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notebooks/pathomics/README.md

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# Introduction to working with digital pathology images in IDC
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This repository contains a short notebook (lung_cancer_cptac_DataExploration.ipynb) giving an idea on how to explore available collections of pathology whole-slide images (WSIs) in the IDC.
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More elaborate tutorials on 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 ["The NCI Imaging Data Commons as a platform for reproducible research in computational pathology"](https://doi.org/10.1016/j.cmpb.2023.107839).
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More elaborate tutorials on 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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> Schacherer, D. P., Herrmann, M. D., Clunie, D. A., Höfener, H., Clifford, W., Longabaugh, W. J. R., Pieper, S., Kikinis, R., Fedorov, A. & Homeyer, A. The NCI Imaging Data Commons as a platform for reproducible research in computational pathology. _Computer Methods and Programs in Biomedicine_. 107839 (2023). [doi:10.1016/j.cmpb.2023.107839](https://doi.org/10.1016/j.cmpb.2023.107839)
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<img src="IDCportal.png" width="700"/>

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