Merge pull request #79 from DanielaSchacherer/bulk_annotations_notebook

Bulk annotations notebook added

Author: fedorov

README.md

@@ -54,6 +54,7 @@ This folders contains notebooks that demonstrate the usage of the data in the sp
 This folder is dedicated to the notebooks focused on the digital pathology (pathomics) applications. The use of DICOM standard is relatively new in digital pathology, and this field is being actively developed, thus a dedicated folder for this.
 * [Getting started with pathology images in IDC](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/pathomics/getting_started_with_digital_pathology.ipynb): all of the pathology images in IDC are in DICOM Slide Microscopy format; this notebook will help you get started with using this representation and also searching IDC pathology images.
 * [Exploring IDC slide microscopy images metadata](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/pathomics/slide_microscopy_metadata_search.ipynb): introduction to the key metadata accompanying IDC slide microscopy images that can be used for subsetting data and building cohorts.
+* [Working with DICOM Microscopy Bulk Simple annotations](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/pathomics/Tutorial_MicroscopyBulkSimpleAnnotations.ipynb): introduction to working with bulk annotations encoded in DICOM using the example of nuclei annotations. 
 
 ## [`analysis`](https://github.com/ImagingDataCommons/IDC-Tutorials/tree/master/notebooks/analysis)
 

notebooks/pathomics/README.md

@@ -1,5 +1,8 @@
 # Introduction to working with digital pathology images in IDC
-This repository contains a short notebook (getting_started_with_digital_pathology.ipynb) giving an idea on how to explore and work with available collections of pathology whole-slide images (WSIs) in the IDC. 
+This repository contains 
+* a short notebook (getting_started_with_digital_pathology.ipynb) giving an idea on how to explore and work with available collections of pathology whole-slide images (WSIs) in the IDC. 
+* an notebook (slide_microscopy_metadata_search.ipynb) to introduce the key metadata accompanying IDC slide microscopy images that can be used for subsetting data and building cohorts.
+* a notebook (Tutorial_MicroscopyBulkSimpleAnnotations.ipynb) that shows how to work with bulk annotations encoded in DICOM using the example of nuclei annotations. 
 
 More tutorials that show, for example, how to train a tissue classification model can be found in the Github repository [idc-comppath-reproducibility](https://github.com/ImagingDataCommons/idc-comppath-reproducibility) as part of the publication below: