adapted query to use ann_index

Author: DanielaSchacherer

notebooks/pathomics/microscopy_dicom_ann_intro.ipynb

@@ -140,7 +140,7 @@
    },
    "source": [
     "## Accessing DICOM ANNs from the IDC\n",
-    "To access and download the ANNs files, we utilize the Python package [idc-index](https://github.com/ImagingDataCommons/idc-index) that facilitates querying metadata and downloading DICOM files from the IDC. Since all available ANN documents in the IDC have a combined size of 1.82 TB - for the demonstration in this tutorial we will use only a single ANN from the TCGA-BRCA collection as an example."
+    "To access and download the ANNs files, we utilize the Python package [idc-index](https://github.com/ImagingDataCommons/idc-index) that facilitates querying metadata and downloading DICOM files from the IDC. Since all available ANN objects in the IDC have a combined size of 1.82 TB - for the demonstration in this tutorial we will use only a single ANN from the TCGA-BRCA collection as an example."
    ]
   },
   {
@@ -152,7 +152,8 @@
    "outputs": [],
    "source": [
     "idc_client = index.IDCClient() # set-up idc_client\n",
-    "idc_client.fetch_index('sm_instance_index')"
+    "idc_client.fetch_index('sm_instance_index') # fetch additional sm_instance_index containing all slide microscopy (SM) instances available in the IDC\n",
+    "idc_client.fetch_index('ann_index') # fetch additional ann_index containing all ANN series available in the IDC"
    ]
   },
   {
@@ -163,24 +164,24 @@
    },
    "outputs": [],
    "source": [
-    "query_sr = '''\n",
+    "query_ann = '''\n",
     "SELECT\n",
-    "    SeriesInstanceUID,\n",
+    "    index.SeriesInstanceUID,\n",
     "    StudyInstanceUID,\n",
     "    PatientID,\n",
     "    collection_id\n",
     "FROM\n",
     "    index\n",
-    "WHERE\n",
+    "JOIN \n",
+    "    ann_index ON ann_index.SeriesInstanceUID = index.SeriesInstanceUID\n",
+    "WHERE \n",
     "    analysis_result_id = 'Pan-Cancer-Nuclei-Seg-DICOM' \n",
-    "    # Microscopy Bulk Simple Annotations SOP Class UID - more reliable than Modality = \"ANN\"\n",
-    "    AND SOPClassUID = \"1.2.840.10008.5.1.4.1.1.91.1\"\n",
     "    AND collection_id = 'tcga_luad'\n",
     "ORDER BY\n",
     "    crdc_series_uuid\n",
     "LIMIT 1\n",
     "'''\n",
-    "pan_ann = idc_client.sql_query(query_sr)"
+    "pan_ann = idc_client.sql_query(query_ann)"
    ]
   },
   {