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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -79,6 +79,7 @@ This folder is dedicated to the notebooks focused on the digital pathology (path
* [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/microscopy_dicom_ann_intro.ipynb): introduction to working with bulk annotations encoded in DICOM using the example of nuclei annotations.
* [Working with DICOM Segmentations](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/pathomics/microscopy_dicom_seg_intro.ipynb): introduction to working with segmentations encoded in DICOM using the example of nuclei segmentations.

## [`analysis`](https://github.com/ImagingDataCommons/IDC-Tutorials/tree/master/notebooks/analysis)

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1 change: 1 addition & 0 deletions notebooks/pathomics/README.md
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Expand Up @@ -6,6 +6,7 @@ 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 (**microscopy_dicom_ann_intro.ipynb**.ipynb**) that shows how to work with bulk annotations encoded in DICOM using the example of nuclei annotations.
* a notebook (**microscopy_dicom_seg_intro.ipynb**.ipynb**) that shows how to work with segmentations encoded in DICOM using the example of nuclei segmentations.

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:

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