Designing smart spatial omics experiments with S2-omics v1
A protocol describing the application of S2-omics on a colorectal cancer tissue section, designing 10x VisiumHD experiment. S2-omics is an end-to-end workflow that automatically selects regions of interest for spatial omics experiments using histology images. Additionally, S2-omics utilizes the resulting spatial omics data to virtually reconstruct spatial molecular profiles across entire tissue sections, providing valuable insights to guide subsequent experimental steps. Our histology image-guided design significantly reduces experimental costs while preserving critical spatial molecular variations, thereby making spatial omics studies more accessible and cost-effective. We demonstrate S2-omics’s utility in selecting a 6.5mm × 6.5mm ROI and predicting the cell-type labels for the whole slide image after conducting VisiumHD experiment on the selected ROI.
Authors
- Kaidi Jin (ORCID: https://orcid.org/0009-0007-7843-1133)
- Amelia Schroeder
- Idania Carolina Lubo Julio (ORCID: https://orcid.org/0009-0002-0545-1444)
- Tae Hyun Hwang (ORCID: https://orcid.org/0000-0002-6668-7269)
- Sicong Yao (ORCID: https://orcid.org/0009-0001-4636-6812)
- Hanying Yan (ORCID: https://orcid.org/0000-0002-9227-1742)
- Emma E. Furth (ORCID: https://orcid.org/0000-0002-9309-985X)
- Linghua Wang (ORCID: https://orcid.org/0000-0001-9380-0266)
- Tianhao Luo
- Jonathan Levinsohn (ORCID: https://orcid.org/0000-0003-0263-2362)
- Katalin Suszták (ORCID: https://orcid.org/0000-0002-1005-3726)
- Musu Yuan (ORCID: https://orcid.org/0000-0002-5674-1639)
- Parker C. Wilson (ORCID: https://orcid.org/0000-0001-8647-9662)
- Jean R. Clemenceau (ORCID: https://orcid.org/0000-0002-6222-6457)
- Anupma Nayak (ORCID: https://orcid.org/0000-0002-7445-1897)
- Luisa M. Solis Soto (ORCID: https://orcid.org/0000-0002-1253-630X)
- Inyeop Jang
- Min‐Ji Kim (ORCID: https://orcid.org/0000-0001-5102-0536)
- Jeong Hwan Park (ORCID: https://orcid.org/0000-0003-4522-9928)
- Yunhe Liu (ORCID: https://orcid.org/0000-0002-2120-952X)
- Mingyao Li (ORCID: https://orcid.org/0000-0001-8180-0621)
- Minghua Deng (ORCID: https://orcid.org/0009-0003-2871-7089)
- Chunyu Luo
- Bernhard Domoulin
Publication Details
- Published
- 2025-10-08
- DOI
- https://doi.org/10.17504/protocols.io.bp2l6zpnkgqe/v1
- Primary Topic
- Cognitive Science and Mapping
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- University of Pennsylvania