https://github.com/mhturner/SC-FC

Analysis scripts for structural / functional connectivity using Drosophila hemibrain connectome and whole brain calcium imaging
https://github.com/mhturner/SC-FC

Last synced: 3 months ago
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Analysis scripts for structural / functional connectivity using Drosophila hemibrain connectome and whole brain calcium imaging

• Host: GitHub
• URL: https://github.com/mhturner/SC-FC
• Owner: mhturner
• License: mit
• Created: 2020-04-23T20:40:05.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2021-02-22T21:44:16.000Z (over 3 years ago)
• Last Synced: 2024-01-17T12:12:39.235Z (5 months ago)
• Language: Python
• Size: 451 KB
• Stars: 4
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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• awesome-stars - SC-FC

README

        
# SC-FC

Analysis and figure generation code for Turner, Mann, Clandinin: The connectome predicts resting state functional connectivity across the Drosophila brain

------------

To install, cd to the top level of the repository, where setup.py lives and:

pip install -e .

-or-

pip3 install -e .

Before you can run the Python code, you need to define a config.yaml file. See config_example.yaml and enter the path to the (functional) data directory, the path to where saved analysis should go, and your neuprint token to access the hemibrain dataset.

------------

To run the R code, you should install the natverse (http://natverse.org/) and define the following environment variables in your .Renviron file:

-GITHUB_PAT

-neuprint_server (e.g. "https://neuprint.janelia.org")

-neuprint_token

-neuprint_dataset (e.g. "hemibrain:v1.2")