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Getting Started

How to use the Virtual Fly Brain 3D browser

Below are a few overview pages to help you get started using VFB:

1 - Starting to explore VFB

Text search and query tools and how to explore the 3D images.

VFB integrates data curated from the literature with image data from many bulk sources. The search system allows you to search for neurons and neuroanatomical structures using almost any name found in the literature. The query system can identify neurons innervating any specified neuropil or fasciculating with any specified tract. It also allows queries for genes, transgenes and phenotypes expressed in any brain region or neuron. Search and query results combine referenced textual descriptions with 3D images and links to originating data sources. VFB features tens of thousands of 3D images of neurons, clones and expression patterns, registered to standard template brains. Any combination of these images can be viewed together. A BLAST-type query system (NBLAST) allows you to find similar neurons and drivers starting from a registered neuron.

Search for the item you’re interested in

Hover to explore brain regions in the Stack Viewer

Query for related terms and images

Virtual Fly Brain (VFB) Overview

2 - This is the Slice Viewer tab

The Slice Viewer displays single slices of the template, showing all selected painted anatomy, neurons and expression patterns

Hover to explore, click to list or shift + click to add painted anatomy

Use the arrow icons or scroll with the mouse to move through the stack

Home resets your view

Use the zoom icons or pinch gesture to zoom

Toggles through orthogonal views

Toggles the slice position on the 3D Viewer on/off

Virtual Fly Brain (VFB) Slice Viewer

3 - This is the 3D Viewer tab

The 3D Viewer displays 3D models of the template, showing all selected painted anatomy, neurons and expression patterns

Point and click to select neurons/expression

Click and drag with the mouse or use the directional icons to rotate/move

Use the zoom icons or scroll with the mouse to zoom in/out

Home resets your view

The camera icon starts/stops a rotation animation of the scene

The sphere icon toggles wireframes on/off

Virtual Fly Brain (VFB) 3D Viewer

4 - This is the Term Info tab

Term Info displays information on the currently selected painted anatomy region, neuron, expression pattern or non-image term definitions

Click on thumbnails to add that image to the viewer

Click on terms to select them

Click on download items to begin downloading

Run term related queries

Virtual Fly Brain (VFB) 3D Viewer

5 - This is the Term Context tab

Term Context displays grapical information on the currently selected term’s location or classification

Home resets your view

Use the zoom icons or scroll with the mouse to zoom in/out

Click to refresh to the current focus term

Select either the location or the classification for the current term

Virtual Fly Brain (VFB) 3D Viewer

6 - This is the Circuit Browser tab

The Circuit Browser allows you to find the strongest paths from one neuron (the source neuron) to another (the target neuron).

The ‘strongest’ paths are the shortest/highest weighted paths. Paths are arranged from the ‘strongest’ at the bottom to the ‘weakest’ at the top. A detailed explanation for the algorithm used to determine path strengths can be found here.

Search for the source neuron to start from (Note: query is directional)

Search for the target neuron

Maximum number of paths to return (only the ‘strongest’ paths will be returned)

A minimum weight for the synapse count of each connection can be applied, paths containing individual connections below this minimum will not be returned

Virtual Fly Brain (VFB) 3D Viewer