User manual

How to use the Horta application

The sections below describe Horta’s basic and advanced features. Generally the sections listed below should be read in the order listed.

Note on Horta versions

The Horta application exists in two versions that come from a common code base. The cloud version (HortaCloud) that is available here is a reduced version of the desktop version (Janelia Workstation). In fact, we’ll often use the word “workstation” to refer to the Horta application in either form.

When there are differences between the two versions, they will be noted with “(HortaCloud)” and “(desktop)”. If the differences are more substantial, they will be presented like this:

The major user-visible differences between the two versions are:

  • HortaCloud does not have access to the local file system or clipboard and requires additional steps to import or export data via those routes (see AppStream Basics section for details)
  • HortaCloud datasets typically only include low-resolution 2D data, so some 2D tools are not as useful or may not function in the absence of high-resolution data (eg, automatic path tracing)
  • the desktop Janelia Workstation contains tools for viewing, annotating, and managing other unrelated Janelia datasets

This is a work in progress!

The original documentation for the desktop version of Horta and the Janelia Workstation are being adapted for HortaCloud, and this website. If something doesn’t make sense for HortaCloud, it probably only applies to the desktop version and hasn’t been revised yet.


High-level description of the data, the software, and the jargon

AppStream Basics

Some general information about running HortaCloud in the AppStream environment


Some Horta tutorials: how to login and start HortaCloud, how to view images, and how to trace neurons

Basic Operations

Description of some basic operations: how to navigate images, how to trace neurons in 2D and 3D, and how to import and export neuron data


Horta features


Horta reference

Synchronized Folders

How to use Synchronized Folders to make data available to Horta

Reporting issues

How to report issues with HortaCloud

Last modified June 16, 2022: fixed some spelling etc. (4177d09)