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notebooks/pathomics/README.md

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This repository contains
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* 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.
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* 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.
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* a notebook (**Tutorial_MicroscopyBulkSimpleAnnotations.ipynb**) that shows how to work with bulk annotations encoded in DICOM using the example of nuclei annotations.
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* 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.
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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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