Usage

How to use BG-brainrender-GUI

Usage

You can start brainrender-gui directly from your terminal with the command

brainrender-gui

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 brainrender scene.

To specify which atlas to use: use the -a argument when calling brainrender-gui:

brainrender-gui -a allen_human_500um # the GUI will use the human atlas

Adding actors

The first set of buttons is used to add elements to the brainrender scene:

  • 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 csv file).

  • Add from file: clicking on this button opens a dialog to select and load a file for a 3d mesh (e.g. a .obj file).

  • Add sharptrack: clicking on this button opens a dialog to select and load a .m file with the output of SHARPTRACK.

Editing actors

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.

The hierarchy view

Pressing the 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.

Taking screenshots

This functionality is currently not working. We are aware of the problem and working on it!

Under the main canvas there is a button that can be used to save a screenshot with the current view of the brainrender scene.

To specify where to save the screenshot, use the -o argument when calling brainrender-gui:

brainrender-gui -o path/to/screenshots/folder

Camera control

To the right of the screenshots button is a panel of buttons used to set the camera position in the brainrender Scene:

  • Reset resets the camera to what is defined as default in brainrender (i.e. brainrender.CAMERA).

  • Top moves the camera so that the brain is viewed from the top

  • Side1 and 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.