Overview

HortaCloud is a streaming 3D annotation platform for large microscopy data that runs entirely in the cloud. It is a free, open source research software tool, developed by Janelia Research Campus.

It 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. HortaCloud takes advantage of cloud-based Virtual Desktop Infrastructure (VDI) to perform all 3D rendering in cloud-leased GPUs which are data-adjacent, and only transfer a high-fidelity interactive video stream to each annotator’s local compute platform through a web browser.

• What is it good for?: HortaCloud is a powerful tool for 3D visualization and annotation of large-scale microscopy data. It has been used to trace axons across the entire mouse brain by Janelia’s MouseLight Team Project.

• What is it not good for?: HortaCloud is a very specialized tool for sparse microscopy data. It is not intended for annotation of dense data sets, such as electron microscopy (EM) imagery.

• What makes HortaCloud unique?: Leveraging state-of-the-art services on AWS allows HortaCloud to run entirely in the cloud, making it possible to visualize terabyte-scale 3D volumes without moving all of that data over the Internet (see diagram below).

Where should I go next?

If you are a HortaCloud user, read through the User Manual to get familiar with the tools.

If you are a system administrator or developer looking to deploy an instance of HortaCloud, start with the AWS Deployment Guide.