Grant Number:	5UH3CA225021-05 Interpret this number
Primary Investigator:	Saltz, Joel
Organization:	State University New York Stony Brook
Project Title:	Methods and Tools for Integrating Pathomics Data Into Cancer Registries
Fiscal Year:	2022

The goal of this project is to enrich SEER registry data with high‐quality population‐based biospecimen data in the form of digital pathology, machine learning based classifications and quantitative pathomics feature sets. We will create a well‐curated repository of high‐quality digitized pathology images for subjects whose data is being collected by the registries. These images will be processed to extract computational features and establish deep linkages with registry data, thus enabling the creation of information‐rich, population cohorts containing objective imaging and clinical attributes. Specific examples of digital Pathology derived feature sets include quantification of tumor infiltrating lymphocytes and segmentation and characterization of cancer or stromal nuclei. Features will also include spectral and spatial signatures of the underlying pathology. The scientific premise for this approach stems from increasing evidence that information extracted from digitized pathology images (pathomic features) are a quantitative surrogate of what is described in a pathology report. The important distinction being that these features are quantitative and reproducible, unlike human observations that are highly qualitative and subject to a high degree of inter‐ and intra‐observer variability. This dataset will provide, a unique, population‐wide tissue based view of cancer, and dramatically accelerate our understanding of the stages of disease progression, cancer outcomes, and predict and assess therapeutic effectiveness. This work will be carried out in collaboration with three SEER registries. We will partner with The New Jersey State Cancer Registry during the development phase of the project (UG3). During the validation phase of the project (UH3), the Georgia and Kentucky State Cancer Registries will join the project. The infrastructure will be developed in close collaboration with SEER registries to ensure consistency with registry processes, scalability and ability support creation of population cohorts that span multiple registries. We will deploy visual analytic tools to facilitate the creation of population cohorts for epidemiological studies, tools to support visualization of feature clusters and related whole‐slide images while providing advanced algorithms for conducting content based image retrieval. The scientific validation of the proposed environment will be undertaken through three studies in Prostate Cancer, Lymphoma and NSCLC, led by investigators at the three sites.




Attention De-sparsification Matters: Inducing diversity in digital pathology representation learning.
Authors: Kapse S. , Das S. , Zhang J. , Gupta R.R. , Saltz J. , Samaras D. , Prasanna P. .
Source: Medical Image Analysis, 2024 Apr; 93, p. 103070.
EPub date: 2023-12-28 00:00:00.0.
PMID: 38176354
Related Citations

Keratin 17 modulates the immune topography of pancreatic cancer.
Authors: Delgado-Coka L.A. , Horowitz M. , Torrente-Goncalves M. , Roa-Peña L. , Leiton C.V. , Hasan M. , Babu S. , Fassler D. , Oentoro J. , Karen Bai J.D. , et al. .
Source: Research Square, 2024-02-20 00:00:00.0; , .
EPub date: 2024-02-20 00:00:00.0.
PMID: 38464123
Related Citations

Understanding metric-related pitfalls in image analysis validation.
Authors: Reinke A. , Tizabi M.D. , Baumgartner M. , Eisenmann M. , Heckmann-Nötzel D. , Kavur A.E. , Rädsch T. , Sudre C.H. , Acion L. , Antonelli M. , et al. .
Source: Nature Methods, 2024 Feb; 21(2), p. 182-194.
EPub date: 2024-02-12 00:00:00.0.
PMID: 38347140
Related Citations

Metrics reloaded: recommendations for image analysis validation.
Authors: Maier-Hein L. , Reinke A. , Godau P. , Tizabi M.D. , Buettner F. , Christodoulou E. , Glocker B. , Isensee F. , Kleesiek J. , Kozubek M. , et al. .
Source: Nature Methods, 2024 Feb; 21(2), p. 195-212.
EPub date: 2024-02-12 00:00:00.0.
PMID: 38347141
Related Citations

Image-based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer.
Authors: Jahangir C.A. , Page D.B. , Broeckx G. , Gonzalez C.A. , Burke C. , Murphy C. , Reis-Filho J.S. , Ly A. , Harms P.W. , Gupta R.R. , et al. .
Source: The Journal Of Pathology, 2024-01-17 00:00:00.0; , .
EPub date: 2024-01-17 00:00:00.0.
PMID: 38230434
Related Citations

An Intelligent Search & Retrieval System (IRIS) and Clinical and Research Repository for Decision Support Based on Machine Learning and Joint Kernel-based Supervised Hashing.
Authors: Foran D.J. , Chen W. , Kurc T. , Gupta R. , Kaczmarzyk J.R. , Torre-Healy L.A. , Bremer E. , Ajjarapu S. , Do N. , Harris G. , et al. .
Source: Cancer Informatics, 2024; 23, p. 11769351231223806.
EPub date: 2024-02-04 00:00:00.0.
PMID: 38322427
Related Citations

PathLDM: Text conditioned Latent Diffusion Model for Histopathology.
Authors: Yellapragada S. , Graikos A. , Prasanna P. , Kurc T. , Saltz J. , Samaras D. .
Source: Ieee Winter Conference On Applications Of Computer Vision. Ieee Winter Conference On Applications Of Computer Vision, 2024 Jan; 2024, p. 5170-5179.
EPub date: 2024-04-09 00:00:00.0.
PMID: 38808304
Related Citations

ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification.
Authors: Kaczmarzyk J.R. , Gupta R. , Kurc T.M. , Abousamra S. , Saltz J.H. , Koo P.K. .
Source: Computer Methods And Programs In Biomedicine, 2023 Sep; 239, p. 107631.
EPub date: 2023-05-30 00:00:00.0.
PMID: 37271050
Related Citations

Spatial analyses of immune cell infiltration in cancer: current methods and future directions. A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer.
Authors: Page D.B. , Broeckx G. , Jahangir C.A. , Verbandt S. , Gupta R.R. , Thagaard J. , Khiroya R. , Kos Z. , Abduljabbar K. , Acosta Haab G. , et al. .
Source: The Journal Of Pathology, 2023-08-23 00:00:00.0; , .
EPub date: 2023-08-23 00:00:00.0.
PMID: 37608771
Related Citations

Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: a report of the international immuno-oncology biomarker working group.
Authors: Thagaard J. , Broeckx G. , Page D.B. , Jahangir C.A. , Verbandt S. , Kos Z. , Gupta R. , Khiroya R. , Abduljabbar K. , Acosta Haab G. , et al. .
Source: The Journal Of Pathology, 2023-08-23 00:00:00.0; , .
EPub date: 2023-08-23 00:00:00.0.
PMID: 37608772
Related Citations

Unsupervised Stain Decomposition via Inversion Regulation for Multiplex Immunohistochemistry Images.
Authors: Abousamra S. , Fassler D. , Yao J. , Gupta R. , Kurc T. , Escobar-Hoyos L. , Samaras D. , Shroyer K. , Saltz J. , Chen C. .
Source: Proceedings Of Machine Learning Research, 2023 Jul; 227, p. 74-94.
PMID: 38817539
Related Citations

Topology-Guided Multi-Class Cell Context Generation for Digital Pathology.
Authors: Abousamra S. , Gupta R. , Kurc T. , Samaras D. , Saltz J. , Chen C. .
Source: Proceedings. Ieee Computer Society Conference On Computer Vision And Pattern Recognition, 2023 Jun; 2023, p. 3323-3333.
EPub date: 2023-08-22 00:00:00.0.
PMID: 38741683
Related Citations

Effective and efficient active learning for deep learning-based tissue image analysis.
Authors: Meirelles A.L.S. , Kurc T. , Kong J. , Ferreira R. , Saltz J. , Teodoro G. .
Source: Bioinformatics (oxford, England), 2023-04-03 00:00:00.0; 39(4), .
PMID: 36943380
Related Citations

Deep Learning for Survival Analysis in Breast Cancer with Whole Slide Image Data.
Authors: Liu H. , Kurc T. .
Source: Bioinformatics (oxford, England), 2022-06-08 00:00:00.0; , .
EPub date: 2022-06-08 00:00:00.0.
PMID: 35674341
Related Citations

Spatial Characterization of Tumor-Infiltrating Lymphocytes and Breast Cancer Progression.
Authors: Fassler D.J. , Torre-Healy L.A. , Gupta R. , Hamilton A.M. , Kobayashi S. , Van Alsten S.C. , Zhang Y. , Kurc T. , Moffitt R.A. , Troester M.A. , et al. .
Source: Cancers, 2022-04-26 00:00:00.0; 14(9), .
EPub date: 2022-04-26 00:00:00.0.
PMID: 35565277
Related Citations

An Expandable Informatics Framework for Enhancing Central Cancer Registries with Digital Pathology Specimens, Computational Imaging Tools, and Advanced Mining Capabilities.
Authors: Foran D.J. , Durbin E.B. , Chen W. , Sadimin E. , Sharma A. , Banerjee I. , Kurc T. , Li N. , Stroup A.M. , Harris G. , et al. .
Source: Journal Of Pathology Informatics, 2022; 13, p. 5.
EPub date: 2022-01-05 00:00:00.0.
PMID: 35136672
Related Citations

Deep learning-based approach to the characterization and quantification of histopathology in mouse models of colitis.
Authors: Kobayashi S. , Shieh J. , Ruiz de Sabando A. , Kim J. , Liu Y. , Zee S.Y. , Prasanna P. , Bialkowska A.B. , Saltz J.H. , Yang V.W. .
Source: Plos One, 2022; 17(8), p. e0268954.
EPub date: 2022-08-29 00:00:00.0.
PMID: 36037173
Related Citations

Multi-Class Cell Detection Using Spatial Context Representation.
Authors: Abousamra S. , Belinsky D. , Van Arnam J. , Allard F. , Yee E. , Gupta R. , Kurc T. , Samaras D. , Saltz J. , Chen C. .
Source: Proceedings. Ieee International Conference On Computer Vision, 2021 Oct; 2021, p. 3985-3994.
EPub date: 2022-02-28 00:00:00.0.
PMID: 38783989
Related Citations

A DICOM Framework for Machine Learning and Processing Pipelines Against Real-time Radiology Images.
Authors: Kathiravelu P. , Sharma P. , Sharma A. , Banerjee I. , Trivedi H. , Purkayastha S. , Sinha P. , Cadrin-Chenevert A. , Safdar N. , Gichoya J.W. .
Source: Journal Of Digital Imaging, 2021 Aug; 34(4), p. 1005-1013.
EPub date: 2021-08-17 00:00:00.0.
PMID: 34405297
Related Citations

Understanding Scanner Utilization With Real-Time DICOM Metadata Extraction.
Authors: Kathiravelu P. , Sharma A. , Sharma P. .
Source: Ieee Access : Practical Innovations, Open Solutions, 2021; 9, p. 10621-10633.
EPub date: 2021-01-11 00:00:00.0.
PMID: 35966128
Related Citations

Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images.
Authors: Fassler D.J. , Abousamra S. , Gupta R. , Chen C. , Zhao M. , Paredes D. , Batool S.A. , Knudsen B.S. , Escobar-Hoyos L. , Shroyer K.R. , et al. .
Source: Diagnostic Pathology, 2020-07-28 00:00:00.0; 15(1), p. 100.
EPub date: 2020-07-28 00:00:00.0.
PMID: 32723384
Related Citations

Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer.
Authors: Le H. , Gupta R. , Hou L. , Abousamra S. , Fassler D. , Torre-Healy L. , Moffitt R.A. , Kurc T. , Samaras D. , Batiste R. , et al. .
Source: The American Journal Of Pathology, 2020 Jul; 190(7), p. 1491-1504.
EPub date: 2020-04-08 00:00:00.0.
PMID: 32277893
Related Citations

AI in Medical Imaging Informatics: Current Challenges and Future Directions.
Authors: Panayides A.S. , Amini A. , Filipovic N.D. , Sharma A. , Tsaftaris S.A. , Young A. , Foran D. , Do N. , Golemati S. , Kurc T. , et al. .
Source: Ieee Journal Of Biomedical And Health Informatics, 2020 Jul; 24(7), p. 1837-1857.
PMID: 32609615
Related Citations

Dataset of segmented nuclei in hematoxylin and eosin stained histopathology images of ten cancer types.
Authors: Hou L. , Gupta R. , Van Arnam J.S. , Zhang Y. , Sivalenka K. , Samaras D. , Kurc T.M. , Saltz J.H. .
Source: Scientific Data, 2020-06-19 00:00:00.0; 7(1), p. 185.
EPub date: 2020-06-19 00:00:00.0.
PMID: 32561748
Related Citations

Optimizing parameter sensitivity analysis of large-scale microscopy image analysis workflows with multilevel computation reuse.
Authors: Barreiros W. , Moreira J. , Kurc T. , Kong J. , Melo A.C.M.A. , Saltz J.H. , Teodoro G. .
Source: Concurrency And Computation : Practice & Experience, 2020-01-25 00:00:00.0; 32(2), .
EPub date: 2019-06-24 00:00:00.0.
PMID: 32669980
Related Citations

Two well-differentiated pancreatic neuroendocrine tumor mouse models.
Authors: Wong C. , Tang L.H. , Davidson C. , Vosburgh E. , Chen W. , Foran D.J. , Notterman D.A. , Levine A.J. , Xu E.Y. .
Source: Cell Death And Differentiation, 2020 01; 27(1), p. 269-283.
EPub date: 2019-06-03 00:00:00.0.
PMID: 31160716
Related Citations

Segmentation and Classification in Digital Pathology for Glioma Research: Challenges and Deep Learning Approaches.
Authors: Kurc T. , Bakas S. , Ren X. , Bagari A. , Momeni A. , Huang Y. , Zhang L. , Kumar A. , Thibault M. , Qi Q. , et al. .
Source: Frontiers In Neuroscience, 2020; 14, p. 27.
EPub date: 2020-02-21 00:00:00.0.
PMID: 32153349
Related Citations

Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer.
Authors: Kos Z. , Roblin E. , Kim R.S. , Michiels S. , Gallas B.D. , Chen W. , van de Vijver K.K. , Goel S. , Adams S. , Demaria S. , et al. .
Source: Npj Breast Cancer, 2020; 6, p. 17.
EPub date: 2020-05-12 00:00:00.0.
PMID: 32411819
Related Citations

Multi-objective Parameter Auto-tuning for Tissue Image Segmentation Workflows.
Authors: Taveira L.F.R. , Kurc T. , Melo A.C.M.A. , Kong J. , Bremer E. , Saltz J.H. , Teodoro G. .
Source: Journal Of Digital Imaging, 2019 Jun; 32(3), p. 521-533.
PMID: 30402669
Related Citations

Robust Histopathology Image Analysis: to Label or to Synthesize?
Authors: Hou L. , Agarwal A. , Samaras D. , Kurc T.M. , Gupta R.R. , Saltz J.H. .
Source: Proceedings. Ieee Computer Society Conference On Computer Vision And Pattern Recognition, 2019 Jun; 2019, p. 8533-8542.
EPub date: 2020-01-09 00:00:00.0.
PMID: 34025103
Related Citations

Sensitivity analysis in digital pathology: Handling large number of parameters with compute expensive workflows.
Authors: Gomes J. , Barreiros W. , Kurc T. , Melo A.C.M.A. , Kong J. , Saltz J.H. , Teodoro G. .
Source: Computers In Biology And Medicine, 2019 05; 108, p. 371-381.
EPub date: 2019-03-13 00:00:00.0.
PMID: 31054503
Related Citations

Sparse Autoencoder for Unsupervised Nucleus Detection and Representation in Histopathology Images.
Authors: Hou L. , Nguyen V. , Kanevsky A.B. , Samaras D. , Kurc T.M. , Zhao T. , Gupta R.R. , Gao Y. , Chen W. , Foran D. , et al. .
Source: Pattern Recognition, 2019 Feb; 86, p. 188-200.
EPub date: 2018-09-13 00:00:00.0.
PMID: 30631215
Related Citations

Unsupervised Domain Adaptation for Classification of Histopathology Whole-Slide Images.
Authors: Ren J. , Hacihaliloglu I. , Singer E.A. , Foran D.J. , Qi X. .
Source: Frontiers In Bioengineering And Biotechnology, 2019; 7, p. 102.
EPub date: 2019-05-15 00:00:00.0.
PMID: 31158269
Related Citations

Statistical Analysis of Survival Models Using Feature Quantification on Prostate Cancer Histopathological Images.
Authors: Ren J. , Singer E.A. , Sadimin E. , Foran D.J. , Qi X. .
Source: Journal Of Pathology Informatics, 2019; 10, p. 30.
EPub date: 2019-09-27 00:00:00.0.
PMID: 31620309
Related Citations

Recurrence analysis on prostate cancer patients with Gleason score 7 using integrated histopathology whole-slide images and genomic data through deep neural networks.
Authors: Ren J. , Karagoz K. , Gatza M.L. , Singer E.A. , Sadimin E. , Foran D.J. , Qi X. .
Source: Journal Of Medical Imaging (bellingham, Wash.), 2018 Oct; 5(4), p. 047501.
EPub date: 2018-11-15 00:00:00.0.
PMID: 30840742
Related Citations

Adversarial Domain Adaptation for Classification of Prostate Histopathology Whole-Slide Images.
Authors: Ren J. , Hacihaliloglu I. , Singer E.A. , Foran D.J. , Qi X. .
Source: Medical Image Computing And Computer-assisted Intervention : Miccai ... International Conference On Medical Image Computing And Computer-assisted Intervention, 2018 Sep; 11071, p. 201-209.
EPub date: 2018-09-26 00:00:00.0.
PMID: 30465047
Related Citations

Differentiation among prostate cancer patients with Gleason score of 7 using histopathology whole-slide image and genomic data.
Authors: Ren J. , Karagoz K. , Gatza M. , Foran D.J. , Qi X. .
Source: Proceedings Of Spie--the International Society For Optical Engineering, 2018 Feb; 10579, .
EPub date: 2018-03-06 00:00:00.0.
PMID: 30662142
Related Citations

Computer aided analysis of prostate histopathology images to support a refined Gleason grading system.
Authors: Ren J. , Sadimin E. , Foran D.J. , Qi X. .
Source: Proceedings Of Spie--the International Society For Optical Engineering, 2017 Jan; 10133, .
EPub date: 2017-02-24 00:00:00.0.
PMID: 30828124
Related Citations