STAPLE: automating spatial transcriptomics analysis and AI interpretation
Date: | April 1, 2026 |
PMCID: | |
Category: | N/A |
Authors: | Dmitrijs Lvovs, Jeffrey Quinn, André Forjaz, Ivette Santana-Cruz, Orian Stapleton, Kranthi Vavikolanu, Meredith Wetzel; Demystifying Pancreatic Cancer Therapies TeamLab; Data Science Hub Teamlab; Vincent Bernard, Brian R Herb, Alexander Favorov, Luciane T Kagohara, Ashley L Kiemen, Anirban Maitra, Dimitrios N Sidiropoulos, Wesley Tansey, Laura D Wood, Atul Deshpande, Michael Noble, Elana J Fertig |
Abstract: |
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This is a preprint.
It has not yet been peer reviewed by a journal.
The National Library of Medicine is running a pilot to include preprints that result from research funded by NIH in PMC and PubMed.
Spatial transcriptomics workflows often span separate tools for cell typing, neighborhoods, and cell-cell communication, yielding fragmented outputs that hinder scalability, interpretation, and reproducibility. STAPLE systematizes analyses across distinct methods into a modular framework, unifying data structures and cross-tool interoperability. End-to-end analyses are performed unassisted with a single invocation, fostering rigorous, reproducible spatial transcriptomics analysis. Its novel, AI-enabled reporting layer synthesizes quantitative results into summaries of biological findings, facilitating analysis interpretation.
Acknowledgements:
The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute, or the National Institute of Health.
The Translational and Basic Science Research in Early Lesions (TBEL) Research Consortia is supported and funded by grants from the National Cancer Institute and the National Institutes of Health under the following award numbers:
Project Number: | Awardee Organization |
U54CA274374 | Fred Hutchinson Cancer Center |
U54CA274375 | Houston Methodist Research Institute |
U54CA274370 | Johns Hopkins University |
U54CA274371 | UT MD Anderson Cancer Center |
U54CA274367 | Vanderbilt University Medical Center |
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