Collaborative neuron annotation in the cloud

Documentation Login to HortaCloud-Janelia

HortaCloud software provides an efficient production environment for collaborative and accurate reconstruction of long range projection neurons in light microscopy data. This software, originally developed for Janelia’s MouseLight Team Project, has allowed annotators to efficiently reconstruct entire axonal arbors of individual neurons from whole-brain light microscopy data.

Automated deployment

Using the AWS CDK, you or your system administrator can easily deploy the entire software stack to an AWS Account with a single installation script.

Browser-based access

We use a virtual desktop environment (VDI) called AWS AppStream to run the 3D rendering in the cloud, so you users don’t need to install any software or have access to a powerful workstation.

Big brains, big data

Mouse brain data as large as 30 TB has been successfully traced by our annotators. You can run a distributed data import tool to bring your data to HortaCloud.

The Next-Generation Platform for Neuron Tracing

HortaCloud combines state-of-the-art volumetric visualization, advanced features for 3D neuronal annotation, and real-time multi-user collaboration with a set of enterprise-grade backend microservices for moving and processing large amounts of data rapidly and securely. Users can load multi-terabyte image volumes with up to three signal channels, and visualize them in 3D with multiscale volume rendering. An optimized workflow allows annotators to efficiently trace long range projection neurons in light microscopy data, including easy merging/splitting of skeletal reconstructions. Collaboration features allow a team of annotators to work together to annotate different neurons in a single volume, or build consensus by annotating the same neurons.

Horta also provides other useful features, including:

  • Movie scripting and rendering
  • Import/export in SWC format
  • Text annotations
  • Color adjustments
  • Shared workspaces

Software architecture

This software is built on the Janelia Workstation platform, leveraging Java NetBeans to provide modularity and extensibility. The backend consists of Java-based microservices that scale to handle large volumes of data. Metadata is stored in MongoDB and real-time event handling is implemented using RabbitMQ. We deploy both the client and backend services to the AWS Cloud, leveraging AWS AppStream to process the 3D rendering and virtualize the desktop infrastructure.

Image data is stored on AWS S3, and we provide many open data sets on AWS Open Data registry that are immediately accessible in the application.

Open Science

In support of Open Science, Janelia’s MouseLight project has shared all of their code and data with the scientific community. We have started the HortaCloud community as a way to share this software platform and allow others to leverage and extend it.

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Contributions welcome

As an open source community project, we greatly welcome contributions and Pull Requests. The current project status can be viewed on our Kanban board.
Let us know if you would like to collaborate!

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