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MRI Pathology slides Prostate

Prostate Fused-MRI-Pathology

Fused Radiology-Pathology Prostate Dataset (PROSTATE-FUSED-MRI-PATHOLOGY)

Prostate MRI before prostatectomy paired with digitized histology of the removed glands, cancer annotations and registration files, for mapping tumor extent from pathology onto MRI. 28 men with prostate cancer scanned at 3 T.

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Overview

The Fused Radiology-Pathology Prostate Dataset pairs in vivo prostate MRI with digitized histology of the same glands after radical prostatectomy. It was contributed by Anant Madabhushi (Case Western Reserve University) and Michael D. Feldman (Hospital of the University of Pennsylvania) and published on The Cancer Imaging Archive in 2016. Version 2 (April 2023) added a table that links MR slices to pathology slides; the images did not change. The collection supports work on MRI-histology registration, tumor mapping on MRI and imaging markers of tumor grade.

Composition

All 28 subjects are men with prostate cancer, each with one MR study (324 DICOM series, 32,508 images). Every subject has T2-weighted and multiphase dynamic contrast-enhanced series, 25 have separate pre-contrast T1-weighted series and 12 have diffusion-weighted series with ADC maps. Annotated pseudo-whole-mount H&E pathology images exist for 16 subjects (114 images), and registration files in MATLAB and MHA format for 15. Spreadsheets list the slice correspondences between MRI and pathology.

Acquisition

All series come from a 3 T Siemens Verio, according to the DICOM headers. The paper recommended by the authors describes an endorectal coil and a T1-weighted VIBE sequence for DCE in its 23-patient analysis. Each excised gland was cut into sections, each section into quarters, and each quarter slide was scanned at 20x on an Aperio scanner. The four quarter images were then stitched into one pseudo-whole-mount section.

Annotations

An expert pathologist outlined cancer on the stitched sections. Software matched each section to a T2-weighted MR slice, and a pathologist and a radiologist checked the matches. Deformable registration then carried the cancer outlines from histology onto the MRI, giving a map of tumor extent on the MR images.

Known limitations

  • Pathology images and registration files cover only about half of the subjects (16 and 15 of 28).
  • The protocol varies between subjects: diffusion imaging is missing for more than half, and series naming differs.
  • Age and Gleason grade are not given for the 28 subjects on the collection page.
  • All MR data come from a single scanner model.

Cohort

Aggregate numbers from the sources below. Bars are relative to the 28 subjects.

Sex

  • Male 28 100%

getPatientStudy, PatientSex in TCIA public NBIA API, series and patient metadata of the collection (CC BY 3.0, no account needed), getSeries and getPatientStudy

Contrast / sequence

Groups can overlap

  • T2-weighted 28 100%
  • DCE perfusion 28 100%
  • T1-weighted 25 89%
  • Diffusion-weighted 12 43%
  • T1-weighted, contrast enhanced 7 25%

PatientID, SeriesDescription, PatientID, SeriesDescription, ImageCount in TCIA public NBIA API, series and patient metadata of the collection (CC BY 3.0, no account needed), getSeries and getPatientStudy

Field strength

  • 3 T 28 100%

Summary in TCIA PROSTATE-FUSED-MRI-PATHOLOGY collection page (version 2, updated 2023/04/10)

Modality

  • MRI 28 100%
  • Pathology slides 16 57%

Data Access table in TCIA PROSTATE-FUSED-MRI-PATHOLOGY collection page (version 2, updated 2023/04/10)

Condition

Groups can overlap

  • Prostate cancer 28 100%

Summary in TCIA PROSTATE-FUSED-MRI-PATHOLOGY collection page (version 2, updated 2023/04/10)

Scanner vendor

  • Siemens Healthineers 28 100%

Manufacturer, ManufacturerModelName in TCIA public NBIA API, series and patient metadata of the collection (CC BY 3.0, no account needed), getSeries and getPatientStudy

Contrast combinations

How many subjects have exactly each set of contrasts.

T1wT1w_ceT2wdwidceSubjects with exactly this set
13
7
5
3

PatientID, SeriesDescription, ImageCount in TCIA public NBIA API, series and patient metadata of the collection (CC BY 3.0, no account needed), getSeries and getPatientStudy

License and access

Our reading of the license, not legal advice. Before you use the data, read the original license and confirm that your use is allowed. We take no responsibility for how you use a dataset. Full disclaimer

Access
Open download

Download without an account

MRI as DICOM via the TCIA Data Retriever, whole-slide pathology images and annotations via IBM Aspera, and the registration MATLAB files and correspondence tables as direct downloads.

Access page

Creative Commons Attribution 3.0 Unported

Older version of CC BY. Use, share and adapt the data for any purpose, including commercial use, as long as you credit the creators.

Every item on the TCIA collection page is listed under CC BY 3.0. TCIA also asks users to follow its Data Usage Policy and to cite the dataset DOI.

Original license text Version read: 3.0 Checked 2026-10-07

What you can do

  • Yes
  • Yes
  • Yes
  • Yes
  • Yes

What you can share

  • Yes
  • Yes
  • Yes

What you must do

  • Yes
  • Share alike No
  • No
  • No
  • Manuscript review No
  • Release code No
  • Return results No
  • Delete after use No

Limits

  • No
  • Location limits No

Citation

Madabhushi A, Feldman M. (2016). Fused Radiology-Pathology Prostate Dataset (Prostate Fused-MRI-Pathology). The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.TLPMR1AM

Sources

Every number on this page comes from one of these documents. Each chart names the table or page it is taken from. The raw numbers are in stats.csv.