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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
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adjusted title and included tutorial header.
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DanielaSchacherer committed Feb 17, 2026
commit 30d5c3190e654743425210447465501c1e8fe768
48 changes: 46 additions & 2 deletions notebooks/collections_demos/bonemarrowwsi_pediatricleukemia.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,29 @@
"id": "vBC86EhVsKql"
},
"source": [
"# TBD: better title - BoneMarrowWSI-PediatricLeukemia\n"
"# Where cells come from: exploring bone marrow with the `BoneMarrowWSI-PediatricLeukemia` collection\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This tutorial is shared as part of the tutorials prepared by the Imaging Data Commons team and available at https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks.\n",
"\n",
"If you are new to IDC and DICOM for digital pathology applications, you may want to check out other introductory tutorials on this topic available here: https://github.com/ImagingDataCommons/IDC-Tutorials/tree/master/notebooks/pathomics.\n",
"\n",
"This tutorial is aimed for the users of Imaging Data Commons that are interested in **bone marrow smear analysis**. You will learn how to:\n",
"* select and access images and annotations of the comprehensive bone marrow collection `BoneMarrowWSI-PediatricLeukemia`\n",
"* parse and understand the available annotations stored in DICOM Bulk Simple Annotations (ANN) format\n",
"\n",
"To learn more about the IDC, please visit the [IDC user guide](https://learn.canceridc.dev).\n",
"\n",
"If you have any questions, bug reports, or feature requests please feel free to contact us at the [IDC discussion forum](https://discourse.canceridc.dev)!\n",
"\n",
"----------------------\n",
"\n",
"Initial version: Feb 2026 \n",
"Updated: Feb 2026"
]
},
{
Expand All @@ -33,7 +55,7 @@
" - For some slides: Unlabeled cell bounding boxes\n",
" - For some slides: Cell bounding boxes with cell type labels for each annotation session plus the finally obtained consensus.\n",
"\n",
"Both images and annotations are made available in the DICOM format. For the annotations, more specifically, the **DICOM Microscopy Bulk Simple Annotation format (ANNs)** was used, which is one of multiple options to store pathology annotation data in DICOM. As a general introduction to this format, we recommend having a look at [this tutorial notebook](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/pathomics/microscopy_dicom_ann_intro.ipynb).\n",
"Both images and annotations are made available in the DICOM format. For the annotations, more specifically, the **DICOM Microscopy Bulk Simple Annotation format (ANN)** was used, which is one of multiple options to store pathology annotation data in DICOM. As a general introduction to this format, we recommend having a look at [this tutorial notebook](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/pathomics/microscopy_dicom_ann_intro.ipynb).\n",
"This notebook demonstrates **how to access and explore** the `BoneMarrowWSI-PediatricLeukemia` collection with a focus on its extensive annotation data. \n",
"\n",
"\n",
Expand Down Expand Up @@ -11627,6 +11649,28 @@
"\n",
"If you are interested in tissue type annotations or want to learn about DICOM Structured Reporting, you can take a look at [this notebook](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/collections_demos/rms_mutation_prediction/RMS-Mutation-Prediction-Expert-Annotations_exploration.ipynb) navigating expert-generated region annotations for rhabdomyosarcoma tumor slides."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Support\n",
"\n",
"If you have any questions about this notebook, please post your question on the [IDC User Forum](https://discourse.canceridc.dev) or [open an issue](https://github.com/ImagingDataCommons/IDC-Tutorials/issues/new) in the [IDC Tutorials repository](https://github.com/ImagingDataCommons/IDC-Tutorials)."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Acknowledgments\n",
"\n",
"Imaging Data Commons has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN261201500003I.\n",
"\n",
"If you use IDC in your research, please cite the following publication:\n",
"\n",
"> Fedorov, A., Longabaugh, W. J. R., Pot, D., Clunie, D. A., Pieper, S. D., Gibbs, D. L., Bridge, C., Herrmann, M. D., Homeyer, A., Lewis, R., Aerts, H. J. W., Krishnaswamy, D., Thiriveedhi, V. K., Ciausu, C., Schacherer, D. P., Bontempi, D., Pihl, T., Wagner, U., Farahani, K., Kim, E. & Kikinis, R. _National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial Intelligence_. RadioGraphics (2023). [https://doi.org/10.1148/rg.230180](https://doi.org/10.1148/rg.230180)"
]
}
],
"metadata": {
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