STAPLE: automating spatial transcriptomics analysis and AI interpretation
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.
Authors
- Kranthi Vavikolanu
- André Forjaz (ORCID: https://orcid.org/0009-0002-5115-2293)
- Wesley Tansey (ORCID: https://orcid.org/0000-0002-5294-4228)
- Dimitrios N. Sidiropoulos (ORCID: https://orcid.org/0000-0001-5716-3917)
- Brian R. Herb (ORCID: https://orcid.org/0000-0002-5910-9647)
- Ivette Santana-Cruz (ORCID: https://orcid.org/0000-0002-8111-0361)
- Dmitrijs Lvovs (ORCID: https://orcid.org/0009-0003-2152-6853)
- Alexander V. Favorov (ORCID: https://orcid.org/0000-0003-2595-1091)
- Luciane T. Kagohara (ORCID: https://orcid.org/0000-0003-1706-0950)
- Orian Stapleton
- Meredith Wetzel (ORCID: https://orcid.org/0009-0005-6955-3521)
- Demystifying Pancreatic Cancer Therapies TeamLab
- Atul Deshpande
- Ashley L Kiemen
- Elana J. Fertig
- Jeffrey Quinn
- Anirban Maitra
- Michael Noble
- Laura Wood
Institutions
- Human Genome Sciences (United States) (US)
- University of Maryland, Baltimore (US)
- Memorial Sloan Kettering Cancer Center (US)
- The University of Texas MD Anderson Cancer Center (US)
- Johns Hopkins University (US)
- Johns Hopkins Medicine (US)
- NYU Langone Health (US)
- Cancer Research Center (US)
- New York University (US)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-04-01
- DOI
- https://doi.org/10.64898/2026.03.30.715127
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Johns Hopkins University
- Break Through Cancer
- National Institutes of Health
- National Institute on Aging
- National Institute on Drug Abuse
- National Cancer Institute