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.

CASTalign is described in the coppaFISH 3D preprint: Prankerd and Shinn et al., 2026.

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

Contents