The Cancer Imaging Archive (TCIA) Public Access

Space shortcuts

Child pages
  • Fused Radiology-Pathology Prostate Dataset (Prostate Fused-MRI-Pathology)

Versions Compared

Old Version 2

changes.mady.by.user Ashish Sharma

Saved on

compared with

New Version Current

changes.mady.by.user Jeff Tobler

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

Summary

Redirect
delay5
locationhttps://www.cancerimagingarchive.net/collection/prostate-fused-mri-pathology/

Excerpt

This is a fused rad-path prostate collection

...

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.

Acknowledgement

  • 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.

...


400
Localtab Group



Click the Versions tab for more info about data releases.

Data Access (Pathology)

 Browse the table below to view reconstructed, annotated whole slide pathology as well as fused Rad-Path matlab objects.

https://pathology.cancerimagingarchive.net/pathdata/

800
Localtab
activetrue
titleData Access

Data

Access (Radiology) Choosing the Download option will provide you with a file to launch the TCIA Download Manager to download the entire collection. If you want to browse or filter the data to select only specific scans/studies please use the Search option.

Access 


Data TypeDownload all or Query/FilterLicense
Images (DICOM,
xxxGB)
Image Removed Image Removed
Widget Connector
width
4.4 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/23691514/doiJNLP-auLIj9wT-Prostate_Fused-MRI-Pathologyv1.tcia?version=1&modificationDate=1534787026838&api=v2



Tcia button generator
labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?CollectionCriteria=Prostate%20Fused-MRI-Pathology

Prostate Fused-MRI-Pathology

  

(Download requires the NBIA Data Retriever)

Tcia cc by 3

Annotated Whole Slide Pathology Images & Annotations (Tiff, XML 76.8 GB)


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6Ijc0NSIsInBhc3Njb2RlIjoiM2RmNWQwYjc5M2QzZGU0N2YwNTExOTc4YWFmNmFkNjBlMTYwMTA1YyIsInBhY2thZ2VfaWQiOiI3NDUiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=



Tcia button generator
labelSearch
urlhttps://pathdb.cancerimagingarchive.net/imagesearch?f[0]=collection:prostate_fused_mri_pathology



   

(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 

Tcia cc by 3

Fused Rad-Path Matlab Files (zip, 65 kB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/23691514/fused_prostate_matlab.zip?version=1&modificationDate=1476802701461&api=v2



Tcia cc by 3

Correspondence tables (XLSX, 22 kB)


Tcia button generator
urlhttps://
pathology
wiki.cancerimagingarchive.net/download/
pathdata/		height
attachments/23691514/histo_MR_Correspondence.xlsx?api=v2



Tcia cc by 3


Click the Versions tab for more info about data releases.

Nci_crdc additional resources




Localtab
titleDetailed Description

Detailed Description


Collection Statistics

 

Radiology Image Statistics

Pathology Image Statistics

Modalities

MRI

Pathology,
Path,
Matlab

Number of

Patients

Participants

28

 
16

Number of Studies

 

28

N/A

Number of Series

324
 
N/A

Number of Images

 

32,508

114
Image Size (GB)
 
4.476.8


Supporting Documentation

The dataset data set is most fully described in detail in

 

Info
titleReferences

1

 

the following publications:

  1. 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: https://doi.org/10.1002/jmri.24975 (PMID:26110513).

  2. 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
  3. 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
  4. 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





Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy 

 This collection is freely available to browse, download, and use for commercial, scientific and educational purposes as outlined in the Creative Commons Attribution 3.0 Unported License.  See TCIA's Data Usage Policies and Restrictions for additional details. Questions may be directed to help@cancerimagingarchive.net.

Please be sure to include the following citations in your work if you use this data set:

Info
titleData Citation

 

Info
titlePublication Citation

 

Tcia limited license policy

Info
titleData 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


Info
titlePublication Citation

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).


Info
titlePublication Citation

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


Info
titlePublication Citation

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


Info
titlePublication Citation

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

Info
titlePublication Citation

 


Info
titleTCIA Citation

Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. (paper). DOI: https://doi.org/10.1007/s10278-013-9622-7


Other Publications Using This Data

TCIA maintains a list of publications which leverage our data. At this time we are not aware of any publications based on this data. If you have a publication you'd like to add, please contact the TCIA's Helpdesk.

  1. 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
  2. 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 
  3. 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 





Localtab
titleVersions

Version 2 (Current): Updated 2023/04/10

Data TypeDownload all or Query/FilterLicense
Images (DICOM, 4.4 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/23691514/doiJNLP-auLIj9wT-Prostate_Fused-MRI-Pathologyv1.tcia?version=1&modificationDate=1534787026838&api=v2



Tcia button generator
labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?CollectionCriteria=Prostate%20Fused-MRI-Pathology

Prostate Fused-MRI-Pathology

  

(Download requires the NBIA Data Retriever)

Tcia cc by 3

Annotated Whole Slide Pathology Images & Annotations (Tiff, XML 76.8 GB)

Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6Ijc0NSIsInBhc3Njb2RlIjoiM2RmNWQwYjc5M2QzZGU0N2YwNTExOTc4YWFmNmFkNjBlMTYwMTA1YyIsInBhY2thZ2VfaWQiOiI3NDUiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=


Tcia button generator
labelSearch
urlhttps://pathdb.cancerimagingarchive.net/imagesearch?f[0]=collection:prostate_fused_mri_pathology


(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 

Tcia cc by 3

Fused Rad-Path Matlab Files


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/23691514/fused_prostate_matlab.zip?version=1&modificationDate=1476802701461&api=v2



Tcia cc by 3

Correspondence tables (XLSX)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/23691514/histo_MR_Correspondence.xlsx?api=v2



Tcia cc by 3

Added a correspondence xlsx between MR and Pathology slides, imaging data are unchanged. 

Version 1: Updated 2016/11/30


Data TypeDownload all or Query/Filter
Images (DICOM, 4.4 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/23691514/doiJNLP-auLIj9wT-Prostate_Fused-MRI-Pathologyv1.tcia?version=1&modificationDate=1534787026838&api=v2



Tcia button generator
labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?CollectionCriteria=Prostate%20Fused-MRI-Pathology


  

(Download requires the NBIA Data Retriever)

Annotated Whole Slide Pathology Images & Annotations (Tiff, XML 76.8 GB)


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjUzNSIsInBhc3Njb2RlIjoiMGUwNWFjMmU0MWNkYWRmZTA1ZGYxNzZjNjRiMzM5MDc3OGNjMTI5MyIsInBhY2thZ2VfaWQiOiI1MzUiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=



Tcia button generator
labelSearch
urlhttps://pathdb.cancerimagingarchive.net/imagesearch?f[0]=collection:prostate_fused_mri_pathology



       

(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package)             

Fused Rad-Path MATLAB Files


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/23691514/fused_prostate_matlab.zip?version=1&modificationDate=1476802701461&api=v2