UCSF-ProstateMR: The University of California - San Francisco (UCSF) Prostate MRI (UCSF-ProstateMR) Dataset

This dataset provides a large dataset of 973 prostate MRI exams performed between January 2016 to March 2019 of all patients that underwent subsequent MRI/ultrasound fusion biopsy within one year at UCSF. Each exam includes registered T2, ADC and high B value DWI as well as a contoured whole gland segmentation of the prostate gland, up to 4 lesion segmentations in the form of bounding boxes, and approximated sextant segmentations. Corresponding fusion biopsy and nontargeted sextant (i.e. systematic) biopsy results in the form of gleason score converted to an ISUP/Gleason grade (with “0” corresponding to benign result) as well as PI-RADS scores, PSA density, presence of endorectal coil, prostate volume, patient age, an anonymized patient identifier, and patient race are available.

Citations

Publications that used this dataset

Velarde N, Westphalen AC, Nguyen HG, Neuhaus J, Shinohara K, Simko JP, Larson PE, Magudia K. 
US lesion visibility predicts clinically significant upgrade of prostate cancer by systematic biopsy. 
Abdominal Radiology. 2022 Mar;47(3):1133-41. doi: 10.1007/s00261-021-03389-x
https://pmc.ncbi.nlm.nih.gov/articles/PMC8863714/

Rajagopal A, Redekop E, Kemisetti A, Kulkarni R, Raman S, Sarma K, Magudia K, Arnold CW, Larson PE. 
Federated learning with research prototypes: application to multi-center MRI-based detection of prostate cancer with diverse histopathology. 
Academic radiology. 2023 Apr 1;30(4):644-57. doi: 10.1016/j.acra.2023.02.012
https://pmc.ncbi.nlm.nih.gov/articles/PMC10869141/

Rajagopal A, Westphalen AC, Velarde N, Simko JP, Nguyen H, Hope TA, Larson PE, Magudia K. 
Mixed supervision of histopathology improves prostate cancer classification from MRI. 
IEEE transactions on medical imaging. 2024 Mar 28;43(7):2610-22. doi: 10.1109/TMI.2024.3382909
https://pmc.ncbi.nlm.nih.gov/articles/PMC11361281/

Data Access (In Progress)

Tutorials

Get to Know the Dataset Notebook

Contributors

Project initiation and leadership - Kirti Magudia, MD, Peder Larson, PhD, and Antonio Westphalen, MD

Dataset Extraction - Kirti Magudia, MD

Curation - Kirti Magudia, MD, Nathan Velarde, Jeffry Simko, MD PhD, Hao Ngyuen, MD PhD

Data Management - Kirti Magudia, PhD, Abhejit Rajagopal, PhD, Mansour Abtahi, PhD