Chrysalis

Chrysalis uncovers tissue compartments in spatial transcriptomics data through spatially variable gene detection and archetypal analysis without requiring external reference data.

Key Features:

• Reference-free analysis: Performs archetypal analysis without dependence on single-cell reference data.
• Spatially variable gene detection: Identifies spatially variable genes as part of the compartment uncovering process.
• Visualisation approach: Provides a unique visualisation method for swift tissue characterisation.
• Gene expression signature access: Enables retrieval of underlying gene expression signatures for identifying spatially and functionally distinct cellular niches.
• Cross-technology compatibility: Supports multiple spatial transcriptomics technologies including Visium, Visium HD, Slide-seq, and Stereo-seq.

Scientific Applications:

• Tissue compartment dissection: Decodes tissue compartments in spatial transcriptomics data with limited spatial resolution.
• Cellular niche identification: Identifies spatially and functionally distinct cellular niches through gene expression signatures.
• Performance benchmarking: Validated against deconvolution, independently obtained cell type abundance data, and histopathological annotations on in silico and real-world examples.

Methodology:

Chrysalis rapidly uncovers tissue compartments through spatially variable gene detection and archetypal analysis.