Coppafish, Antibody Staining, and Two-photon alignment: 3D alignment framework for microscopy and in vivo imaging
Project description
CASTalign: Coppafish, Antibody Staining, and Two-photon alignment
CASTalign allows you to register 3D microscopy images to each other and to in vivo two-photon imaging. It is optimised to allow registration between CoppaFISH 3D, antibody staining (e.g., immunofluorescence), 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.
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