Evidence map›Paper›PMID 39564562›Full record

ArticleIEEE open journal of engineering in medicine and biology2025

Optimized Whole-Slide-Image H&E Stain Normalization: A Step Towards Big Data Integration in Digital Pathology.

Jose L Agraz, Carlos Agraz, Andrew A Chen, Charles Rice, Robert S Pozos, Sven Aelterman, Amanda Tan, Angela N Viaene, MacLean P Nasrallah, Parth Sharma and 8 more

Abstract read
In one paragraph

Article in IEEE open journal of engineering in medicine and biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

18 authors.

Jose L AgrazWilson Laboratory and Department of Pathology and Laboratory Medicine, Perelman School of MedicineUniversity of Pennsylvania Philadelphia PA 19104-4238 USA.ORCID https://orcid.org/0000-0001-6582-2783
Carlos AgrazWilson Laboratory, Perelman School of MedicineUniversity of Pennsylvania Philadelphia PA 19104-4238 USA.ORCID https://orcid.org/0009-0009-4036-2106
Andrew A ChenMedical University of South Carolina Charleston SC 29425 USA.ORCID https://orcid.org/0000-0002-5027-6422
Charles RiceMicrosoft Austin TX 78759 USA.ORCID https://orcid.org/0009-0009-5667-5406
Robert S PozosDepartment of BiologySan Diego State University San Diego CA 92182 USA.ORCID https://orcid.org/0000-0002-8498-8276
Sven AeltermanMicrosoft Nashville TN 37209 USA.ORCID https://orcid.org/0009-0002-1474-7335
Amanda TanInternet2 Washington DC 20036 USA.ORCID https://orcid.org/0000-0003-4891-7435
Angela N ViaeneDepartment of Pathology and Laboratory Medicine, Children's Hospital of PhiladelphiaUniversity of Pennsylvania Philadelphia PA 19104 USA.ORCID https://orcid.org/0000-0001-6430-8360
MacLean P NasrallahDepartment of Pathology and Laboratory Medicine, Perelman School of MedicineUniversity of Pennsylvania Philadelphia PA 19104-4238 USA.ORCID https://orcid.org/0000-0003-4861-0898
Parth SharmaSymphony Health Philadelphia PA 19422 USA.ORCID https://orcid.org/0000-0002-5701-0619
Caleb M GrenkoDepartment of Pathology and Laboratory Medicine, Perelman School of MedicineUniversity of Pennsylvania Philadelphia PA 19104-4238 USA.ORCID https://orcid.org/0000-0002-3926-5503
Tahsin KurcDepartment of Biomedical InformaticsStony Brook University Stony Brook NY 11794 USA.ORCID https://orcid.org/0000-0001-9237-4306
Joel SaltzDepartment of Biomedical InformaticsStony Brook University Stony Brook NY 11794 USA.ORCID https://orcid.org/0000-0002-3451-2165
Michael D FeldmanDepartment of Pathology and Laboratory Medicine, Perelman School of MedicineUniversity of Pennsylvania Philadelphia PA 19104-4238 USA.ORCID https://orcid.org/0000-0002-6661-4940
Hamed AkbariDepartment of Bioengineering, School of EngineeringSanta Clara University Santa Clara CA 95053 USA.ORCID https://orcid.org/0000-0001-9786-3707
Russell T ShinoharaCBICA and Penn Statistical Imaging and Visualization Endeavor (PennSIVE)University of Pennsylvania Philadelphia PA 19104 USA.ORCID https://orcid.org/0000-0001-8627-8203
Spyridon BakasPerelman School of MedicineUniversity of Pennsylvania Philadelphia PA 19104 USA.ORCID https://orcid.org/0000-0001-8734-6482
Parker WilsonDepartment of Pathology and Laboratory Medicine, Perelman School of MedicineUniversity of Pennsylvania Philadelphia PA 19104-4238 USA.ORCID https://orcid.org/0000-0001-8647-9662

Funding

Tumor Microenvironment and Metastasis ProgramP30CA082709 · NCI · INDIANA UNIV-PURDUE UNIV AT INDIANAPOLIS · PI Sara K Quinney · 1999 to 2026
$59.3M
The Single Cell Landscape of Early Human Diabetic NephropathyK08DK126847 · NIDDK · WASHINGTON UNIVERSITY · PI Parker C. Wilson · 2022 to 2026
$840k
NCI NIH HHS P30 CA082709NIDDK NIH HHS K08 DK126847
6 · The paper itself

Abstract

In the medical diagnostics domain, pathology and histology are pivotal for the precise identification of diseases. Digital histopathology, enhanced by automation, facilitates the efficient analysis of massive amount of biopsy images produced on a daily basis, streamlining the evaluation process. This study focuses in Stain Color Normalization (SCN) within a Whole-Slide Image (WSI) cohort, aiming to reduce batch biases. Building on published graphical method, this research demonstrates a mathematical population or data-driven method that optimizes the dependency on the number of reference WSIs and corresponding aggregate sums, thereby increasing SCN process efficiency. This method expedites the analysis of color convergence 50-fold by using stain vector Euclidean distance analysis, slashing the requirement for reference WSIs by more than half. The approach is validated through a tripartite methodology: 1) Stain vector euclidean distances analysis, 2) Distance computation timing, and 3) Qualitative and quantitative assessments of SCN across cancer tumors regions of interest. The results validate the performance of data-driven SCN method, thus potential to enhance the precision and reliability of computational pathology analyses. This advancement is poised to enhance diagnostic processes, therapeutic strategies, and patient prognosis.

Indexed as

Glioblastomanormalizationoptimizingpreprocessingstain-vectorswhole-slide-image

Identifiers

PMID39564562
PMCPMC11573418

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.