Cellular neighborhood | Average Nearest Neighbour Index (ANNI) | You can access the vignettes for other modules of SPIAT here: | Reproducibility | Author Contributions

Cells In Neighbourhood (CIN) | Mixing Score (MS) and Normalised Mixing Score (NMS) | Cross K function | Cross-K Intersection (CKI) | You can access the vignettes for other modules of SPIAT here: | Reproducibility | Author Contributions

Cell percentages | Cell distances | Pairwise cell distances | Minimum cell distances | You can access the vignettes for other modules of SPIAT here: | Reproducibility | Author Contributions

Characterising the distribution of the cells of interest in identified tissue regions | Determining whether there is a clear tumour margin | Automatic identification of the tumour margin | Classification of cells based on their locations relative to the margin | You can access the vignettes for other modules of SPIAT here: | Reproducibility | Author Contributions

Introduction | You can access the vignettes for other modules of SPIAT here: | Data reading and formatting | Quality control and visualisation | Basic analysis | Cell colocalisation | Spatial heterogeneity | Tissue structure | Cellular neighborhood | Installing SPIAT | Citing SPIAT | Author Contributions

Visualise marker levels | Boxplots of marker intensities | Scatter plots of marker levels | Heatmaps of marker levels | Identifying incorrect phenotypes | Removing cells with incorrect phenotypes | Dimensionality reduction to identify misclassified cells | Visualising tissues | Categorical dot plot | 3D surface plot | 3D stacked surface plot | You can access the vignettes for other modules of SPIAT here: | Reproducibility | Author Contributions

Reading in data | Reading in data through the 'general' option (RECOMMENDED) | Reading in data pre-formatted by other software | Reading in data from inForm | Reading in data from HALO | Inspecting the SpaitalExperiment object | Structure of a SPIAT SpatialExperiment object | Nomenclature | Splitting images | Predicting cell phenotypes | Specifying cell types | You can access the vignettes for other modules of SPIAT here: | Reproducibility | Author Contributions

Localised Entropy | Fishnet grid | Gradients (based on concentric circles) | You can access the vignettes for other modules of SPIAT here: | Reproducibility | Author Contributions