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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
Data import
Build an
InSituData
object from custom data
Addition of data segmented with proseg
Plotting
Spatial plotting functionalities
Plot colorlegends for publication
Analysis from manuscript
Differential gene expression analysis for publication Figure 4
API
insitupy.InSituData
insitupy.InSituExperiment
insitupy.MultiCellData
insitupy.CellData
insitupy.BoundariesData
insitupy.ImageData
insitupy.AnnotationsData
insitupy.RegionsData
insitupy.read_xenium
insitupy.io.read_qupath_geojson
insitupy.io.read_celldata
insitupy.io.read_multicelldata
insitupy.io.read_shapesdata
insitupy.plotting.plot_spatial
insitupy.plotting.plot_cellular_composition
insitupy.plotting.cell_abundance_along_axis
insitupy.plotting.cell_expression_along_axis
insitupy.plotting.volcano_plot
insitupy.plotting.plot_colorlegend
insitupy.plotting.plot_overview
Repository
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.rst
.pdf
insitupy.io.read_shapesdata
Contents
read_shapesdata()
insitupy.io.read_shapesdata
#
insitupy.io.
read_shapesdata
(
path
,
mode
,
scale_factor
=
None
)
#
Contents
read_shapesdata()
