You can start
brainrender-gui directly from your terminal with the command
Once the GUI is started it will open a window visualizing the
root mesh of the atlas selected and several buttons to add and remove elements to the
The first set of buttons is used to add elements to the
Add brain regions: clicking on this button opens a new window where you can input the names of the brain regions to be added to the brainrender scene.
Add cells: clicking on this button opens a dialog to select and load a file containing cell coordinates data (e.g. a
Add from file: clicking on this button opens a dialog to select and load a file for a 3d mesh (e.g. a
Add sharptrack: clicking on this button opens a dialog to select and load a
.m file with the output of SHARPTRACK.
Whenever an actor is added to the scene, its name will be added to the
Actors list. The list can also be used to edit rendered actors:
Double clicking an actor's name will toggle the visibility of the corresponding mesh.
A single click on an actor's name selects it for editing with the
alpha (transparency) and
color options below the actors list. Once an actor is selected from the
Actors list, its color and alpha will appear in the text boxes below. Editing the values in these textboxes change the corresponding actor's properties.
Show structures tree button at the bottom right of the window shows a panel with the hierarchy view of brain regions in the selected atlas:
The hierarchy view can be used to explore the structures hierarchy as well as to add brain regions to the scene: clicking on a region's tick box will add it to the list of actors in the scene. Press the same button again to hide the hierarchy view.
Under the main canvas there is a button that can be used to save a screenshot with the current view of the
To specify where to save the screenshot, use the
-o argument when calling
brainrender-gui -o path/to/screenshots/folder
To the right of the screenshots button is a panel of buttons used to set the camera position in the
Reset resets the camera to what is defined as default in
Top moves the camera so that the brain is viewed from the top
Side2 move the camera to view the brain from the side (left and right sides).
Front moves the camera to view the brain from the fron.