Installation and Use
The Universal Renderer for Neuroscience (Urchin) allows you to connect your Python scripts to a standalone rendering program, to create graphics like the ones above.
pip install oursin
No additional installation is required if you plan to run Urchin in a browser. A standalone desktop application is also available from the releases page. Linux standalone available on request.
import oursin as urchin urchin.setup()
setup() opens a web browser and links it to your Python client. Set the parameter
standalone = True to connect to a standalone Desktop application.
When opening the renderer your ID should be set automatically. If this fails or you need to change your ID press
I and enter your account username. If you aren’t sure what that is, try running:
python import os os.getlogin()
You can press
C to open the console in the renderer to confirm your ID was set correctly.
Left click + drag along the Y axis to pitch the brain
Left click + drag along the X axis to yaw the brain
Hold shift while left clicking and dragging along the X axis to spin the brain
Scroll to zoom
Right click + drag to pan
Hold [SHIFT] or [CTRL] while moving on any axis to increase or decrease the speed, respectively.
You can use
urchin.camera.capture_image(filename) to take screenshots.
Grids and Axes
In orthographic camera mode these will look a bit weird, use the perspective camera.
Press [G] to bring up a flat grid
Press [A] to bring up a set of 3D axes (I know… they’ll get better eventually)
Press [S] to hide the settings menus
When individual brain areas are loaded, e.g. by using
urchin.ccf.load_beryl(), you can “explode” the brain using the slider option. Options allow you to explode just one side as well as set the default colors on one side of the brain. Additional “explode” axes can be added on request.
The camera rotation button continuously increments the spin angle to rotate the camera around the current camera target. The speed is controlled by the slider. You can then capture videos using the windows screen capture features [WINDOWS + G].
We’re in full beta mode right now – asking Dan to build you an example is probably the best way to get started.
You can also browse the Examples and [API](file:///C:/proj/VBL/vbl-docs/docs/build/html/_autosummary/unityneuro.render.html#module-unityneuro.render) for inspiration.
If you use this to make figures for a publication you should cite this repo, email me (email@example.com) and I can generate a DOI.