brainreg3D

A pipeline for manual registration of cortical regions using 3D projection onto an experimentally obtained 2D image.

Register a widefield image using the command line:

$ python -m brainreg3D ./your_image.tif

Write custom python scripts to register images:

#!/usr/bin/python3

from brainreg3D import BrainReg3D
reg = BrainReg3D('./your_image.tif')
reg.run()

description.md contains a more thorough overview of the workflow.

Installation

Installation can be done in one of two ways: install using pip, or through repo cloning and manual installation. The latter is recommended for the example scripts and data to be included in the install.

Clone repository

Windows

python -m venv .venv
./.venv/Scripts/Activate.ps1

git clone https://github.com/JoeRicotta/brainreg3D.git
cd brainreg3D

python -m pip install -r requirements.txt
python example.py

Mac

python3 -m venv .venv
source .venv/bin/activate

git clone https://github.com/JoeRicotta/brainreg3D.git
cd brainreg3D

pip install -r requirements.txt

python example.py

Install with pip

(pypi repo is in alpha, no guarantees on successful install.)

python -m pip install -i https://test.pypi.org/simple/ brainreg3D

Acknowledgements

brainreg3D relies heavily upon the vedo and brainrender frameworks. Thank you to these teams for making this pipeline possible.