Neuroglancer Guide

Neuroglancer is a browser-based viewer for large volumetric datasets. This guide is a quick visual reference for finding your way around the interface and navigating in both the 2D image panels and the 3D view. Each animation shows the action; the note beside it gives the key combination.

Note

The exact toolbar and panels vary a little between deployments (for example Spelunker, the MICrONS viewer). The controls and shortcuts shown here work the same way across all of them.

The Neuroglancer interface

When you open a Neuroglancer link you will see one or more panels showing the data, a row of layer tabs across the top, a coordinate readout, and a toolbar in the top-right corner (see Toolbar & settings below).

Layer tabs

The tabs across the top of the viewer are the layers — the separate pieces of data in the scene (for example an EM image layer and a segmentation layer).

A layer tab showing the tooltip: click to hide, control+click to show side panel, drag to move, shift+drag to copy.

  • Click a tab to turn that layer on or off.
  • a tab to open its side panel.
  • Drag a tab to reorder it, or to copy it.

Coordinates

The coordinate readout shows the current position (in nanometers). Click it to paste in a coordinate, or click the copy icon to copy the current location.

The coordinate readout showing x, y, and z positions with a copy button.

Panel layout

Switch between layouts with the key, or by clicking the box-in-box icon in the upper corner of any panel. You can choose a 1-panel, 2-panel, or 4-panel view.

The box-in-box layout toggle icons.

Two-panel layout.

2 panel — a 2D slice beside the 3D view.

Four-panel layout.

4 panel — three 2D slices plus the 3D view.

Single 3D panel layout.

3D only — just the 3D view.

The xy plane is in the plane of imaging and has the highest resolution; the default 2-panel view is xy-3d.

3D navigation

These actions work in the 3D panel (the right panel by default).

Left click and drag rotates the 3D view around the centered point.

Rotate — + drag.

Shift plus left click and drag pans the 3D view.

Pan — + + drag.

Hovering over the 3D panel and Ctrl plus scroll zooms.

Zoom — .

Right clicking an object centers it in every panel.

Center in every panel — .

2D navigation

These actions work in the 2D image panels (the left panel by default).

Click and drag pans the 2D EM image.

Pan — + drag.

Hovering over the image panel and Ctrl plus scroll zooms.

Zoom — .

Double clicking a cell selects it; double clicking again deselects it.

Select / deselect a cell — .

Right clicking centers the clicked point in every panel.

Center in every panel — .

Controlling perspective and overlays

These toggles change how the scene is displayed.

Scrolling over the image panel moves between slices of the volume.

Add section overlay — toggles to add the current section(s) from the 2D views to 3D.

Move through the section slices — mouse wheel, or / .

Pressing space cycles through the panel layouts.

Cycle panel layouts — .

Pressing O toggles between perspective and orthographic projection; a scale bar appears in the orthographic view.

Toggle projection style — . Switches between perspective and orthographic views. Orthographic equalizes depth, so a scale bar appears.

Visualization

Pressing L assigns a fresh random color to every visible segment.

Recolor all segments — . Assigns a fresh random color to every segment, which can help when neighboring cells overlap.

Toolbar & settings

The toolbar in the upper-right corner opens the side panels and tools:

The Neuroglancer top-right toolbar with Share, Layers, Selection, Controls, JSON, Help, and Settings icons.

Icon Opens What it does
Share Share Creates a shareable, shortened link that captures your current view, visible segments, and annotations.
Wrench Palette Shows the tool palette list (includes default Shader Controls).
Layers Layers Shows the list of data layers (images, segmentations, annotations).
Bullet List Details Shows details submenu for whatever you have selected.
Sliders Controls Opens layer side panel, controls for the active layer (color, opacity, shaders).
Curly brackets JSON Opens the raw JSON state — the full, editable definition of the scene.
Camera Screenshot Opens the built in screenshot tool.
Clipboard Copy URL Copy the full URL to the clipboard.
Question Mark Shortcuts Lists every keyboard and mouse binding.
Gear Settings Global settings (axis lines, scale bar, memory limits, backgrounds).

The Settings (gear) panel controls display options for the whole viewer:

The Neuroglancer Settings side panel with options such as Show axis lines and Show scale bar.

Keyboard shortcuts

Key Action
+ drag Rotate (3D) / pan (2D)
+ + drag Pan (3D)

Center the clicked point in every panel

Zoom
Mouse wheel Move between slices
/ Move between slices

Cycle panel layouts

Show / hide the colored axis lines

Show / hide the 2D slice in the 3D view

Recolor all segments globally

Switch between 3D orthographic and projection views

Snap to the nearest axis (also undoes a sheared 2D view)
Tip

Pressing is handy if you have “sheared” the 2D view with + + drag and want to return to the original orientation.

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