added AnnotationCoordinateType to query and reference in text

Author: DanielaSchacherer

notebooks/collections_demos/bonemarrowwsi_pediatricleukemia.ipynb

@@ -123,20 +123,20 @@
       },
       "source": [
         "## Finding the `BoneMarrowWSI-PediatricLeukemia` dataset on IDC\n",
-        "To access and download image and ANNs files, we utilize the Python package [idc-index](https://github.com/ImagingDataCommons/idc-index) and fetch `ann_index` and `ann_group_index`, specific to DICOM ANN objects. You can have a look [here](https://idc-index.readthedocs.io/en/latest/indices_reference.html) for details on all available indices in idc-index."
+        "To access and download image and ANNs files, we utilize the Python package [idc-index](https://github.com/ImagingDataCommons/idc-index) and fetch `ann_index` and `ann_group_index`, specific to DICOM ANN objects. Have a look [here](https://idc-index.readthedocs.io/en/latest/indices_reference.html) for details on all available indices in idc-index and what information you can query from them. "
       ]
     },
     {
       "cell_type": "code",
-      "execution_count": 3,
+      "execution_count": null,
       "metadata": {
         "id": "D6XmpjYFsaJy"
       },
       "outputs": [],
       "source": [
         "idc_client = IDCClient() # set-up idc_client\n",
         "idc_client.fetch_index('ann_index') # fetch index for ANN objects\n",
-        "idc_client.fetch_index('ann_group_index') # fetch index for ANN groups"
+        "idc_client.fetch_index('ann_group_index') # fetch index for the AnnotationGroups within ANN objects"
       ]
     },
     {
@@ -519,6 +519,7 @@
         "SELECT\n",
         "    ann_index.SeriesInstanceUID, -- SeriesInstanceUID of the annotation object\n",
         "    ann_index.referenced_SeriesInstanceUID, -- SeriesInstanceUID of the slide that the annotation is associated with\n",
+        "    ann_index.AnnotationCoordinateType, -- whether coordinates are 2D (image coordinate system) or 3D (frame-of-reference coordinate system)\n",
         "    index.SeriesDescription,\n",
         "    index.StudyInstanceUID,\n",
         "FROM\n",
@@ -540,13 +541,13 @@
         "id": "kBWUmv6qHZ48"
       },
       "source": [
-        "We can see, that for each slide (i.e. **referencedSeriesInstanceUID**) there are multiple ANN Series. Looking at the **SeriesDescription**, we can assert what is described in the [Background](#Background) section of this notebook.\n",
+        "We can see, that for each slide (i.e. **referencedSeriesInstanceUID**) there are multiple ANN Series. All annotations have an **AnnotationCoordinateType** of \"2D\", meaning that the coordinates are two-dimensional coordinates in the image coordinate system (more information [here](https://highdicom.readthedocs.io/en/latest/package.html#highdicom.ann.AnnotationCoordinateTypeValues)). Looking at the **SeriesDescription**, we can assert what is described in the [Background](#Background) section of this notebook.\n",
         "\n",
         "*   Each slide has \"Monolayer regions of interest for cell classification\" annotations.\n",
         "*   For some slides, there is one ANN Series with \"Unlabeled cell bounding boxes\", while for others, there are multiple ANN Series containing \"Cell bounding boxes with cell type labels\" for different annotation sessions and the consensus labels.\n",
         "\n",
-        "ANN files contain one or multiple \"AnnotationGroups\" (for more explanation see the aforementioned [tutorial notebook]((https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/pathomics/microscopy_dicom_ann_intro.ipynb)) on DICOM ANNs).\n",
-        "Using `ann_group_index` we can get a little more information on what the individual annotation groups contain exactly. The following code cell queries the AnnotationGroupLabel - a human-readable label for the annotation group - as well as [coded values from controlled vocabularies](https://learn.canceridc.dev/dicom/coding-schemes) like SNOMED-CT for the category and type of the annotation.\n"
+        "ANN files contain one or multiple **\"AnnotationGroups\"** (for more explanation see the aforementioned [tutorial notebook]((https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/pathomics/microscopy_dicom_ann_intro.ipynb)) on DICOM ANNs).\n",
+        "Using `ann_group_index` we can get a little more information on what the individual annotation groups contain exactly. The following code cell queries the AnnotationGroupLabel - a human-readable label for the annotation group - as well as [coded values from controlled vocabularies](https://learn.canceridc.dev/dicom/coding-schemes) such as SNOMED-CT for the category and type of the annotation.\n"
       ]
     },
     {