About

This repository contains scripts for programmatic access to Lichtman Lab datasets hosted by CAVE (Connectome Annotation and Versioning Engine). The scripts are written in Python and use the CAVEClient.

Supported Datasets

• H01 - (Shapson-Coe at al. 2024) - Latest Proofread Version
• Fish 1.0 - Latest Proofread Version (more coming soon)

Interactive proofreading can be done through this link - also check out the proofreading tutorial.

Getting Started

Local Environment

Setup a virtual environment using virtualenv.

For MacOS or Linux Users

git clone https://github.com/VCG/cave-scripts.git
cd cave-scripts
virtualenv -p python3.9 venv
source venv/bin/activate
pip install -r requirements.txt

For Windows Users

git clone https://github.com/VCG/cave-scripts.git
cd cave-scripts
python -m venv venv
.\venv\Scripts\Activate
pip install -r requirements.txt

Troubleshooting

• If you receive the error message virtualenv is not recognized, please install virtualenv using pip install virtualenv.

• When you try to activate the virtualenv with .\venv\Scripts\Activate and you have an error message cannot be loaded because running scripts is disabled on this system., you need to change the execution policy of the Powershell.

  Get-ExecutionPolicy # check this returns Restricted
  Set-ExecutionPolicy RemoteSigned -Scope CurrentUser
  Get-ExecutionPolicy # check this returns RemoteSigned
  

  Now, you can activate the virtualenv.

Request CAVE permission

Submit this form to request access. We will respond within 24h. If you don't hear back, please email us.

CAVE credentials

Use this script to get your CAVE credentials. This assumes you have been approved in the previous step already.

Tutorials

• Creating Custom Annotation Tables - notebook
• Visualizing CAVE annotation tables in Neuroglancer - notebook
• Downloading Meshes of Proofread Neurons - notebook
• Query Materialized Annotation Tables - notebook
• Uploading Custom Annotations to CAVE - notebook
• View Segment Proofreading Changelog - website_service
• Count Edits over Time (Admins only) - notebook
• Query Synapses - notebook

Limitations / Known Issues

Programmatic access to H01 & Fish 1.0 through CAVE is fairly new. So expect improvements, and please report bugs by opening an issue in the repository.

Acknowledgements

We thank Akhilesh Halageri, Sven Dorkenwald, Forrest Collman, Casey Schneider-Mizell, Chris Jordan, Nico Kemnitz, Derrick Brittain, and Will Silversmith for their efforts in making CAVE open-source.

Cite

Please consider citing the following articles, when using code from this repository.

@article{dorkenwald2023cave,
  title={CAVE: Connectome annotation versioning engine},
  author={Dorkenwald, Sven and Schneider-Mizell, Casey M and Brittain, Derrick and Halageri, Akhilesh and Jordan, Chris and Kemnitz, Nico and Castro, Manual A and Silversmith, William and Maitin-Shephard, Jeremy and Troidl,    Jakob and others},
  journal={bioRxiv},
  year={2023},
  publisher={Cold Spring Harbor Laboratory Preprints}
}

@article{shapson2024petavoxel,
  title={A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution},
  author={Shapson-Coe, Alexander and Januszewski, Micha{\l} and Berger, Daniel R and Pope, Art and Wu, Yuelong and Blakely, Tim and Schalek, Richard L and Li, Peter H and Wang, Shuohong and Maitin-Shepard, Jeremy and others},
  journal={Science},
  volume={384},
  number={6696},
  pages={eadk4858},
  year={2024},
  publisher={American Association for the Advancement of Science}
}