API

Core Dataclasses

InSituData([path, metadata, slide_id, sample_id])	InSituData class for managing and analyzing spatially resolved transcriptomics data.
InSituExperiment()	Class to manage and analyze multiple spatially resolved single-cell transcriptomics experiments.
MultiCellData()	Data object containing multiple CellData objects.
CellData(matrix, boundaries[, config])	Data object containing an AnnData object and a boundary object which are kept in sync.
BoundariesData(cell_names, seg_mask_value)	Object to read and load boundaries of cells and nuclei.
ImageData([img_files, img_names, pixel_size])	Object to read and load images.
AnnotationsData([files, keys, pixel_size])
RegionsData([files, keys, pixel_size])

Core reading functions

read_xenium(path[, nuclei_type, ...])

Reads Xenium In Situ data from the specified directory.

IO

io.read_qupath_geojson(file)	Reads a QuPath-compatible GeoJSON file and transforms it into a flat DataFrame.
io.read_celldata(path)
io.read_multicelldata(path[, path_upper, ...])
io.read_shapesdata(path, mode[, scale_factor])

Plotting

plotting.plot_spatial(data, keys[, ...])
plotting.plot_cellular_composition(data, ...)	Plots the composition of cell types for specified regions or annotations.
plotting.cell_abundance_along_axis(adata, axis)	Plot cell abundance along a specified observation value.
plotting.cell_expression_along_axis(adata, ...)	Plot gene expression along a specified axis for a given cell type.
plotting.volcano_plot(data[, ...])	Create a volcano plot from the DataFrame and label the top 20 most significant up and down-regulated genes.
plotting.plot_colorlegend(viewer[, ...])
plotting.plot_overview(data[, cells_layer, ...])	Plots an overview table with metadata and quality control metrics.