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Summary

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

Excerpt

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&EstainedE stained) images of corresponding radical prostatectomy specimens. The MRI scans also have a mapping of extent of prostate cancer on them [110.1002/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 [2PMCID: 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 [310.1016/j.compmedimag.2010.12.003] and checked for accuracy by an expert pathologist and radiologist. Deformable co-registration [4PMC3078156] 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

...

References

...

  • .


Localtab Group



Localtab
activetrue
titleData Access

Data Access 


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)

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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) 

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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



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Correspondence tables (XLSX, 22 kB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/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, Matlab

Number of Participants

28

16

Number of Studies

28

N/A

Number of Series

324N/A

Number of Images

32,508

114
Image Size (GB)4.476.8


Supporting Documentation

The data set is fully described in 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

...

  1. microvessel architecture and gleason grades of prostate cancer. J. Magn. Reson. Imaging, 43: 149-158. doi: https://doi.org/10.1002/jmri.24975

...

  1. (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)

...

  1. . https://doi.org/10.1118/1.3560879





Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy 

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

 

Localtab Group
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.

Data TypeDownload all or Query/Filter
Images (DICOM, 4.4 GB)Image Removed Image Removed
Annotated Whole Slide Pathology ImagesImage Removed
Fused Rad-Path Matlab FilesImage Removed Image Removed

Click the Versions tab for more info about data releases.

Localtab
titleDetailed Description

Detailed Description

Collection Statistics

 

Modalities

MRI, Pathology, Matlab

Number of Patients

28

Number of Studies

29

Number of Series

325

Number of Images

32508

Image Size (GB)4.4

Supporting Documentation

The data set is fully described in the following publications:

 

Singanamalli, A, Sparks, R, Rusu, M, Shih, N, Ziober, A, Tomaszewski, J, Rosen, M, Feldman, M, Madabhushi, A, “Identifying

in vivo DCE MRI markers associated with

Microvessel Architecture and Gleason Grades of Prostate Cancer—Preliminary Findings”, Journal of Magnetic Resonance Imaging,

microvessel architecture and gleason grades of prostate cancer. J. Magn. Reson. Imaging, 43: 149-158. doi:10.1002/jmri.24975

. [Epub ahead of print]

 (PMID:26110513).


Info
titlePublication Citation

Toth, R, Feldman, M, Yu, D, Tomaszewski, J, Madabhushi, A,

“Histostitcher™

“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

“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

“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).

Pathology and Matlab Data

Reconstructed, annotated whole slide pathology as well as fused Rad-Path matlab objects are also available at

https

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

 

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

Madabhushi, A., & Feldman, M. (2016). Fused Radiology-Pathology Prostate Dataset. The Cancer Imaging Archive.http://doi.org/10.79371118/K9/TCIA.2016.TLPMR1AM1.3560879


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

1

2 (Current)

Updated 11-30-2016

: 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)
Image Removed Image Removed


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
Image Removed
& 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
Image Removed Image Removed


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