castalign 0.3.2

Coppafish, Antibody Staining, and Two-photon alignment: 3D alignment framework for microscopy and in vivo imaging

CASTalign: Coppafish, Antibody Staining, and Two-photon alignment

CASTalign allows you to register hundreds of 3D microscopy images to each other and to in vivo two-photon imaging. It is optimised to allow registration between large datasets including coppaFISH 3D, immunofluorescence labelling, and in vivo imaging.

Installation

To install:

pip install castalign

You may also want to install (optional) GPU acceleration with cupy. Depending on the version of CUDA, install one of these:

pip install cupy-cuda13x # For CUDA 13.x
pip install cupy-cuda12x # Fox CUDA 12.x

Alternatively, you can install from github:

pip install git+https://github.com/mwshinn/castalign.git

Usage

See the tutorial in the documentation.