The Python interface to Neuroglancer

The Python interface to Neuroglancer provides several advantages over using fixed links to your data, such as the visualization links generated at the site. The main advantage is that it gives you programmatic control over your Neuroglancer session. A popular use case is for making reproducible figures and movies via the screenshot feature. It also allows you to keep the Neuroglancer session open indefinitely, whereas the links on braincogs00 expire after a few hours of inactivity. If you are making annotations for longer than a single sitting, you could lose your progress if the Neuroglancer session is closed while you are away from your computer. By using the Python interface, you don’t have to worry about that happening.

A tutorial on how to start using the Python interface to Neuroglancer is written up here: The basic idea is you boot up a jupyter notebook and make a connection to a Neuroglancer session. As long as the jupyter notebook is running, the connection to Neuroglancer will remain open. Here is what is covered in the notebook:

  • Start a Neuroglancer session from Python and load in public data
  • Manipulate the Neuroglancer session from Python
  • Add custom annotations to Neuroglancer using Python
  • Configure and take a screenshot and movie reproducibly
  • Load in private light-sheet data from bucket

There is a lot more that can be done with the Python interface, such as defining your own keyboard shortcut that executes a custom Python program. We will explore this feature in a future post.

19. March 2021 by ahoag
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