This section provides a step-by-step introduction to the visualization of anatomical regions, e.g.,
Rhombencephalon, in the 2D viewer.
FishExplorer superimposes anatomical regions as solid or dashed contours. In this section we consider
the simplest case, namely displaying
the reference zebrafish brain, which is stored at the server. To load, follow these steps:
When FishExplorer is started, a default window, as you can see like the one shown below appears on
the screen. It is a 3D-viewer,
as you can see on the top, where this tab is highlighted. By moving the mouse you can intuitively
rotate the displayed 2D-slice.
Click the adjacent tap “2d-viewer” (highlighted as red in the image above) on the top left. Then a
2D viewer, like the one
shown in the image below, appears on the screen.
Imagine now that you want to display e.g. the Rhombencephalon. In order to do that, search
the anatomical region by typing the first letters
in the white searching box (encircled with a red line) in the list viewer on the right.
Alternatively, you can scroll through the list of
regions. The list of regions matching the search criteria will appear on the screen as shown below.
Next, select the checkbox in front of the region name, e.g. Rhombencephalon (encircled with
a green line). If the current slice contains
the selected region, i.e. Rhombencephalon, the outlined region will be displayed in the
2D-viewer. The depicted slice is slice 1,
as you can see at the bottom of the 2D-viewer. This slice, however, does not contain
Rhombencephalon. Therefore, go to slice 31,
using the next slice button, where the Rhombencephalon first appears.
