Welcome to corgie! corgie is a toolkit for registration of large 3D volumes.
The recommended installation method is pip-installing into a virtualenv:
git clone [email protected]:seung-lab/corgie.git cd corgie pip install -e .
Installation typically takes under 10 minutes.
To install the pinned versions of the package requirements, refer to the requirements-release.txt:
pip install -r requirements-release.txt
Corgie uses boto3 under the hood, so follow boto3's instructions to get credentials installed for Amazon SQS.
You can find demo walkthrough with links to the demo dataset and expected output in the Documentation.
- License: MIT
- Source Code: https://github.com/seung-lab/corgie
- Documentation: https://corgie.readthedocs.io/en/latest/
- Supported Python Versions: 3.7, 3.8, 3.9
- Supported OS: Ubuntu 18.04
@article {Popovych2022.03.25.485816,
author = {Popovych, Sergiy and Macrina, Thomas and Kemnitz, Nico and Castro, Manuel and Nehoran, Barak and Jia, Zhen and Bae, J. Alexander and Mitchell, Eric and Mu, Shang and Trautman, Eric T. and Saalfeld, Stephan and Li, Kai and Seung, Sebastian},
title = {Petascale pipeline for precise alignment of images from serial section electron microscopy},
elocation-id = {2022.03.25.485816},
year = {2022},
doi = {10.1101/2022.03.25.485816},
URL = {https://www.biorxiv.org/content/early/2022/03/27/2022.03.25.485816},
eprint = {https://www.biorxiv.org/content/early/2022/03/27/2022.03.25.485816.full.pdf},
journal = {bioRxiv}
}