Getting started
Installation
Requirements
Recommended: conda environment
PyPI
From source (latest development version)
Optional dependencies
WSI support (SVS, NDPI, CZI files)
Getting Started with
goatpy
Tutorial
Loading and Aligning Data
Manual MALDI/H&E Alignment
Automatic MALDI/H&E Alignment
Loading with specific m/z values
Adding Pathologist annotations
Adding Annotations Using Manual Alignment
Adding Annotations Using Automatic Alignment
Assigning Annotations to the Pixel Level
Subsetting Data
Saving and Loading
goatpy
Ojects
Plotting and Visualising Results
Adjusting Plot Colour Palettes
Tutorial Session Info
Tutorials
Aligning Spatial Glycomics and IHC images
Manual Alignment
Automatic Alignment
Spatially Informed Clustering (GraphPCA)
Align Additional Image Layers
Tutorial Session Info
Multi-Sample
goatpy
Analysis Tutorial
Loading Data
Data Preprocessing
Merging Data
Using
scanpy
function with
goatpy
Batch Correction with
goatpy
m/z peak glycan annotation
Differential Abundance Analysis
Comparing Pathologist Annotation
Tutorial Session Info
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
IHC support
Coordinate system
Functions
Module Contents
goatpy.batch_correction
USAGE
Functions
Module Contents
goatpy.bin
Key concepts
Usage
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.plotting
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