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Installation
Getting started
Preparations
Download of datasets
Extract images of individual samples from whole slide image
Step-by-step analysis
Automated image registration
Data preprocessing and analysis
Working with histological annotations and regions
Cropping the data
Cell type annotation
Investigate gene expression and cell density along an axis
Differential gene expression and GO term enrichment analysis
Multi-sample analysis
Introduction to the
InSituExperiment
class
Performing pseudobulking on the
InSituExperiment
object
Data import
Addition of data segmented with proseg
Build an
InSituData
object from custom data
Reading data from QuPath projects
Plotting
Spatial plotting functionalities
Plot colorlegends for publication
Analysis from manuscript
Differential gene expression analysis for publication Figure 4
API
insitupy.InSituData
insitupy.InSituData.read
insitupy.InSituExperiment
insitupy.InSituExperiment.read
insitupy.InSituExperiment.from_config
insitupy.InSituExperiment.from_regions
insitupy.InSituExperiment.concat
insitupy.dataclasses.CellData
insitupy.dataclasses.MultiCellData
insitupy.dataclasses.BoundariesData
insitupy.dataclasses.ImageData
insitupy.dataclasses.ShapesData
insitupy.dataclasses.AnnotationsData
insitupy.dataclasses.RegionsData
insitupy.dataclasses.read_celldata
insitupy.dataclasses.read_multicelldata
insitupy.dataclasses.read_shapesdata
insitupy.io.read_qupath
insitupy.io.read_xenium
insitupy.io.read_qupath_project
insitupy.plotting.spatial
insitupy.plotting.cellular_composition
insitupy.plotting.cell_abundance_along_axis
insitupy.plotting.cell_expression_along_axis
insitupy.plotting.volcano
insitupy.plotting.colorlegend
insitupy.plotting.overview
Repository
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