
3f3b1c5
Smaller style changes
DanielaSchacherer Dec 3, 2025
bdff1a9
adapted Colab link, added warning about flawed session labels.
DanielaSchacherer Dec 9, 2025
ffce1c3
ready to be tested on complete dataset for first time
DanielaSchacherer Feb 2, 2026
f512884
removed contraint to bmdeep collection
DanielaSchacherer Feb 2, 2026
aff0d46
minor changes
fedorov Feb 2, 2026
376de03
adapted query on ANN files
DanielaSchacherer Feb 3, 2026
5483e3a
Integrated first round of feedback from Andrey.
DanielaSchacherer Feb 3, 2026
d3b22c6
adapted queries to use ann_index
DanielaSchacherer Feb 3, 2026
bde5c4c
text changes, demo replaced by ann_to_process and warning in the last…
DanielaSchacherer Feb 3, 2026
c2d33e6
adjusted numbers in text
DanielaSchacherer Feb 3, 2026
0d660e1
working if idc-index-data is force-upgraded
DanielaSchacherer Feb 4, 2026
015a485
updated information about ann_groups
DanielaSchacherer Feb 14, 2026
2801aaa
updated to query ann_group_index.
DanielaSchacherer Feb 15, 2026
65f1ea4
added correct colab link (for when notebook is merged)
DanielaSchacherer Feb 15, 2026
40ace17
Merge branch 'ImagingDataCommons:master' into bmdeep_tutorial
DanielaSchacherer Feb 15, 2026
e9e40bb
Merge branch 'ImagingDataCommons:master' into bmdeep_tutorial
DanielaSchacherer Feb 16, 2026
ca46d14
updated introduction
DanielaSchacherer Feb 17, 2026
30d5c31
adjusted title and included tutorial header.
DanielaSchacherer Feb 17, 2026
384505f
small cosmetic changes
DanielaSchacherer Feb 17, 2026
2b89ce7
added AnnotationCoordinateType to query and reference in text
DanielaSchacherer Feb 19, 2026
91b06ed
added confusion matrix (to be tested with v24!), tiny text changes
DanielaSchacherer Feb 20, 2026
9c8c3a5
Merge branch 'ImagingDataCommons:master' into bmdeep_tutorial
DanielaSchacherer Mar 4, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file added notebooks/collections_demos/bmdeep_annotations_example.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading