General Navigation

From Endrov

While there are many windows for different purposes, for looking at images there are two you should know about:


Getting help


First of all, if you need help on a task, you can be pointed to the right article using the built-in help button in the help menu. See the image above.

The 3D viewer

This window is for anything, not just images. Annotations can be shown independently of the images.

modw with neuron.svg

To show images they have to be given a 3D interpretation. The most common ones are:

  • Isosurfaces - The object is defined as the region for which pixels are above a certain value. Finding a good value can be difficult.
  • Volumes - The data is rendered as a cloud, with opacity and color as a function of the intensity of each pixel. This is the easiest to work with.

The controls are:

  • Left mouse button+drag - Rotate camera around camera itself
  • Right mouse button+drag - Rotate camera around center
  • Scroll wheel - Zoom
  • Alt+Left mouse button+drag - Pan camera
  • Alt+Scroll wheel - Roll camera
  • Key 'a' and 'd' - Fast back and forward stepping
  • Key 'w' and 's' - Slow back and forward stepping

The 2D viewer

This window is primarily for displaying images in 2D and allows very fast browsing of the opened dataset. We strongly advise learning the keyboard shortcuts!

Image window

Whenever you open up a new image it makes sense to first adjust contrast and brightness. You can use "Fit intensity range" to do this automatically. Any number of channels can be overlaid. Add new channels using (+) and give it another color. Some tools require one channel to be the active one; this is controlled by the selection (.) to the left.

  • Scroll wheel - zoom
  • Right mouse button+drag - Pan
  • Key 'a' and 'd' - Back and forward stepping
  • Key 'w' and 's' - Up and down stepping
  • Space bar - temporarily hide all annotation.

Synchronizing windows

Spatio-temporal windows can be grouped:


Windows with the same group number will be synchronized i.e. if the current frame is changed in one window, it will be changed in all other windows. This is useful to see the model while you browse the images, or if you want to see several channels separately. The image window has an additional check box to synchronize current Z (slice).

The console window

Many things can be done from the console. Indeed, some of the mouse and keyboard commands are sent as commands to the console. Features that require input beyond what is shown in other windows can only be executed in the console. The program was designed for specialist users and so all operations should be as easily accessible as possible.

Pressing Esc when some window is selected (in focus) will move the focus to the console ready for input. If the console isn't open then it will automatically open. Focus will automatically move back once the command has been entered. If you want focus to stay, then manually select the console.

Press up and down to retrieve old commands from history.