Introduction | What this package does | Scope | The workflow | Installation | Quick start | The data model | Reading your own data | Loading the acquisitions | Pieces of one tissue | Selecting tissue pixels | Labelling regions of interest | What the labels look like downstream | Ion images | Colour-scale treatment | Quantile heatmaps across samples | Seeing which sample carried a group effect | Signal-to-noise filtering | Running a full study from a YAML config | Samples made of several acquisitions | Comparing regions of interest | The configuration as a record of the analysis | References | Session information

Introduction | Scope, and where this sits among related packages | Assumptions and limitations | How the package is organised | Installation | Quick start | Stage 1: data parse | The curated workbook | The TargetLynx export | The simulated dataset used from here on | Assembling a DatasetExperiment | Stage 2: peak-matrix processing | Blank filter | Detection filters | Batch correction | Normalise | Concentration adjustment | Impute missing values | The whole matrix in one call | Stage 3: QC check | How well was each compound measured? | Analytical drift | Normality | PCA | Loadings | What was reported, and what was dropped | Stage 4: statistics | Selecting the biological samples | Group summaries | Comparisons | Per-compound plots | Volcano | Heatmap | When the sample axis runs out | Feature correlations | Metabolite ratios | Driving it from a YAML config | Merging several acquisition panels | References | Session info

Introduction | On-slide versus on-tissue calibration | Scope and assumptions | Installation | Calibration workflow overview | The bundled calibration dataset | Fitting and diagnosing calibration models | Applying the models to a study section | Checking calibration coverage | Handling out-of-range pixels | Driving calibration from a study YAML | Interpretation and limitations | References | Session information