Getting started
Installation
Requirements
Recommended: conda environment
PyPI
From source (latest development version)
Optional dependencies
WSI support (SVS, NDPI, CZI files)
Quickstart
Load and register MALDI + H&E
Normalise
Dimensionality reduction
Clustering
Visualise
Add annotations to an existing sdata object
User guide
Loading and aligning MALDI + H&E
Overview
Basic usage
Parameters
Output SpatialData structure
Custom peaks
Registration quality
QuPath annotations
During registration
After registration
Exporting from QuPath
Accessing annotation labels
Visualising with spatialdata-plot
GraphPCA and clustering
GraphPCA
Spatial smoothing
K-means clustering
Visualising clusters as a pseudo-image
Pseudo-image generation
Categorical columns
Continuous columns
Parameters
Output
Landmark alignment GUI
Launch the GUI
Workflow
Apply the alignment
Multiscale images
API reference
goatpy
Submodules
goatpy.annotation
Functions
Module Contents
goatpy.auto_align
Key design decisions
Coordinate system
Functions
Module Contents
goatpy.data
goatpy.filter
Usage
Functions
Module Contents
goatpy.graphpca_mod
Functions
Module Contents
goatpy.he_image
Functions
Module Contents
goatpy.io
Functions
Module Contents
goatpy.landmark_alignment
Classes
Functions
Module Contents
goatpy.preprocessing
Functions
Module Contents
goatpy.pseudo_image
Functions
Module Contents
goatpy.tools
Functions
Module Contents
Development
Changelog
0.1.0 (2025)
New features
Breaking changes from 0.0.1
Contributing
Development setup
Running tests
Building the docs locally
goatpy
goatpy
goatpy.data
Edit on GitHub
goatpy.data