updated introduction

Author: DanielaSchacherer

notebooks/collections_demos/bonemarrowwsi_pediatricleukemia.ipynb

@@ -13,7 +13,7 @@
         "id": "vBC86EhVsKql"
       },
       "source": [
-        "# BoneMarrowWSI-PediatricLeukemia\n"
+        "# TBD: better title - BoneMarrowWSI-PediatricLeukemia\n"
       ]
     },
     {
@@ -24,7 +24,7 @@
       "source": [
         "## Background\n",
         "\n",
-        "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",
+        "The analysis of bone marrow aspirate smears serves as the foundation for assessing haematopoiesis (the process of blood cell formation in the bone marrow) and amongst other systemic diseses, the diagnosis of leukemia. This notebook introduces the `BoneMarrowWSI-PediatricLeukemia` collection, a commprehensive dataset of bone marrow smears and cell annotations. The dataset is presented in detail in [this preprint](https://www.arxiv.org/pdf/2509.15895) and is publicly available via the [Imaging Data Commons](https://portal.imaging.datacommons.cancer.gov/). \n",
         "\n",
         "- **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",
         "- **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",
@@ -33,7 +33,8 @@
         "    - 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",
-        "This notebook concentrates on **how to access and work with the annotation data**, that are made available in **DICOM Microscopy Bulk Simple Annotation format (ANNs)**. 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 (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",
+        "This notebook demonstrates **how to access and explore** the `BoneMarrowWSI-PediatricLeukemia` collection with a focus on its extensive annotation data. \n",
         "\n",
         "\n",
         "<img src=\"https://raw.githubusercontent.com/ImagingDataCommons/IDC-Tutorials/master/notebooks/pathomics/bmdeep_annotations_example.png\" alt=\"Example visualization of BoneMarrowWSI-PediatricLeukemia annotations\" width=\"1000\"/>\n",
@@ -162,7 +163,9 @@
         "id": "1-ZR8MkhFqKX"
       },
       "source": [
-        "Next, we have a look at the available annotation (ANN) files. The following query collects information about ANN files on series-level from idc-index's `ann_index`."
+        "Next, we have a look at the available annotation (ANN) files. The following query collects information about ANN files on series-level from idc-index's `ann_index`.\n",
+        "\n",
+        "# TOdO: explain why join on SeriesInstanceUID"
       ]
     },
     {