Display and navigation

The 3D dataset rendering happens inside BigVolumeViewer window (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.
• ⌃ Ctrl + ⇧ Shift + Mouse Wheel, or ↑ Up and ↓ Down keys to zoom in and out.
• N and M (or [ and ]) pairs are used to change the current timepoint (in the case of timelapse data).

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. It is used to return "focus" on a currently visible part of the dataset.

The extent of "zoom-in" is defined by the "Zoom box volume size" parameter in the Panel View/Crop#zoom-settings. If the "Crop volume when zooming in" option of Panel View/Crop#zoom-settings is activated, the plugin performs automatic clipping of the volume to the zoom box (see below). It can be helpful when there is a need to focus on some specific part of the volume.

In this video, pressing D leads to a zoom-and-crop. Shortcut X removes the crop and C centers dataset in the viewer.

Additional shortcuts that help to position the dataset to axis planes are:

• button 1 - zoom out and align to XY plane;
• button 2 - zoom out and align to YZ plane;
• button 3 - zoom out and align to XZ plane;

The rest of the display options (rendering method, voxel dimensions/anisotropy, volume clipping) are described
in detail on the Panel View/Crop page.

After getting familiar with dataset navigation, continue to Creating ROIs.

Bookmarks

To save a specific location/orientation, you can press ⇧ Shift + B, and a short message "set bookmark" will appear. Press a button on a keyboard to assign/bookmark this location. To return to it, first press B and then the button for the corresponding bookmark.