Thinking spatially: a conceptual roadmap for designing spatial transcriptomics studies
Recent advances in spatial transcriptomics technologies have enabled researchers to address biological questions that depend on the spatial organization of cells and tissues. In this roadmap, we provide an intuitive, conceptually driven introduction to spatial transcriptomics for life science researchers new to the field. Rather than focusing on technical details, we emphasize how to design research and computational analysis starting from a biological question. Through conceptual explanations and practical examples, we aim to provide question-driven guidance for designing, generating, analyzing, and interpreting a spatial transcriptomics study.
Authors
- Sadia Afrin Bristy
- Mishal Roy (ORCID: https://orcid.org/0000-0001-7560-4392)
- Prashanna Koirala (ORCID: https://orcid.org/0000-0002-7920-0771)
- Anita Shrestha (ORCID: https://orcid.org/0000-0001-9581-8750)
- Prabin Dawadi (ORCID: https://orcid.org/0000-0003-1927-7221)
- Sayaka Miura (ORCID: https://orcid.org/0000-0001-9881-2848)
- Nusrath Jahan Emu (ORCID: https://orcid.org/0009-0002-7921-3895)
- Saroj Nepal
- Anupa Wasti (ORCID: https://orcid.org/0009-0009-8485-6554)
- Dikshya Niraula
- Md Tarikul Islam
- Bivek Pokharel
- Nick Nighswander
- Kent G. Bynum
- Anand P. Singh
Institutions
- University of Mississippi (US)
Publication Details
- Journal
- Frontiers in Genetics
- Published
- 2026-11-03
- DOI
- https://doi.org/10.3389/fgene.2026.1958622
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.00