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https://github.com/janeliascicomp/workstation

Janelia Workstation
https://github.com/janeliascicomp/workstation

confocal-microscopy connectomics janelia neuroimaging neuroscience scientific-computing volume-rendering

Last synced: about 7 hours ago
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Janelia Workstation

Host: GitHub
URL: https://github.com/janeliascicomp/workstation
Owner: JaneliaSciComp
License: other
Created: 2019-03-23T17:10:49.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2024-10-24T20:13:13.000Z (15 days ago)
Last Synced: 2024-10-26T11:22:37.020Z (13 days ago)
Topics: confocal-microscopy, connectomics, janelia, neuroimaging, neuroscience, scientific-computing, volume-rendering
Language: Java
Size: 98.2 MB
Stars: 23
Watchers: 15
Forks: 11
Open Issues: 11
Metadata Files:
- Readme: README.md
- License: LICENSE.md

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README

# Janelia Workstation

[![Java CI with Maven](https://github.com/JaneliaSciComp/workstation/actions/workflows/maven.yml/badge.svg)](https://github.com/JaneliaSciComp/workstation/actions/workflows/maven.yml)

The Janelia Workstation is a neuroscience discovery platform for processing, analysis, annotation, and sharing of large-scale 3D microscopy data.

![Workstation Screenshot](docs/screenshot.png)

The Janelia Workstation currently supports two large-scale team projects at Janelia Research Campus:
* The **HortaCloud** application built for [MouseLight](https://www.janelia.org/project-team/mouselight) has been fully open sourced and made available here with complete documentation. These tools enable neuron tracing and connectomics on terabyte-scale Mouse brain volumes.
* The [FlyLight](https://www.janelia.org/project-team/flylight) tools have been partially open sourced, but are not yet officially supported. At Janelia, these tools support search, browsing, and annotation of millions of confocal-imaged Fly nervous systems.

## License and Citation Agreement

This software uses a modified Janelia Open Source License, and requiring [citation](https://doi.org/10.25378/janelia.8182256.v1) when used for studies or publications. [For details see here](LICENSE.md).

## For Users

Read the [User Manual](docs/UserManual.md) to find out more about the Workstation's capabilities and how to use them.

## For System Administrators

### Deployment

The Workstation Client (this repository) is supported by a set of back-end services. Deploying all of these services is easily accomplished through the use of Docker containers orchestrated with either Docker Compose or Docker Swarm. Complete documentation about deploying the entire system is available in the [jacs-cm](https://github.com/JaneliaSciComp/jacs-cm) repository.

### MouseLight Deployment

The canonical two-server deployment of the MouseLight neuron tracing tools is described [here](https://github.com/JaneliaSciComp/jacs-cm/blob/master/docs/MouseLightDeployment.md).

## For Developers

For information about building this code base, see the [Development](docs/Development.md). To create an official release, see the [Release](docs/ReleaseProcess.md) documentation.