Package: MultiAssaySpatialExperiment 0.99.2

Installation | Citing MultiAssaySpatialExperiment | Why another spatial data structure? | When to use MASE | Anatomy of a MultiAssaySpatialExperiment | Overview | Components | ExperimentList: assay data | colData: specimen metadata | sampleMap: assay-to-specimen mapping | points: spatial coordinates | shapes: spatial geometries | images: raster images | labels: segmentation masks | spatialMap: assay-to-spatial mapping | imgData: specimen-to-image mapping | Quick Start: Building a MASE object | Accessors | Inherited from MultiAssayExperiment | Spatial element accessors | Mapping accessors | Subsetting | Spatial operations | Coercion | Quick reference | Next steps | Session info

Introduction | Building MASE objects | prepMASE and buildSpatialMap | Optional: lazy Parquet I/O via BiocDuckDB | Minimal MASE | Adding spatial coordinates | Adding spatial shapes | Building from multiple SingleCellExperiment objects | Validation checklist | Subsetting operations | Overview of subsetting operations | Basic subsetting | Subset by specimen (colData) | Subset by assay columns | Bracket notation | Spatial subsetting | Subset by bounding box | Subset by polygon | Multi-region subsets | Buffer-based subsets | Spatial annotation and aggregation | Example setup | Annotate with regions | Aggregate by region | Count points per region | Sum expression per region | Mean expression per region | Lower-level spatial joins | Aggregation strategies | Visualizing aggregated data | Labels ↔ shapes interoperability | Rasterization: shapes → labels | Vectorization: labels → shapes | Use cases | Next steps | Session info

Introduction | Part 1: Data Import | Reading Xenium data | Basic usage | Options | When to load transcripts | Reading Visium data | Visium HD support | Reading CosMx data | FOV (Field of View) handling | Reading MERSCOPE data (MERFISH) | Choosing a reader | Converting from other Bioconductor classes | From SpatialExperiment | From SpatialFeatureExperiment | Reading multiple samples | Part 2: Real-World Workflows | Workflow 1: Xenium + Visium integration | Background | Data preparation | Build MASE object | Exploratory analysis | Visualize spatial distribution | Gene expression overlap | Spatial annotation: Cell types in Visium spots | Visualize deconvolution results | Spatial aggregation: Summarize Xenium by regions | Comparative analysis | Integration insights | Workflow 2: Coordinate transformation and alignment | Converting Visium grid to microns | Applying affine transformations | Landmark-based alignment | Storing transformed coordinates | Visualizing alignment | Workflow 3: Multi-sample analysis | Workflow 4: Iterative analysis pattern | Summary | Session info