Display and navigation

The 3D dataset rendering happens using BigVolumeViewer (or actually its modified version). It has a lot in common with BDV, including basic navigation.

If after loading a dataset all you can see is a black cube, a standard way to proceed is to adjust
Brightness and color (and opacity) using shortcut S.

Once you see your dataset, to manipulate it in 3D, start with (similar to BDV):

• Left Mouse button drag anywhere on the canvas to rotate the volume.
• Right Mouse button anywhere on the canvas to translate the volume.
• Use ⌃ Ctrl + ⇧ Shift + Mouse Wheel, or ↑ Up and ↓ Down keys to zoom in and out.

And for the rest (axis rotation, etc), please check the corresponding BDV documentation. It is helpful to study navigation shortcuts to browse datasets easily.

Since left/right mouse buttons are reserved for navigation, the majority of additional functionality is implemented by positioning a mouse pointer to a desired space of the viewer and pressing specific keyboard buttons (so they serve as "extra" mouse buttons).

The 3D view is a little bit more overwhelming compared to a single-slice view, there are extra tools to make navigation easier.

Zooming in/out, center

By positioning the mouse cursor at the desired area of the canvas and pressing shortcut D, the viewer will zoom in to this point.
To zoom-out use the shortcut C.

The shortcut C can be useful in other cases, when you completely lost your volume, for example.