Reference ownership and reproducibility | Build once, inspect before testing | Annotate experiment features without altering expression | Use the whole measured panel as the universe | One membership index for enrichment, expression and plots

Analysis questions determine the workflow | Supply modalities and study design explicitly | Compare representations using the same observations and features | Region characterization is richer than a mean difference | Keep biological-replicate inference separate | Ask whether colocalization survives regional composition | Map identities before pathway statistics | Apply the workflow to complete reference sections | Render and retain a reviewable analysis

Overview | RaMP snapshot and identifiers | A small 2-hydroxyglutarate example | From functional groups to ion-mode behaviour | Validated adduct rules | Build the reusable index | Chemical validity pruning | Query and rank candidates | Adduct-family support | Mass-defect heuristic | Annotate individual values or a SpaMTP object | Choose thresholds without re-annotation | Production use with the complete RaMP table | Carry the annotation threshold into real pathway analysis | Interpretation and limitations

One container, public accessors | Read a binned MSI table | Pixel and feature metadata | Coordinates and optical images | Paired modalities and standard subsetting | Optional Seurat boundary

Membership and topology are separate resources | Identifier consolidation | Interaction correction | Loading and inspecting corrected graphs | Reproducing the correction

Clear responsibilities | Data to a native analysis container | Database discovery without network access | Annotate without inventing a downloaded database | Published native datasets and historical archives

Overview | Bioconductor container model | A binned MSI workflow | Alignment and pixel mapping | Binning and statistical reuse | Native feature plots and annotation ranking | Optional Seurat conversion boundary | Inspect available database resources | Create a small structure-aware database | Build and query an indexed search space | Reproducibility

Introduction | A native example without downloads | Published native datasets | Loading a published native dataset | Session information

Introduction | Where the resources are stored | Inspecting resources without downloading | Retrieving a resource | Retrieving a coherent bundle | Working from a staged directory | The three-package workflow | Recording the version used | Session information