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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)
  • 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
  • Overview: module code

All modules for which code is available

  • goatpy.annotation
  • goatpy.auto_align
  • goatpy.filter
  • goatpy.graphpca_mod
  • goatpy.he_image
  • goatpy.io
  • goatpy.landmark_alignment
  • goatpy.preprocessing
  • goatpy.pseudo_image
  • goatpy.tools

© Copyright 2025, Andrew Causer.

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