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Prostate Fused-MRI-Pathology | Fused Radiology-Pathology Prostate Dataset
DOI: 10.7937/k9/TCIA.2016.tlpmr1am | Data Citation Required | Image Collection
| Location | Species | Subjects | Data Types | Cancer Types | Size | Status | Updated | |
|---|---|---|---|---|---|---|---|---|
| Prostate | Human | 28 | MR, Histopathology | Prostate Cancer | Image Analyses | Public, Complete | 2023/04/10 |
Summary
This collection comprises a total of 28 3 Tesla T1-weighted, T2-weighted, Diffusion weighted and Dynamic Contrast Enhanced prostate MRI along with accompanying digitized histopathology (H&E stained) images of corresponding radical prostatectomy specimens. The MRI scans also have a mapping of extent of prostate cancer on them [10.1002/jmri.24975]. Each surgically excised prostate specimen was originally sectioned and quartered resulting in 4 slides for each section. Each of these individual slides was digitized at 20x magnification using an Aperio slide scanner resulting in a set of 4 .svs images. Each of the 4 .svs images were then digitally stitched together to constitute a pseudo-whole mount section (.tiff) using the program in [PMCID: PMC4023035]. Annotations of cancer presence on the pseudo-whole mount sections were made by an expert pathologist. Slice correspondences were established between the individual T2w MRI and stitched pseudo-whole mount sections by the program in [10.1016/j.compmedimag.2010.12.003] and checked for accuracy by an expert pathologist and radiologist. Deformable co-registration [PMC3078156] was employed to spatially co-registered the corresponding radiologic and histopathologic tissue sections to map disease extent onto the corresponding MRI scans.
Data Access
Version 2: Updated 2023/04/10
Added a correspondence xlsx between MR and Pathology slides, imaging data are unchanged.
| Title | Data Type | Format | Access Points | Subjects | License | |||
|---|---|---|---|---|---|---|---|---|
| Images | MR | DICOM | Download requires NBIA Data Retriever |
28 | 28 | 324 | 32,508 | CC BY 3.0 |
| Annotated Whole Slide Pathology Images & Annotations | Histopathology | XML and TIFF | Download requires IBM-Aspera-Connect plugin |
16 | 114 | CC BY 3.0 | ||
| Fused Rad-Path Matlab Files | ZIP, MHA, and MATLAB | 15 | CC BY 3.0 | |||||
| Correspondence tables | XLSX | CC BY 3.0 |
Additional Resources for this Dataset
The NCI Cancer Research Data Commons (CRDC) provides access to additional data and a cloud-based data science infrastructure that connects data sets with analytics tools to allow users to share, integrate, analyze, and visualize cancer research data.
- Imaging Data Commons (IDC) (Imaging Data)
Citations & Data Usage Policy
Data Citation Required: Users must abide by the TCIA Data Usage Policy and Restrictions. Attribution must include the following citation, including the Digital Object Identifier:
Data Citation |
|
|
Madabhushi, A., & Feldman, M. (2016). Fused Radiology-Pathology Prostate Dataset (Prostate Fused-MRI-Pathology) . The Cancer Imaging Archive. doi; 10.7937/k9/TCIA.2016.tlpmr1am |
Acknowledgements
- Data collection and analysis was provided by Anant Madabhushi, PhD, Case Western Reserve University and Michael D. Feldman, MD, PhD, Hospital at the University of Pennsylvania.
- This work was supported by NIH R01CA136535.
Related Publications
Publications by the Dataset Authors
The authors recommended this paper as the best source of additional information about this dataset:
Singanamalli, A. , Rusu, M. , Sparks, R. E., Shih, N. N., Ziober, A. , Wang, L. , Tomaszewski, J. , Rosen, M. , Feldman, M. and Madabhushi, A. (2016), Identifying in vivo DCE MRI markers associated with microvessel architecture and gleason grades of prostate cancer. J. Magn. Reson. Imaging, 43: 149-158. doi: 10.1002/jmri.24975 (PMID:26110513).
Toth, R, Feldman, M, Yu, D, Tomaszewski, J, Madabhushi, A, “Histostitcher™: An Informatics Software Platform for Reconstructing Whole-Mount Prostate Histology using the Extensible Imaging Platform (XIP™) Framework,” Journal of Pathology Informatics, vol. 5, pg. 8, 2014 (PMID: 24843820, PMCID: PMC4023035). https://doi.org/10.4103/2153-3539.129441
Xiao, G, Bloch, N, Chappelow, J, Genega, E, Rofsky, N, Lenkinsky, R, Tomaszewski, J, Feldman, M, Rosen, M, Madabhushi, A, “Determining Histology-MRI Slice Correspondences for Defining MRI-based Disease Signatures of Prostate Cancer,” Special Issue of Computerized Medical Imaging and Graphics on Whole Slide Microscopic Image Processing, vol. 35[7-8], pp. 568-78, 2011 (PMID: 21255974). https://doi.org/10.1016/j.compmedimag.2010.12.003
Chappelow, J, Bloch, N., Rofsky, N, Genega, E, Lenkinski, R, DeWolf, W, Madabhushi, A, “Elastic Registration of Multimodal Prostate MRI and Histology via Multi-Attribute Combined Mutual Information,” Medical Physics, vol. 38[4], pp. 2005-2018, 2011 (PMID: 21626933). https://doi.org/10.1118/1.3560879
No publications by dataset authors were found.
Research Community Publications
TCIA maintains a list of publications which leverage our data. If you have a publication you’d like to add, please contact TCIA’s Helpdesk.
The below were found to have cited this dataset:
- Brunese, L., Mercaldo, F., Reginelli, A., & Santone, A. (2020). Formal methods for prostate cancer gleason score and treatment prediction using radiomic biomarkers. Magnetic resonance imaging, 66, 165-175. doi:https://doi.org/10.1016/j.mri.2019.08.030
- Chatzoudis, P. (2018). MRI prostate cancer radiomics: Assessment of effectiveness and perspectives. (Master of Biomedical Engineering). Delft University of Technology, Delft, Netherlands. Retrieved from http://resolver.tudelft.nl/uuid:b8459bdb-1761-4f17-8807-e3b1cf7da629
- Duran, A., Dussert, G., Rouviere, O., Jaouen, T., Jodoin, P. M., & Lartizien, C. (2022). ProstAttention-Net: A deep attention model for prostate cancer segmentation by aggressiveness in MRI scans. Medical image analysis, 77, 102347. doi:https://doi.org/10.1016/j.media.2021.102347
The authors recommend that the below publications fully describe the data:
Previous Versions
Version 1: Updated 2016/11/30
| Title | Data Type | Format | Access Points | License | ||||
|---|---|---|---|---|---|---|---|---|
| Images | DICOM | Download requires NBIA Data Retriever |
||||||
| Annotated Whole Slide Pathology Images & Annotations | XML and TIFF | Download requires IBM-Aspera-Connect plugin |
||||||
| Fused Rad-Path MATLAB Files |