Papers and publications

A mix of papers published by contributors to the Digital Slide Archive and by unaffiliated researchers who have found the system useful in their work.

• NimbusImage: A Cloud-Computing Platform for Image Analysis.
  Niu, Zijian, Thibault Bruyère, David Manthey, Jingxin Li, Aoife O’Farrell, and Arjun Raj. 2025. “NimbusImage: A Cloud-Computing Platform for Image Analysis.” Nature Methods 23 (1): 6–8.
  DOI · Publisher · PubMed 41266644

• FUSION: A Web-Based Application for in-Depth Exploration of Multi-Omics Data with Brightfield Histology.
  Border, Samuel P., Ricardo Melo Ferreira, Nicholas Lucarelli, Suhas Katari Chaluva Kumar, Anindya S. Paul, David Manthey, Laura Barisoni, et al. 2025. “FUSION: A Web-Based Application for in-Depth Exploration of Multi-Omics Data with Brightfield Histology.” Nature Communications 16 (1).
  DOI · Publisher · PubMed 40998789

• HistomicsTK: A Python Toolkit for Pathology Image Analysis Algorithms.
  Pourakpour, Fattaneh, Ákos Szölgyén, Ramin Nateghi, David A Gutman, David Manthey, and Lee AD Cooper. 2025. “HistomicsTK: A Python Toolkit for Pathology Image Analysis Algorithms.” SoftwareX 31 (September): 102318.

• ComPRePS 2.0: Enabling Massive-Scale Distributed Computing on High-Performance Computing Cluster for Histopathological Data Processing.
  Katari Chaluva Kumar, Suhas, Anindya S. Paul, Haitham Abdelazim, Will Dunklin, David Manthey, Oleksandr Moskalenko, Sayat Mimar, Erik Deumens, and Pinaki Sarder. 2025. “ComPRePS 2.0: Enabling Massive-Scale Distributed Computing on High-Performance Computing Cluster for Histopathological Data Processing.” Edited by John E. Tomaszewski and Aaron D. Ward. Medical Imaging 2025: Digital and Computational Pathology. SPIE.

• Efficiently Writing and Visualizing Many-Dimension Large Images.
  Haley, Anne, David Manthey, Lee Cooper, and David Gutman. 2024. “Poster Presentations: Efficiently Writing and Visualizing Many-Dimension Large Images.” Digital Pathology & AI Congress, May 7-8, 2024.
  PDF

• A User-Friendly Tool for Cloud-Based Whole Slide Image Segmentation with Examples from Renal Histopathology.
  Lutnick, Brendon, David Manthey, Jan U. Becker, Brandon Ginley, Katharina Moos, Jonathan E. Zuckerman, Luis Rodrigues, et al. 2022. “A User-Friendly Tool for Cloud-Based Whole Slide Image Segmentation with Examples from Renal Histopathology.” Communications Medicine. Springer Science and Business Media LLC.
  PubMed 35996627

• PodoCount: A Robust, Fully Automated, Whole-Slide Podocyte Quantification Tool.
  Santo, Briana A., Darshana Govind, Parnaz Daneshpajouhnejad, Xiaoping Yang, Xiaoxin X. Wang, Komuraiah Myakala, Bryce A. Jones, et al. 2022. “PodoCount: A Robust, Fully Automated, Whole-Slide Podocyte Quantification Tool.” Kidney International Reports. Elsevier BV.
  PubMed 35694561

• A Tool for Federated Training of Segmentation Models on Whole Slide Images.
  Lutnick, Brendon, David Manthey, Jan U. Becker, Jonathan E. Zuckerman, Luis Rodrigues, Kuang-Yu Jen, and Pinaki Sarder. 2022. “A Tool for Federated Training of Segmentation Models on Whole Slide Images.” Journal of Pathology Informatics. Elsevier BV.
  PubMed 35910077

• Explainable Nucleus Classification Using Decision Tree Approximation of Learned Embeddings
  Amgad, Mohamed, LameesA Atteya, Hagar Hussein, Kareem Hosny Mohammed, Ehab Hafiz, Maha A T Elsebaie, Pooya Mobadersany, et al. 2021. “Explainable Nucleus Classification Using Decision Tree Approximation of Learned Embeddings.” Edited by Jinbo Xu. Bioinformatics, September.
  PubMed 34586355

• PodoSighter: A Cloud-Based Tool for Label-Free Podocyte Detection in Kidney Whole Slide Images
  Govind, Darshana, Jan Becker, Jeffrey Miecznikowski, Avi Rosenberg, Julien Dang, Pierre Louis Tharaux, Rabi Yacoub, et al. 2021. “PodoSighter: A Cloud-Based Tool for Label-Free Podocyte Detection in Kidney Whole Slide Images.” Journal of the American Society of Nephrology, September, ASN.2021050630.
  PubMed 34479966

• User Friendly, Cloud Based, Whole Slide Image Segmentation.
  Lutnick, Brendon, Avinash Kammardi Shashiprakash, David Manthey, and Pinaki Sarder. 2021. “User Friendly, Cloud Based, Whole Slide Image Segmentation.” In Medical Imaging 2021: Digital Pathology, edited by John E. Tomaszewski and Aaron D. Ward. SPIE.
  PubMed 34366542

• A Distributed System Improves Inter-Observer and AI Concordance in Annotating Interstitial Fibrosis and Tubular Atrophy.
  Kammardi Shashiprakash, Avinash, Brendon Lutnick, Brandon Ginley, Darshana Govind, Nicholas Lucarelli, Kuang-Yu Jen, Avi Z. Rosenberg, et al. 2021. “A Distributed System Improves Inter-Observer and AI Concordance in Annotating Interstitial Fibrosis and Tubular Atrophy.” In Medical Imaging 2021: Digital Pathology, edited by John E. Tomaszewski and Aaron D. Ward. SPIE.
  PubMed 34366540

• Machine-based detection and classification for bone marrow aspirate differential counts - initial development focusing on nonneoplastic cells.
  Chandradevan, Ramraj, Ahmed A. Aljudi, Bradley R. Drumheller, Nilakshan Kunananthaseelan, Mohamed Amgad, David A. Gutman, Lee A. D. Cooper, and David L. Jaye. “Machine-Based Detection and Classification for Bone Marrow Aspirate Differential Counts: Initial Development Focusing on Nonneoplastic Cells.” Laboratory Investigation 100, no. 1 (September 30, 2019): 98–109.
  DOI · Publisher · PubMed 31570774

• Phosphoinositide 3-Kinase Signaling Can Modulate MHC Class I and II Expression.
  Chandrasekaran, Sanjay, Maiko Sasaki, Christopher D. Scharer, Haydn T. Kissick, Dillon G. Patterson, Kelly R. Magliocca, John T. Seykora, et al. “Phosphoinositide 3-Kinase Signaling Can Modulate MHC Class I and II Expression.” Molecular Cancer Research 17, no. 12 (September 23, 2019): 2395–2409.
  DOI · Publisher · PubMed 31548239

• Structured crowdsourcing enables convolutional segmentation of histology images.
  Amgad, Mohamed, Habiba Elfandy, Hagar Hussein, Lamees A Atteya, Mai A T Elsebaie, Lamia S Abo Elnasr, Rokia A Sakr, et al. “Structured Crowdsourcing Enables Convolutional Segmentation of Histology Images.” Edited by Robert Murphy. Bioinformatics 35, no. 18 (February 6, 2019): 3461–67.
  DOI · Publisher · PubMed 30726865

• Multi-faceted computational assessment of risk and progression in oligodendroglioma implicates NOTCH and PI3K pathways.
  Halani, Sameer H., Safoora Yousefi, Jose Velazquez Vega, Michael R. Rossi, Zheng Zhao, Fatemeh Amrollahi, Chad A. Holder, et al. “Multi-Faceted Computational Assessment of Risk and Progression in Oligodendroglioma Implicates NOTCH and PI3K Pathways.” Npj Precision Oncology 2, no. 1 (November 6, 2018).
  DOI · Publisher · PubMed 30417117

• PanCancer insights from The Cancer Genome Atlas - the pathologist's perspective.
  Cooper, Lee AD, Elizabeth G Demicco, Joel H Saltz, Reid T Powell, Arvind Rao, and Alexander J Lazar. “PanCancer Insights from The Cancer Genome Atlas: The Pathologist’s Perspective.” The Journal of Pathology 244, no. 5 (February 22, 2018): 512–24.
  DOI · Publisher · PubMed 29288495

• Predicting cancer outcomes from histology and genomics using convolutional networks.
  Mobadersany, Pooya, Safoora Yousefi, Mohamed Amgad, David A. Gutman, Jill S. Barnholtz-Sloan, José E. Velázquez Vega, Daniel J. Brat, and Lee A. D. Cooper. “Predicting Cancer Outcomes from Histology and Genomics Using Convolutional Networks.” Proceedings of the National Academy of Sciences 115, no. 13 (March 12, 2018): E2970–79.
  DOI · Publisher · PubMed 29531073

• Informatics Approaches to Address New Challenges in the Classification of Lymphoid Malignancies.
  Jordan, Jacob, Jordan S. Goldstein, David L. Jaye, Metin Gurcan, Christopher R. Flowers, and Lee A.D. Cooper. “Informatics Approaches to Address New Challenges in the Classification of Lymphoid Malignancies.” JCO Clinical Cancer Informatics, no. 2 (December 2018): 1–9.
  DOI · Publisher · PubMed 30637363

• Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas.
  Abeshouse, Adam, Clement Adebamowo, Sally N. Adebamowo, Rehan Akbani, Teniola Akeredolu, Adrian Ally, Matthew L. Anderson, et al. “Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas.” Cell 171, no. 4 (November 2017): 950–965.e28.
  DOI · Publisher · PubMed 29100075

• The Digital Slide Archive - A Software Platform for Management, Integration, and Analysis of Histology for Cancer Research.
  Gutman, David A., Mohammed Khalilia, Sanghoon Lee, Michael Nalisnik, Zach Mullen, Jonathan Beezley, Deepak R. Chittajallu, David Manthey, and Lee A.D. Cooper. “The Digital Slide Archive: A Software Platform for Management, Integration, and Analysis of Histology for Cancer Research.” Cancer Research 77, no. 21 (October 31, 2017): e75–78.
  DOI · Publisher · PubMed 29092945

• Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.
  Ceccarelli, Michele, Floris P. Barthel, Tathiane M. Malta, Thais S. Sabedot, Sofie R. Salama, Bradley A. Murray, Olena Morozova, et al. “Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.” Cell 164, no. 3 (January 2016): 550–63.
  DOI · Publisher · PubMed 26824661

• Novel genotype-phenotype associations in human cancers enabled by advanced molecular platforms and computational analysis of whole slide images.
  Cooper, Lee AD, Jun Kong, David A Gutman, William D Dunn, Michael Nalisnik, and Daniel J Brat. “Novel Genotype-Phenotype Associations in Human Cancers Enabled by Advanced Molecular Platforms and Computational Analysis of Whole Slide Images.” Laboratory Investigation 95, no. 4 (January 19, 2015): 366–76.
  DOI · Publisher · PubMed 25599536

• Cancer Digital Slide Archive - an informatics resource to support integrated in silico analysis of TCGA pathology data.
  Gutman, David A, Jake Cobb, Dhananjaya Somanna, Yuna Park, Fusheng Wang, Tahsin Kurc, Joel H Saltz, Daniel J Brat, Lee A D Cooper, and Jun Kong. “Cancer Digital Slide Archive: An Informatics Resource to Support Integrated in Silico Analysis of TCGA Pathology Data.” Journal of the American Medical Informatics Association 20, no. 6 (November 2013): 1091–98.
  DOI · Publisher · PubMed 23893318

Source and version

This list is consolidated from the upstream project website, docs/papers-publications/index.md in DigitalSlideArchive/digital_slide_archive, on 2026-11-01. Citations are reproduced as published upstream; links resolve to the publisher, PubMed, or the upstream PDF. The list has not been independently checked against a citation database.