Evidence map›Paper›PMID 41889839›Full record

ArticlebioRxiv : the preprint server for biology2026

CROCHET: a versatile pipeline for automated analysis and visual atlas creation from single-cell spatialomic data.

Behnaz Bozorgui, Guillaume Thibault, Chunyu Yuan, Zeynep Dereli, Huamin Wang, Michael J Overman, John N Weinstein, Anil Korkut

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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

8 authors.

Behnaz BozorguiDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Guillaume ThibaultBiomedical Engineering, Oregon Health & Science University, Portland, OR, 97239, USA.
Chunyu YuanDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Zeynep DereliDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Huamin WangDepartment of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Michael J OvermanDepartment of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
John N WeinsteinDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Anil KorkutDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

Funding

Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Fabien Delerue · 1985 to 2026
$290.8M
Mechanistic maps of adaptive responses to therapeutic stress to optimize combination therapies.U01CA253472 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI KORKUT, ANIL, LIANG, HAN · 2021 to 2025
$2.6M
NCI NIH HHS P30 CA016672NCI NIH HHS U01 CA253472
6 · The paper itself

Abstract

Spatial biology technologies offer a unique opportunity to link tissue composition with function. However, analytical methods for quantifying and interpreting highly complex spatial data remain limited. We present CROCHET (ChaRacterization Of Cellular HEterogeneity in Tissues), an end-to-end analysis pipeline for construction of spatially resolved cell atlases from raw data covering millions of cells across large sample cohorts. Its modular architecture supports the integration of diverse data modalities and novel analytical methods for image processing and segmentation, spatialomics quantification and downstream analyses. With comprehensive, open-source, user-friendly, interactive, and visual analysis modules, CROCHET aims to democratize spatial omics for a broad community of users.

Identifiers

PMID41889839
PMCPMC13015496

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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.