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 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.
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
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
(pypi repo is in alpha, no guarantees on successful install.)
python -m pip install -i https://test.pypi.org/simple/ brainreg3D
brainreg3D relies heavily upon the vedo and brainrender frameworks. Thank you to these teams for making this pipeline possible.