visiumStitched

visiumStitched facilitates stitching images and gene expression data from multiple overlapping Visium capture areas into unified SpatialExperiment objects for downstream spatial transcriptomics analysis.

Key Features:

• SpaceRanger output preparation: Prepares 10x Genomics SpaceRanger output files for image stitching with Fiji (ImageJ).
• SpatialExperiment construction: Builds SpatialExperiment objects containing stitched images and gene expression data from multiple capture areas.
• Artificial hexagonal grid generation: Constructs an artificial hexagonal array grid enabling seamless use of spatial clustering methods that rely on such grids to identify neighboring spots, such as PRECAST and BayesSpace.
• spatialLIBD compatibility: Creates SpatialExperiment objects compatible with spatialLIBD for interactive visualization of stitched data.
• Seurat conversion: Enables casting SpatialExperiment objects as Seurat objects.

Scientific Applications:

• Multi-capture area spatial transcriptomics: Enables analysis of larger tissue structures that exceed standard Visium capture area dimensions (6.5mm by 6.5mm) by combining overlapping images and associated gene expression data.
• Spatially-aware clustering: Supports downstream spatial clustering analyses including PRECAST and BayesSpace without discarding data from overlapping spots.
• Interactive visualization: Allows interactive web-based visualization of stitched spatial transcriptomics datasets through spatialLIBD compatibility.

Methodology:

visiumStitched relies on affine transformations performed by Fiji (ImageJ) for image alignment and stitching of Visium capture areas.