Awesome Spatial Omics Niche¶
A curated guide to spatial niche analysis — organized by how each method defines "niche," not by publication date.
This site is the companion to the Awesome Spatial Omics Niche list. While the awesome list provides a curated index of the best resources, this site goes deeper with concept explanations, paper analyses, method comparisons, and practical guides.
The Core Question¶
Every spatial niche method makes an implicit choice: what does "niche" mean? A composition-based method counts neighboring cell types. An expression method averages neighboring transcriptomes. A communication method detects active signaling. These are genuinely different biological lenses, and the right choice depends on your question.
This site makes those implicit choices explicit.
How to Use This Site¶
- New to spatial niches? Start with What Is a Niche? and Niche vs Domain.
- Choosing a method? Browse the Methods section organized by niche definition type.
- Evaluating papers? See the Deep Reads for honest assessments of key papers.
- Preparing for benchmarks? Read State of Benchmarking and What to Measure.
- Attending the Colin Stroud Hackathon? Check Hackathon Context.
Site Structure¶
| Section | What You'll Find |
|---|---|
| Concepts | What a niche is, how it differs from a domain, and the functional niche frontier. |
| Methods | Methods organized by niche definition: composition, expression, covariance, communication, morphology, foundation models, and domain detection. |
| Deep Reads | 10 paper analyses with architecture details, honest verdicts, and design decisions. |
| Benchmarks | The state of benchmarking and what metrics actually matter. |
| Datasets | Key datasets organized by what niche definitions they support. |
| Synthesis | Cross-cutting essays on how definitions shape discovery and the causation frontier. |
| Glossary | Key terms and concepts defined. |