HortaCloud 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. HortaCloud automates the deployment of the software stack to AWS, and provides a web browser-based interface for annotation with 3D-accelerated volume rendering.
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 process 3D volume rendering in the cloud, so users don’t need to install any software and don’t need a powerful workstation. You can even trace neurons on your iPad (but using a mouse is highly recommended.)
Big brains, big data
Mouse brain data as large as 30 TB has been successfully traced by our annotators. You can load standard OME-Zarr compliant images or run our distributed data import tool to convert your data.
The Next-Generation Platform for Neuron Tracing
Features
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
- 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.
Learn more about HortaCloudOpen 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.
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!