TissueViewer: a web-based multiplexed image viewer.

David Gerardus Pieter van IJzendoorn, Magdalena Matusiak, Rob West, Matt van de Rijn

Abstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

4 authors.

David Gerardus Pieter van IJzendoornDepartment of Pathology, Stanford University, Stanford, CA 94305, United States.ORCID 0000-0002-2249-5919

Magdalena MatusiakDepartment of Pathology, Stanford University, Stanford, CA 94305, United States.

Rob WestDepartment of Pathology, Stanford University, Stanford, CA 94305, United States.

Matt van de RijnDepartment of Pathology, Stanford University, Stanford, CA 94305, United States.

Funding

Studying macrophage polarization in search for predictive and prognostic markers of breast cancerR01CA229529 · NCI · STANFORD UNIVERSITY · PI Robert michael Angelo, Magdalena Matusiak · 2018 to 2026

$3.9M

NCI NIH HHS R01 CA229529Virginia and D.K. Ludwig 2 R01 CA229529

6 · The paper itself

Abstract

motivationDatasets generated by spatial biology techniques such as multiplex immunofluorescence staining or spatial transcriptomics profiling of histologic sections carry a tremendous wealth of information. Several commercial platforms exist that can simultaneously acquire 1-1000 distinct marker signals (e.g. MIBI, CODEX, Orion, Nanostring CosMX SMI, Vizgen). However, due to the large size of these datasets, their viewing and sharing are slow, laborious, and require extensive computational resources.

resultsTo overcome these challenges, we developed TissueViewer, an easy to setup and use web-based viewer designed to deliver high-resolution images over the internet with low bandwidth requirements and at high speed. AVAILABILITY AND IMPLEMENTATION: TissueViewer is available on GitHub (https://github.com/davidvi/tissueviewer) and can be used on the TissueViewer.org platform, where readers can upload their own data with a limit of 50 GB to share with colleagues.

Indexed as

Computational BiologyImage Processing, Computer-AssistedInternetSoftwareHumans

Identifiers

PMID40279289

DOI10.1093/bioinformatics/btaf246

PMCPMC12119129

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.