https://github.com/janeliascicomp/neuronbridge

EM/LM neuron search
https://github.com/janeliascicomp/neuronbridge

aws drosophila janelia neuroimaging neurons neuroscience

Last synced: about 1 month ago
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EM/LM neuron search

• Host: GitHub
• URL: https://github.com/janeliascicomp/neuronbridge
• Owner: JaneliaSciComp
• License: bsd-3-clause
• Created: 2020-04-20T21:29:13.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2024-10-29T18:10:12.000Z (about 2 months ago)
• Last Synced: 2024-10-29T20:13:30.591Z (about 2 months ago)
• Topics: aws, drosophila, janelia, neuroimaging, neurons, neuroscience
• Language: JavaScript
• Homepage: https://neuronbridge.janelia.org
• Size: 36.4 MB
• Stars: 4
• Watchers: 7
• Forks: 1
• Open Issues: 8
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
# NeuronBridge

[![DOI](https://zenodo.org/badge/257408159.svg)](https://zenodo.org/badge/latestdoi/257408159)

[![Node.js CI](https://github.com/JaneliaSciComp/neuronbridge/actions/workflows/node.js.yml/badge.svg)](https://github.com/JaneliaSciComp/neuronbridge/actions/workflows/node.js.yml)

[![bioRxiv](https://img.shields.io/badge/bioRxiv-10.1101%2F2022.07.20.500311%20-red)](https://www.biorxiv.org/content/10.1101/2022.07.20.500311v1)

[![Follow on Twitter](http://img.shields.io/badge/twitter-%40NeuronBridge-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/NeuronBridge)



  



NeuronBridge is a web-based service for neuron matching and searching in _Drosophila melanogaster_. It indexes large data sets of LM and EM imagery to enable finding similar neurons across modalities and data sets. The software is described in [this paper](https://doi.org/10.1186/s12859-024-05732-7).

[![Janelia's production instance of NeuronBridge](https://img.shields.io/static/v1?style=for-the-badge&logo=&label=&message=View%20Production%20Site&color=008B94)](https://neuronbridge.janelia.org/)

## Source Code

This repository contains the web client. Other related repositories:

* [neuronbridge-services](https://github.com/JaneliaSciComp/neuronbridge-services) - Backend implementation

* [neuronbridge-aligners](https://github.com/JaneliaSciComp/neuronbridge-aligners) - Aligner implementation

* [neuronbridge-precompute](https://github.com/JaneliaSciComp/neuronbridge-precompute) - Precompute scripts

* [neuronbridge-python](https://github.com/JaneliaSciComp/neuronbridge-python) - Python API

* [neuronbridge-vol-viewer](https://github.com/JaneliaSciComp/neuronbridge-vol-viewer) - Web-based 3D Volume Viewer

* [colormipsearch](https://github.com/JaneliaSciComp/colormipsearch) - Color Depth MIP Search Algorithms

## Data Availability

The imagery and metadata are stored on AWS S3, and are available for browsing and reuse, subject to the license agreement:

* [Color Depth MIPS](https://open.quiltdata.com/b/janelia-flylight-color-depth)

* [Precomputed CDM match metadata](https://open.quiltdata.com/b/janelia-neuronbridge-data-prod)

* [Precomputed PPPM match metadata](https://open.quiltdata.com/b/janelia-ppp-match-prod)

## Release Notes

View the [Release Notes](public/RELEASENOTES.md) for a history of changes to the web client.

## Development

Read the [Developer's Guide](docs/Development.md) for more information about developing and deploying this service.

## License

All code related to NeuronBridge is made available under the [3-Clause BSD License](LICENSE.md).

All data served by the application is made available under the [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/).

Studies and publications that use this software should cite [doi:10.1101/2022.07.20.500311]().