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notebooks/collections_demos/bonemarrowwsi_pediatricleukemia.ipynb

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"\n",
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"This notebook introduces the `BoneMarrowWSI-PediatricLeukemia` collection, which is presented in [this preprint](https://www.arxiv.org/pdf/2509.15895) and was recently added to [Imaging Data Commons](https://portal.imaging.datacommons.cancer.gov/).\n",
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"\n",
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"- **Images**: The `BoneMarrowWSI-PediatricLeukemia` dataset comprises bone marrow aspirate smear WSIs for 246 pediatric cases of leukemia, including acute lymphoid leukemia (ALL), acute myeloid leukemia (AML), and chronic myeloid leukemia (CML). The smears were prepared for the initial diagnosis (i.e., without prior treatment), stained in accordance with the Pappenheim method, and scanned at 40x magnification.\n",
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"- **Images**: The `BoneMarrowWSI-PediatricLeukemia` dataset comprises bone marrow aspirate smear WSIs for almost 250 pediatric cases of leukemia, including acute lymphoid leukemia (ALL), acute myeloid leukemia (AML), and chronic myeloid leukemia (CML). The smears were prepared for the initial diagnosis (i.e., without prior treatment), stained in accordance with the Pappenheim method, and scanned at 40x magnification.\n",
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"- **Annotations**: The images have been annotated with rectangular regions of interest (ROI) of the evaluable monolayer area and more than 40000 cell bounding box annotations have been placed (with few exceptions) within the ROIs. For a subset of them all cells and other haematological structures have additionally been labelled by multiple experts in a consensus labeling approach with 49 distinct (cell type) classes. The consensus labelling approach worked as follows: each bounding box was successively labelled by different experts in so-called \"annotation sessions\" until (a) the bounding box had been labelled by at least two experts, and (b) the most frequent label had constituted at least half of all labels given to that bounding box (and had then been termed \"consensus class\"). In summary, the following annotations are available: \n",
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" - For each slide: ROI annotations of the monolayer area for each slide\n",
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": null,
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"metadata": {
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"id": "tacxH-AusHPT"
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"metadata": {
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"id": "dgtRNVatzl2s"
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"metadata": {
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"id": "D6XmpjYFsaJy"
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"id": "0HEq03G4EFtv"
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},
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"source": [
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"First, we verify that we have indeed 246 slides (=distinct SeriesInstanceUIDs of SM modality) in the `BoneMarrowWSI-PediatricLeukemia` collection:"
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"First, we count the number of slides (=distinct SeriesInstanceUIDs of SM modality) available in the `BoneMarrowWSI-PediatricLeukemia` collection:"
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]
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": null,
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"metadata": {
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"colab": {
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"base_uri": "https://localhost:8080/"

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