ArticleCommunications medicine2022
A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology.
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Article in Communications medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33citing papers in PubMed
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Who cites it
33 citing papers in PubMed.
- CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images.Nature protocols · 2026Review
- Machine Learning-Enabled Quantification of Hepatocellular Necrosis in the Liver After Lethal Marburg and Ebola Virus Exposures.The Journal of infectious diseases · 2026Article
- A Machine learning pipeline to investigate tissue ingrowth in cerebral aneurysms using preclinical animal models.Scientific reports · 2026Article
- Morphometry-based detection of deep learning faults in glomerular segmentation.bioRxiv : the preprint server for biology · 2025Article
- FUSION: a web-based application for in-depth exploration of multi-omics data with brightfield histology.Nature communications · 2025Article
- Chronic Changes on Kidney Histology by a Multiclass Artificial Intelligence Model.Kidney international reports · 2025Article
- Comparative analysis of a 5G campus network and existing networks for real-time consultation in remote pathology.Journal of pathology informatics · 2025Article
- Advancing open-source visual analytics in digital pathology: A systematic review of tools, trends, and clinical applications.Journal of pathology informatics · 2025Review
- Renal arteriosclerosis in kidney biopsies associated with higher 10-year atherosclerotic cardiovascular disease in lupus nephritis.Rheumatology (Oxford, England) · 2025Article
- Explainable Feature Embeddings from Histopathology Foundation Models: A Case Study for End Stage Kidney Disease Risk Analysis in Diabetic Nephropathy Patients.Proceedings of SPIE--the International Society for Optical Engineering · 2025Article
- A novel automated method for comprehensive renal cast quantification from rat kidney sections using QuPath.American journal of physiology. Renal physiology · 2025Article
- Whole Slide Imaging (WSI) in Pathology: Emerging Trends and Future Applications in Clinical Diagnostics, Medical Education, and Pathology.Iranian journal of pathology · 2025Review
- GNCnn: A QuPath extension for glomerulosclerosis and glomerulonephritis characterization based on deep learning.Computational and structural biotechnology journal · 2025Article
- Computational pathology: A survey review and the way forward.Journal of pathology informatics · 2024Review
- Investigating quantitative histological characteristics in renal pathology using HistoLens.Scientific reports · 2024Article
- Mesangial Expansion by Morphometry at 5 y After Kidney Transplantation: Incidence, Risk Factors, and Association With Graft Loss.Transplantation direct · 2024Article
- ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology.bioRxiv : the preprint server for biology · 2024Article
- Precision Medicine in Nephrology: An Integrative Framework of Multidimensional Data in the Kidney Precision Medicine Project.American journal of kidney diseases : the official journal of the National Kidney Foundation · 2024Article
- ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology.Proceedings of SPIE--the International Society for Optical Engineering · 2024Article
- Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms.Nature communications · 2023Article
Corrections and comments
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Authors and funding
23 authors.
Brendon LutnickDepartment of Pathology and Anatomical Sciences, SUNY Buffalo, Buffalo, USA.ORCID 0000-0001-7360-3302
David MantheyKitware Incorporated, Clifton Park, USA.ORCID 0000-0002-4580-8770
Jan U BeckerInstitute of Pathology, University Hospital Cologne, Cologne, Germany.
Brandon GinleyDepartment of Pathology and Anatomical Sciences, SUNY Buffalo, Buffalo, USA.
Katharina MoosInstitute of Pathology, University Hospital Cologne, Cologne, Germany.
Jonathan E ZuckermanDepartment of Pathology and Laboratory Medicine, University of California at Los Angeles, Los Angeles, USA.
Luis RodriguesUniversity Clinic of Nephrology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
Alexander J GallanDepartment of Pathology, Medical College of Wisconsin, Milwaukee, USA.
Laura BarisoniDepartments of Pathology and Medicine, Duke University, Durham, USA.ORCID 0000-0003-0848-9683
Charles E AlpersDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, USA.ORCID 0000-0002-1859-1772
Xiaoxin X WangDepartments of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC USA.
Komuraiah MyakalaDepartments of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC USA.ORCID 0000-0003-3233-047X
Bryce A JonesDepartment of Pharmacology and Physiology, Georgetown University, Washington, DC USA.ORCID 0000-0002-6950-8414
Moshe LeviDepartments of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC USA.ORCID 0000-0001-6403-2261
Jeffrey B KoppKidney Disease Section, NIDDK, NIH, Bethesda, USA.ORCID 0000-0001-9052-186X
Teruhiko YoshidaKidney Disease Section, NIDDK, NIH, Bethesda, USA.ORCID 0000-0002-2049-7347
Jarcy ZeeDepartment of Biostatistics, Epidemiology, & Informatics, University of Pennsylvania, Philadelphia, USA.ORCID 0000-0003-0586-1160
Seung Seok HanDepartment of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea.ORCID 0000-0003-0137-5261
Sanjay JainDepartment of Medicine, Nephrology, Washington University School of Medicine, St. Louis, USA.
Avi Z RosenbergDepartment of Pathology, Johns Hopkins University, Baltimore, USA.ORCID 0000-0003-2356-950X
Kuang Yu JenDepartment of Pathology and Laboratory Medicine, University of California at Davis, Sacramento, USA.ORCID 0000-0003-2815-5912
Pinaki SarderDepartment of Pathology and Anatomical Sciences, SUNY Buffalo, Buffalo, USA.ORCID 0000-0003-2450-5233
Kidney Precision Medicine Project
Funding
Coordinating and Bioinformatics Unit for the MMPC/DiaCompU24DK076169 · NIDDK · AUGUSTA UNIVERSITY · PI MCINDOE, RICHARD A. · 2006 to 2018
$42.4MPILOT STUDY--CLINICAL NUTRITION RESEARCHP30DK035816 · NIDDK · UNIVERSITY OF WASHINGTON · PI Ellen A Schur · 1986 to 2026
$30.4MCentral Hub for Kidney Precision MedicineU24DK114886 · NIDDK · UNIVERSITY OF WASHINGTON · PI Jonathan Himmelfarb, Matthias Kretzler · 2022 to 2026
$21.1MConProject-002U2CDK114886 · NIDDK · UNIVERSITY OF WASHINGTON · PI HIMMELFARB, JONATHAN, IYENGAR, SRINIVAS RAVI V · 2017 to 2021
$21.0MCoordinating Unit for DiaCompU24DK115255 · NIDDK · AUGUSTA UNIVERSITY · PI MCINDOE, RICHARD A. · 2017 to 2020
$11.6MKPMP Kidney Mapping and Atlas Project (KMAP)U01DK133090 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Jonathan Himmelfarb, Matthias Kretzler · 2022 to 2026
$10.4MOrgan Specific ProjectU54HL145608 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SOLDATOV, RUSLAN · 2018 to 2021
$5.6MChronic Kidney Disease (CKD) Biomarkers Consortium Data Coordinating CenterU01DK103225 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI SCHRAUBEN, SARAH JEANNE · 2014 to 2020
$5.5MComputational Imaging of Renal Structures for Diagnosing DiabeticNephropathyR01DK114485 · NIDDK · UNIVERSITY OF FLORIDA · PI Michael Thomas Eadon, Avi Z Rosenberg · 2018 to 2026
$4.7MRole of Estrogen Related Receptors in Age Related Kidney DiseaseR01DK127830 · NIDDK · GEORGETOWN UNIVERSITY · PI MOSHE LEVI · 2021 to 2026
$4.2MComputational Pathology of Proteinuric DiseasesR01DK118431 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI BARISONI, LAURA MARIACHIARA, HODGIN, JEFFREY BENTON · 2018 to 2025
$3.6MBoston Chronic Kidney Disease Research Biopsy CenterU01DK133092 · NIDDK · BOSTON MEDICAL CENTER · PI Sylvia E Rosas, Sushrut S. Waikar · 2022 to 2026
$3.5MNHLBI NIH HHS U54 HL145608NIDDK NIH HHS F30 DK129003NIDDK NIH HHS P30 DK035816NIDDK NIH HHS R01 DK114485NIDDK NIH HHS R01 DK116567NIDDK NIH HHS R01 DK118431NIDDK NIH HHS R01 DK127830NIDDK NIH HHS U01 DK103225NIDDK NIH HHS U01 DK114866NIDDK NIH HHS U01 DK114907NIDDK NIH HHS U01 DK133090NIDDK NIH HHS U01 DK133092NIDDK NIH HHS U24 DK076169NIDDK NIH HHS U24 DK114886NIDDK NIH HHS U24 DK115255NIDDK NIH HHS U2C DK114886NIDDK NIH HHS UH3 DK114861NIDDK NIH HHS UH3 DK114866NIDDK NIH HHS UH3 DK114870NIDDK NIH HHS UH3 DK114907NIDDK NIH HHS UH3 DK114908NIDDK NIH HHS UH3 DK114915NIDDK NIH HHS UH3 DK114920NIDDK NIH HHS UH3 DK114923NIDDK NIH HHS UH3 DK114926NIDDK NIH HHS UH3 DK114933NIDDK NIH HHS UH3 DK114937
Abstract
Background: Image-based machine learning tools hold great promise for clinical applications in pathology research. However, the ideal end-users of these computational tools (e.g., pathologists and biological scientists) often lack the programming experience required for the setup and use of these tools which often rely on the use of command line interfaces. Methods: We have developed Results: By segmenting glomeruli, interstitial fibrosis and tubular atrophy, and vascular structures from renal and non-renal WSIs, we demonstrate the scalability, best practices for transfer learning, and effects of dataset variability. Finally, we demonstrate an application for animal model research, analyzing glomerular features in three murine models. Conclusions:
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Computational biology and bioinformaticsEnd-stage renal disease
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