Evidence map›Paper›PMID 38902336›Full record

ArticleNPJ digital medicine2024

PatchSorter: a high throughput deep learning digital pathology tool for object labeling.

Cédric Walker, Tasneem Talawalla, Robert Toth, Akhil Ambekar, Kien Rea, Oswin Chamian, Fan Fan, Sabina Berezowska, Sven Rottenberg, Anant Madabhushi and 4 more

Abstract read
In one paragraph

Article in NPJ digital medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Association of Histological Features of Cortical and Medullary Peritubular Capillaries With Progressive CKD.American journal of kidney diseases : the official journal of the National Kidney Foundation · 2026
    Article
  2. Article
  3. bioRxiv : the preprint server for biology · 2025
    Article
  4. Article
  5. Machine learning methods for histopathological image analysis: Updates in 2024.Computational and structural biotechnology journal · 2025
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Cédric WalkerInstitute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.ORCID http://orcid.org/0009-0001-1508-2083
Tasneem TalawallaDepartment of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
Robert TothToth Technology LLC, Toth Technology LLC, New Brunswick, NJ, USA.
Akhil AmbekarDepartment of Pathology, Division of AI & Computational Pathology, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0002-6241-6234
Kien ReaDepartment of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
Oswin ChamianDepartment of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
Fan FanDepartment of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
Sabina BerezowskaInstitute of Pathology, Lausanne University Hospital, Lausanne, Switzerland.
Sven RottenbergInstitute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Anant MadabhushiDepartment of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA.ORCID http://orcid.org/0000-0002-5741-0399
Marie MaillardInstitute of Pathology, Lausanne University Hospital, Lausanne, Switzerland.
Laura BarisoniDepartment of Pathology, Division of AI & Computational Pathology, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0003-0848-9683
Hugo Mark HorlingsDepartment of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.ORCID http://orcid.org/0000-0003-4782-8828
Andrew JanowczykDepartment of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA. andrew.r.janowczyk@emory.edu.ORCID http://orcid.org/0000-0003-2982-4321

Funding

The Impact of COVID-19 on People Living with Rare Diseases and Their FamiliesU2CTR002818 · NCATS · CINCINNATI CHILDRENS HOSP MED CTR · PI Maurizio Macaluso, Michael Wagner · 2019 to 2026
$51.2M
Training Program in Clinical & Translationa Research in Human Glomerular DiseaseU54DK083912 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI KRETZLER, MATTHIAS · 2009 to 2023
$20.3M
CureGNU24DK100845 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CRYSTAL A. GADEGBEKU, Laura H Mariani · 2019 to 2026
$12.1M
KPMP Kidney Mapping and Atlas Project (KMAP)U01DK133090 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Jonathan Himmelfarb, Matthias Kretzler · 2022 to 2026
$10.4M
The Columbia PCC for CureGN: the Cure Glomerulonephropathy networkU01DK100876 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Andrew Stephen Bomback, ALI G GHARAVI · 2019 to 2026
$8.5M
CureGN-Penn PCCU01DK100846 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI LAWRENCE B. HOLZMAN · 2019 to 2026
$8.3M
CUREGN 3.0 - Pediatric Nephrology Consortium - PCCU01DK100866 · NIDDK · RESEARCH INST NATIONWIDE CHILDREN'S HOSP · PI Laurence A Greenbaum, Jon Klein · 2019 to 2026
$7.7M
CureGN-3: UNCPCCU01DK100867 · NIDDK · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Vimal Kumar Derebail, Ronald J Falk · 2019 to 2026
$6.7M
GDPrimeUM1DK100845 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI GIPSON, DEBBIE S, KRETZLER, MATTHIAS · 2013 to 2018
$6.4M
Primary Outcomes in Glomerulonephritis Study (PROGRESS)UM1DK100846 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI HOLZMAN, LAWRENCE B. · 2013 to 2018
$5.8M
Integrative Proteomics & Metabolomics for Pediatric Glomerula Disease BiomarkersUM1DK100866 · NIDDK · RESEARCH INST NATIONWIDE CHILDREN'S HOSP · PI GREENBAUM, LAURENCE A, SMOYER, WILLIAM E · 2013 to 2018
$5.5M
Advancing Clinical Research in Primary Glomerular Diseases (UM1)UM1DK100876 · NIDDK · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI GHARAVI, ALI G · 2013 to 2018
$4.8M
NCATS NIH HHS U2C TR002818NCI NIH HHS U01 CA239055NCI NIH HHS U01 CA248226NIDDK NIH HHS R01 DK118431NIDDK NIH HHS U01 DK100846NIDDK NIH HHS U01 DK100866NIDDK NIH HHS U01 DK100867NIDDK NIH HHS U01 DK100876NIDDK NIH HHS U01 DK133090NIDDK NIH HHS U24 DK100845NIDDK NIH HHS U54 DK083912NIDDK NIH HHS UM1 DK100845NIDDK NIH HHS UM1 DK100846NIDDK NIH HHS UM1 DK100866NIDDK NIH HHS UM1 DK100867NIDDK NIH HHS UM1 DK100876NLM NIH HHS R01 LM013864U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS) U2CTR002818U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) 1U01DK133090U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) 2R01DK118431-04U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) U54DK083912U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM) 1R01LM013864
6 · The paper itself

Abstract

The discovery of patterns associated with diagnosis, prognosis, and therapy response in digital pathology images often requires intractable labeling of large quantities of histological objects. Here we release an open-source labeling tool, PatchSorter, which integrates deep learning with an intuitive web interface. Using >100,000 objects, we demonstrate a >7x improvement in labels per second over unaided labeling, with minimal impact on labeling accuracy, thus enabling high-throughput labeling of large datasets.

Identifiers

PMID38902336
PMCPMC11190251

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.