CASTalign

CASTalign (Coppafish, Antibody Staining, and Two-photon alignment) is a Python library for registering 3D microscopy images to each other and to in vivo two-photon imaging. It is optimized for aligning CoppaFISH 3D volumes, antibody staining (e.g., immunofluorescence), and in vivo imaging.

Main features

• Align images across modalities with shared, composable transforms.

• Edit and fit transforms using interactive Napari GUIs.

• Organize many transforms and images with a graph-based workflow.

Quick Start

Install with pip:

pip install castalign

Then follow the tutorial to learn how transforms, GUIs, and graphs fit together.

Documentation Map

• Tutorial: Conceptual overview, examples, and GUIs.

• Transforms Gallery: Visual transform examples with geometry and parameter defaults.

• FAQs: FAQs

• API Reference: Public classes and functions.

• Contact: Questions, bugs, and feedback.

Contents

• CASTalign
• Tutorial
  • Conceptual summary
  • Transforms
  • GUI
  • Graphs
  • Shifted NDArrays
• Transform Gallery
  • Data Geometries
  • Parametric / Direct Transforms
  • Point-based Transforms
• Frequently asked questions
  • Why is the “Perform transform” button in the GUI slower than I expect?
• API Reference
  • Transforms
  • Graphs
  • GUI
  • Utilities
  • Shifted Arrays
• Contact