public_data.md

Data

TODO

Histopathology (WSI databases)

• https://gtexportal.org/home/histologyPage
• https://cancerimagingarchive.net/datascope/cptac/
• https://camelyon17.grand-challenge.org/Data/
• https://www.cancerimagingarchive.net/histopathology-imaging-on-tcia/
• https://wiki.cancerimagingarchive.net/pages/vi

.action?pageId=33948919

• http://workbench-czi-cpw.mvm.ed.ac.uk/

Lung-specific:

• https://wiki.cancerimagingarchive.net/display/NLST/National+Lung+Screening+Trial

Breast-specific:

• http://gigadb.org/dataset/102207
• CAMELYON16 (lymph node metastasis from breast): https://camelyon17.grand-challenge.org/Data/, https://drive.google.com/drive/folders/0BzsdkU4jWx9BaXVHSXRJTnpLZU0?resourcekey=0-tyfGzeoOMAWlP_ogPt_4pw&usp=sharing
• CAMELYON17 (lymph node metastasis from breast): https://camelyon17.grand-challenge.org/Data/, https://drive.google.com/drive/folders/0BzsdkU4jWx9Bb19WNndQTlUwb2M?resourcekey=0-FREBAxB4QK4bt9Zch_g5Mg

Prostate-specific:

• Prostate cANcer graDe Assessment (PANDA) Challenge: https://www.kaggle.com/competitions/prostate-cancer-grade-assessment/overview

Databases of pathology with WSI (small or for educational purposes)

• https://figshare.com/articles/dataset/Tabula_Sapiens_H_E_Image_Collection/14962947
• https://digitalpathologyassociation.org/whole-slide-imaging-repository
• https://recutclub.com/index.php
• http://www.emouseatlas.org/emap/home.html
• https://www.virtualpathology.leeds.ac.uk/slides/library/index.php
• https://pathologycenter.jp/english/en_index.html

Pre-trained models

• VGGA16

• ResNet

• StarDist

• DeepCell

• CellPose

• Tumor-Infiltrating Lymphocytes Maps from TCGA H&E Whole Slide Pathology Images: https://wiki.cancerimagingarchive.net/pages/vi.action?pageId=33948919, https://stonybrookmedicine.app.box.com/v/cellreportspaper/folder/42003984813

• NuCLS crowdsourcing approach, dataset, and explainable deep-learning method: https://github.com/PathologyDataScience/NuCLS