2020 Publications:
1.Sharma A, Tarbox L, Kurc T, Bona J, Smith K, Kathiravelu P, Bremer E, Saltz J, Prior F. PRISM: A Platform for Imaging in Precision Medicine, JCO Clinical Cancer Informatics, 2020: 4:491-499. DOI: 10.1200/CCI.20.00001. PMID: 32479186, PMCID: PMC7328100
2.Fedorov A, Hancock M, Clunie D, Brochhausen M, Bona J, Kirby J, Freymann J, Pieper S, Aerts H, Kikinis R, Prior F, DICOM re‐encoding of volumetrically annotated Lung Imaging Database Consortium (LIDC) nodules, Medical Physics, 2020; DOI: 10.1002/mp.14445.
3.Fitzgerald T, Followill D, Laurie F, Boterberg T, Hanusik R, Kessel S, Karolczuk K, Iandoli M, Ulin K, Morano K, Bishop-Jodoin M, Kry S, Lowenstein J, Molineu A, Moni J, Cicchetti G, Prior F, Saltz J, Sharma A. Mandeville H, Bernier-Chastagner V, Janssens G. Quality Assurance in Radiation Oncology, Pediatric Blood & Cancer, 2020; DOI: 10.1002/pbc.28609.
4.Fedorov A, Beichel R, Kalpathy-Cramer J, Clunie D, Onken M, Riesmeier J, Herz C, Bauer C, Beers A, Fillion-Robin J-C, Lasso A, Pinter C, Pieper S, Nolden M, Maier-Hein K, Herrmann M, Saltz J, Prior F, Fennessy F, Buatti J, Kikinis R. Quantitative Imaging Informatics for Cancer Research (QIICR), JCO Clinical Cancer Informatics, 2020:4, 444-453. doi: 10.1200/CCI.19.00165. PMID: 32392097, PMCID: PMC7265794
5.Han Le, Rajarsi Gupta, Le Hou, Shahira Abousamra, Danielle Fassler, Luke Torre-Healy, Richard A. Moffitt, Tahsin Kurc, Dimitris Samaras, Rebecca Batiste, Tianhao Zhao, Arvind Rao, Alison L. Van Dyke, Ashish Sharma, Erich Bremer, Jonas S. Almeida, Joel Saltz. Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer, The American Journal of Pathology, 2020, 190(7);1491-1504. doi: https://doi.org/10.1016/j.ajpath.2020.03.012.
6.Reyna MA, Josef CS, Jeter R, Shashikumar SP, Westover MB, Nemati S, Clifford GD, Sharma A. Early Prediction of Sepsis From Clinical Data: The PhysioNet/Computing in Cardiology Challenge 2019. Crit Care Med. 2020 Feb;48(2):210-217. doi: 10.1097/CCM.0000000000004145. PMID: 31939789; PMCID: PMC6964870.
7.Amgad M, Stovgaard ES, Balslev E, Thagaard J, Chen W, Dudgeon S, Sharma A, Kerner JK, Denkert C, Yuan Y. Report on computational assessment of tumor infiltrating lymphocytes from the International Immuno-Oncology Biomarker Working group. NPJ breast cancer. 2020;6(1):1-13.
8.Bremer E, Saltz J, Almeida JS. ImageBox 2–Efficient and rapid access of image tiles from whole-slide images using serverless HTTP range requests. Journal of pathology informatics. 2020;11.
9.Fassler DJ, Abousamra S, Gupta R, Chen C, Zhao M, Paredes D, Batool SA, Knudsen BS, Escobar-Hoyos L, Shroyer KR. Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images. Diagnostic pathology. 2020;15(1):1-11.
10.Hou L, Gupta R, Van Arnam JS, Zhang Y, Sivalenka K, Samaras D, Kurc TM, Saltz JH. Dataset of segmented nuclei in hematoxylin and eosin stained histopathology images of ten cancer types. Scientific data. 2020;7(1):185. Epub 2020/06/21. doi: 10.1038/s41597-020-0528-1. PubMed PMID: 32561748; PubMed Central PMCID: PMCPMC7305328.
11.Kos Z, Roblin E, Kim RS, Michiels S, Gallas BD, Chen W, van de Vijver KK, Goel S, Adams S, Demaria S. Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer. NPJ breast cancer. 2020;6(1):1-16.
12.Kurc T, Bakas S, Ren X, Bagari A, Momeni A, Huang Y, Zhang L, Kumar A, Thibault M, Qi Q, Wang Q, Kori A, Gevaert O, Zhang Y, Shen D, Khened M, Ding X, Krishnamurthi G, Kalpathy-Cramer J, Davis J, Zhao T, Gupta R, Saltz J, Farahani K. Segmentation and Classification in Digital Pathology for Glioma Research: Challenges and Deep Learning Approaches. Frontiers in neuroscience. 2020;14:27. Epub 2020/03/11. doi: 10.3389/fnins.2020.00027. PubMed PMID: 32153349; PubMed Central PMCID: PMCPMC7046596.
13.Le H, Gupta R, Hou L, Abousamra S, Fassler D, Torre-Healy L, Moffitt RA, Kurc T, Samaras D, Batiste R, Zhao T, Rao A, Van Dyke AL, Sharma A, Bremer E, Almeida JS, Saltz J. Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer. The American journal of pathology. 2020;190(7):1491-504. Epub 2020/04/12. doi: 10.1016/j.ajpath.2020.03.012. PubMed PMID: 32277893; PubMed Central PMCID: PMCPMC7369575.
14.Papadiamantis AG, Klaessig FC, Exner TE, Hofer S, Hofstaetter N, Himly M, Williams MA, Doganis P, Hoover MD, Afantitis A. Metadata stewardship in nanosafety research: Community-driven organisation of metadata schemas to support FAIR nanoscience data. Nanomaterials. 2020;10(10):2033.
15.Saltz J, Gupta R, Samaras D, Hou L, Le H, Abousamra S, Batiste R, Zhao T, Zhang J, Chen C. Generating a Comprehensive Map of Cancer Morphology in Whole Slide Tissue Specimens. Bulletin of the American Physical Society. 2020;65.
2019 Publications:
1.Prior F, Almeida J, Kathiravelu P, Kurc T, Smith K, Fitzgerald TJ, Saltz J, Open Access Image Repositories: High Quality Data to Enable Machine Learning Research, Clinical Radiology, 2019; doi: 10.1016/j.crad.2019.04.002. PMID:31040006, PMCID: PMC6499855.
2.Bona JP, Prior FW, Zozus MN, Brochhausen M. Enhancing Clinical Data and Clinical Research Data with Biomedical Ontologies – Insights from the Knowledge Representation Perspective. Yearbook of medical informatics. 2019;28(1):140-51. Epub 2019/08/17. doi: 10.1055/s-0039-1677912. PubMed PMID: 31419826; PubMed Central PMCID: PMCPMC6697506.
3.FitzGerald TJ, Bishop-Jodoin M, Laurie F, Hanusik R, Iandoli M, Karolczuk K, Kessel S, Prior F, Saltz J, Sharma A, Knopp M, Rosen M, Xiao Y, Followill D, Michalski J, Cicchetti G, Moni J. Imaging and Neuro-Oncology Clinical Trials of the National Clinical Trials Network (NCTN). In: Zhou Y, editor. Neuroimaging. London, UK: IntechOpen Limited; 2019; doi: 10.5772/intechopen.89065
4.FitzGerald TJ, Bishop-Jodoin M, Laurie F, Hanusik R, Iandoli M, Karolczuk K, Kessel S, Prior F, Saltz J, Sharma A, Knopp M, Rosen M, Xiao Y, Followill D, Michalski J, Elaimy A, Shen J, Lee P, Cicchetti M, Moni J. Acquisition and Management of Data for Translational Science in Oncology. In: Zhou Y, editor. Neuroimaging. London, UK: IntechOpen Limited; 2019; doi: 10.5772/intechopen.89700
5.Hou L, Nguyen V, Kanevsky AB, Samaras D, Kurc TM, Zhao T, Gupta RR, Gao Y, Chen W, Foran D, Saltz JH. Sparse Autoencoder for Unsupervised Nucleus Detection and Representation in Histopathology Images. Pattern recognition. 2019;86:188-200. Epub 2019/01/12. doi: 10.1016/j.patcog.2018.09.007. PubMed PMID: 30631215; PubMed Central PMCID: PMCPMC6322841.
6.Taveira LFR, Kurc T, Melo A, Kong J, Bremer E, Saltz JH, Teodoro G. Multi-objective Parameter Auto-tuning for Tissue Image Segmentation Workflows. Journal of digital imaging. 2019;32(3):521-33. Epub 2018/11/08. doi: 10.1007/s10278-018-0138-z. PubMed PMID: 30402669; PubMed Central PMCID: PMCPMC6499855.
7.Cooper LA, Demicco EG, Saltz JH, Powell RT, Rao A, Lazar AJ. PanCancer insights from The Cancer Genome Atlas: the pathologist’s perspective. The Journal of pathology. 2018;244(5):512-24. Epub 2017/12/31. doi: 10.1002/path.5028. PubMed PMID: 29288495; PubMed Central PMCID: PMCPMC6240356.
8.Vu QD, Graham S, Kurc T, To MN, Shaban M, Qaiser T, Koohbanani NA, Khurram SA, Kalpathy-Cramer J, Zhao T, Gupta R. Methods for segmentation and classification of digital microscopy tissue images. Frontiers in bioengineering and biotechnology. 2019;7.
9.Hou L, Agarwal A, Samaras D, Kurc TM, Gupta RR, Saltz JH. Robust Histopathology Image Analysis: To Label or to Synthesize?. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition 2019 (pp. 8533-8542).
10.Gomes J, Barreiros Jr W, Kurc T, Melo AC, Kong J, Saltz JH, Teodoro G. Sensitivity analysis in digital pathology: Handling large number of parameters with compute expensive workflows. Computers in biology and medicine. 2019 May 1;108:371-81.
11.Rajarsi Gupta, Tahsin Kurc, Ashish Sharma, Jonas S Almeida, Joel Saltz, “The Emergence of Pathomics”, Current Pathobiology Reports, 7(3), pp. 73-84, 2019
12.H Le, D Samaras, T Kurc, R Gupta, K Shroyer, J Saltz, “Pancreatic Cancer Detection in Whole Slide Images Using Noisy Label Annotations”, Medical Image Computing and Computer-Asisted Intervention (MICCAI 2019), Shenzhen, China, Oct 2019
2018 Publications:
1.Bennett, W., Smith, K., Jarosz, Q., Nolan, T., & Bosch, W. (2018). Reengineering Workflow for Curation of DICOM Datasets. Journal of digital imaging, 1-9.10.1007/s10278-018-0097-4
2.Saltz, Joel, et al. “Spatial organization and molecular correlation of tumor-infiltrating lymphocytes using deep learning on pathology images.” Cell reports 23.1 (2018): 181.
2020 Courses:
1.MICCAI2020 Satellite Event: “Public Cancer Imaging Data Repositories for Biomedical Data Science Research” Presented by F.W. Prior (faculty) MICCAI 2020 Virtual, Lima Peru, 2020
2.RSNA Refresher course: “Novel Discoveries Using the NCI’s Cancer Imaging Archive (TCIA) Public Data Sets,” Chaired by FW. Prior, Course RC653, Radiological Society of North America, Chicago, Il. 2020.
2019 Courses:
1.RSNA Refresher course: “Computer Science ‘Deep Learning’ Research by the Academic Community” Presented by F.W. Prior (faculty) Course RCC55A, Radiological Society of North America, Chicago, Il. 2019.
2.RSNA Hands-on course: “An Introduction to Using the NIH/NCI’s Cancer Imaging Archive (TCIA) (Hands-on),” Presented by F.W. Prior, L. Tarbox (faculty) Course RCB54, Radiological Society of North America, Chicago, Il. 2019.
2018 Courses:
1.RSNA Hands-on course: “Computer Science ‘Deep Learning’ Research by the Academic Community” Presented by F.W. Prior (faculty) Course RCC453A, Radiological Society of North America, Chicago, Il. 2017-2018.
2.RSNA Hands-on course: “Using Publicly Accessible ‘Big Data’ from the NIH/NCI’s Cancer Imaging Archive (TCIA) to Research Quantitative Radiomics, Proteomics, Genetics and Pathology” Presented by F.W. Prior (faculty) Course RCB54, Radiological Society of North America, Chicago, Il. 2016 – 2018.
2020 Presentations:
1.Invited Grand Rounds: “Artificial Intelligence and Digital Pathology in Cancer Research and Clinical Decision Support,” presented by J. Saltz, University of Pennsylvania, January 27, 2020.
2.Invited Keynote address: “AI and Machine Learning in Cancer Imaging,” presented by F.W. Prior, Arkansas Bioinformatics Consortium (ARBIC) Annual meeting, North Little Rock, AR, February 10, 2020.
3.Larson-Prior, L.J., Bona, J.P, Virmani, T., Kemp, A.S., Pillai, L., Prior, F.W. “Leveraging telehealth in underserved populations for open data research,” presented by L.J. Larson-Prior to the Open Science Special Interest Group at the Organization for Human Brain Mapping Virtual Meeting, June 2020.
4.Plenary presentation: “AI Driven Pathomics – the next diagnostic frontier.” presented by J. Saltz, Digital Pathology Visions virtual, October 28, 2020.
5.“Infrastructure for Imaging AI Research- Data Issues,” presented by F.W. Prior, VA Center of Excellence Artificial Intelligence for Medical Imaging (AIMI), Central Virginia VA Health Care System, virtual, October 28, 2020.
6.“Computational Pathology: Deep Learning, Classification and Predicting the Future,” presented by J. Saltz, Digital Pathology & AI Congress virtual, November 19, 2020.
7.“Digital Transformation of Cancer Care.” presented by F.W. Prior, European Cancer Summit 2020 virtual, November 19, 2020.
8.“Pathomics: deep learning, classification and computational diagnostics ,” presented by J. Saltz, European Society of Pathology (ESP), Computational Pathology 2020, December 19, 2020.
2019 Presentations:
1.“Curating High Quality, Open Access Data to Enable Machine Learning Research.” Presented by F.W. Prior, Arlington Imaging Artificial Intelligence (AI-AI) Workshop, Arlington Virginia, May 9, 2019.
2.“Data curation and quantitative analysis – NCI’s cancer imaging archive.” Presented by F.W. Prior, The Wizardry of AI and Machine Learning in Cancer Imaging Conference, Lisbon Portugal, May 17, 2019.
3.Invited Keynote address “Scope of Image Banking in Modern Oncology Practice & Research.” presented by F.W. Prior, Structuring a Collaborative National Image Banking Program, Joint Workshop organized under the initiative of National Digital Library of India – CHAVI, Tata Medical Center, Kolkata, India, July 26, 2019.
4.“Structure and Vision of TCIA.” presented by F.W. Prior, Structuring a Collaborative National Image Banking Program, Joint Workshop organized under the initiative of National Digital Library of India – CHAVI, Tata Medical Center, Kolkata, India, July 26, 2019
5.“Road map for development of artificial intelligence in oncological imaging.” presented by F.W. Prior, International Cancer Imaging Society 19th Annual Teaching Course, Verona, Italy, October 8, 2019.
6.“Digital Pathology – Deep Learning, Imaging Biomarkers and Clinical Decision Support,” presented by J. Saltz, IEEE BHI 2019 Chicago, IL, May 19, 2019
7.“Pathomics: Deep Learning, Surveillance and Precision Medicine,” presented by J. Saltz, FALL CI4CC Napa, CA, October 14, 2019
8.“Deep Learning, Surveillance and Precision Medicine,” presented by J. Saltz, Association of American Cancer Institutes & Cancer Center Administrators Forum Invitation to Speak | 2019 AACI/CCAF Annual Meeting, Washington DC, October 19, 2019
9.“Semantic Integration of Non-Image Data in The Cancer Imaging Archive Collections with Biomedical Ontologies.” Presented by J.P. Bona, Practical Big Data Workshop (PBDW 2019), Ann Arbor, Michigan, June 7, 2019.
10.“ARIES Integrates Neuroinformatics Data Using Open Biomedical Ontologies.” Presented by J.P. Bona, American Medical Informatics Association (AMIA) Knowledge Representation and Semantics Pre-symposium Workshop, November 17, 2019.
2018 Presentations:
1.“Ontology-Enhanced Representations of Non-image Data in The Cancer Imaging Archive,” Presented by J.P. Bona, International Conference on Biological Ontology 2018, Corvallis, OR, August 8, 2018.
2.“Machine Learning in Feature Space – Adding New Dimensions to Imaging Research.” Presented by F.W. Prior, Partnership for Artificial Intelligence and Automation in Healthcare, Washington, DC, October 1, 2018.
3.Invited Keynote address “Big data initiatives changing the future of cancer imaging and therapy.” presented by F.W. Prior, International Cancer Imaging Society 18th Annual Teaching Course, Menton, France, October 8, 2018.
4.“Representing Non-image Data in The Cancer Imaging Archive Collections,” Presented by J.P. Bona, AMIA 2018 Knowledge Representation and Semantics Working Group Pre-Symposium Workshop, San Francisco, CA, November 3, 2018.
5.RSNA Paper No: SSJ13-06 “Kaleidoscope: A Series Projection Visualization Tool for Review of DICOM Images for Protected Health Information.” presented by K. Smith, RSNA, Chicago, Il, November 27, 2018.
2020 Posters and Demonstrations:
1.Bona JP, Li N, PRISM semantic integration and DataScope visual exploration of clinical data in TCIA lung cancer collections. ePoster, ITCR Annual Meeting, May 26-28, 2020.
2.Bremer E, Diprima T, Kurc T, Saltz J, PathDB – Management of Pathology Images and FeatureMaps. ePoster, ITCR Annual Meeting, May 26-28, 2020.
3.Tarbox L, PRISM Architecture Fundamentals. ePoster, ITCR Annual Meeting, May 26-28, 2020.
4.Birmingham R, Li N, Hajoori I, Sharma A, AI Assisted Pathology, A tour of caMicroscope’s Machine Learning Functionality. ePoster, ITCR Annual Meeting, May 26-28, 2020.
2019 Posters and Demonstrations:
1.Fevrier-Sullivan B, Kirby J, Jaffe C, Smith K, Nolan T, Bennett W, Honomichl N, Sharma A, Birmingham R, Prior F, Freymann J, The Cancer Imaging Archive (TCIA): CPTAC Radiology and Pathology Imaging Research Efforts. Abstract and poster, The Clinical Proteomic Tumor Analysis Consortium Steering Committee Meeting, NIH, Bethesda MD, April 30, 2019.
2.Freymann J, Bennett W, Kirby J, Levine B, Nolan T, Smith K, Tarbox L, Prior F, Data and Services Provided by NCI’s Cancer Imaging Archive. Abstract and poster, Co-Clinical Imaging Research Resources Network Annual Meeting, NCI Campus, Rockville, MD, May 20, 2019.
3.Bona JP, Kemp AS, Nolan TS, Larson-Prior L, Das A, Virmani T, Pillai L, Brochhausen M, Prior F, Semantic Integration of Neuroinformatics Data in the Arkansas Image Enterprise System. (ARIES). Abstract and poster, 2019 ITCR Annual Meeting, Deer Valley, UT, May 29 – 31, 2019.
4.Sharma A, Gu P, Kathiravelu P, Marappareddy M, Saha M, Saltz J, Kurc T, Bremmer E, DiPrima T, Gupta R, Prior F, Tarbox L, Brochhausen M, Bona JP, Bennett W, Smith K, Nolan TS, Platform for Imaging in Precision Medicine (PRISM). Abstract and poster, 2019 ITCR Annual Meeting, Deer Valley, UT, May 29 – 31, 2019.
5.Kemp A, Bona J, Nolan T, Larson-Prior L, Virmani T, Pillai L, Brochhausen M, Tarbox L, Prior F, Semantic Representations of Multi-Modal Data, NeuroInformatic Processing Pipelines, and Derived Neuroimaging Results in the Arkansas Image Enterprise System (ARIES). Abstract and poster, AMIA Annual Symposium, Washington DC, November 16-20, 2019.
6.Smith K, Bennett B, Tarbox L, Nolan T, Blake G, Kirby J, Freymann J, Prior F, The Cancer Imaging Archive (TCIA), NCI’s Imaging Data Resource. Abstract and poster, AMIA Annual Symposium, San Washington DC, November 16-20, 2019.
7.Bennett B, Smith K, Jarosz Q, Utecht S, Prior F, Posda: An Open Source Curation Tool for Validation, Editing, and Inspection of DICOM Objects for Large Scale Imaging Archives. Abstract and poster, AMIA Annual Symposium, Washington DC, November 20, 2019.
8.Bona JP, Kemp A, Nolan T, Larson-Prior L, Das A, Virmani T, Pillai L, Brochhausen M, Prior F, Semantic Integration of Neuroinformatics Data in the Arkansas Image Enterprise System with Open Biomedical Ontologies. Abstract and poster. International Conference on Biomedical Ontology (ICBO) 2019, Buffalo, NY, July 30 – August 2, 2019.
9.Bona JP, Utecht J, Brochhausen M, Providing a User-oriented Interface to Enable Semantic Queries in PRISM. Abstract and poster. American Medical Informatics Association 2019 (AMIA) Annual Symposium, Washington, DC, November 16 – 20, 2019.
2018 Posters and Demonstrations:
1.Nolan T, Kirby J, Prior F, “Data Management, Sharing, and Citation Strategies in The Cancer Imaging Archive (TCIA),” Abstract and poster presentation, AMIA Annual Symposium, Washington DC, November, 2017.
2.Prior F, Sharma A, Almeida J, Bennett W, Bona J, Bosch W, Bremer E, Brochhausen M, Fitzgerald TJ, Kurc T, Nolan T, Smith K, Tarbox L, Saltz J, “TCIA Sustainment and Scalability – Platform for Imaging in Precision Medicine,” Abstract and poster presentation, Quantitative Imaging Network Annual Meeting, Rockville, MD, May 17, 2018.
3.Prior F, Sharma A, Almeida J, Bennett W, Bona J, Bosch W, Bremer E, Brochhausen M, Fitzgerald TJ, Kurc T, Nolan T, Smith K, Tarbox L, Saltz J, “Semantic Integration of Non-image Data in TCIA Collections and PRISM Platform,” Abstract and poster presentation, ITCR Annual Meeting, Bethesda, MD, May 23, 2018.
4.Prior F, Sharma A, “The Cancer Imaging Archive (TCIA),” Interactive demonstration, IITCR Annual Meeting, Bethesda, MD, May 23, 2018.
5.Becich MJ, Saltz J, Silverstein J, Bollag RJ, Brochhausen M, Chennubhotla C, Feldman MD, Gaudioso C, Kurc T, London J, Maihle NJ, Prior F, Sharma A, Tarbox L, “The TIES Cancer Research Network (TCRN): Computational Pathology Support for Precision Oncology,” Abstract and poster presentation, IITCR Annual Meeting, Bethesda, MD, May 23, 2018.
6.Prior F, Tarbox L, Kunc T, Larson-Prior L, Sharma A, Saltz J, “PRISM: Neuroinformatics Architecture to Support Research Reproducibility and Data Publication,” Abstract and poster presentation, OHBM Annual Meeting, Singapore, June 17-21, 2018 https://files.aievolution.com/hbm1801/abstracts/31098/2013_Prior.pdf
7.Larson-Prior LJ, Kemp AS, Baghal A, Syed S, Matthews EE, “P17 Sleep abnormalities in non-CNS malignant tumours.” Cancer Imaging. 2018; 18(Suppl 1): 28. https://doi.org/10.1186/s40644-018-0160-x
8.Bona J, Nolan S, Gibson D, Brochhausen M, “Ontologies Enabling Non-image Data Queries in The Cancer Imaging Archive,” Abstract and poster presentation, AMIA Annual Symposium, San Francisco CA, November 5 2018.
9.Towards a Services Oriented Platform for Combined Radiology-Pathology Image Analysis and Interpretation. System demonstration at AMIA 2018, presented by Tahsin Kurc.
