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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
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