How to create neural circuit diagrams (updated)


My diagrams are always a mess, but maybe I could start following this advice a little more carefully?

Diagrams of even simple circuits are often unnecessarily complex, making understanding brain connectivity maps difficult…Encoding several variables without sacrificing information, while still maintaining clarity, is a challenge. To do this, exclude extraneous variables—vary a graphical element only if it encodes something relevant, and do not encode any variables twice…

For neural circuits such as the brainstem auditory circuits, physical arrangement is a fundamental part of function. Another topology that is commonly necessary in neural circuit diagrams is the laminar organization of the cerebral cortex. When some parts of a circuit diagram are anatomically correct, readers may assume all aspects of the figure are similarly correct. For example, if cells are in their appropriate layers, one may assume that the path that one axon travels to reach another cell is also accurate. Be careful not to portray misleading information—draw edges clearly within or between layers, and always clearly communicate any uncertainty in the circuit.

Update: Andrew Giessel pointed me to this collection of blog posts from Nature Methods on how to visualize biological data more generally. Recommended!

4 thoughts on “How to create neural circuit diagrams (updated)

  1. I disagree with the admonition not to encode variables redundantly – I find it useful if, e.g. excitatory and inhibitory connections are distinguished by *both* color (blue vs red) and line caps (arrowsheads vs perpendicular lines). This is like how it’s good when lines on graphs are distinguished redundantly using color, dashed lines and/or labeling the line directly on the graph instead of relying on the legend. It just makes it easier for the eye to spot the difference. Of course if there are many variables that need to be depicted, it does make sense to save color for something else if you can encode E vs I using line caps. But generally I don’t see the problem with redundantly encoding variables on diagrams.

  2. Hey Adam,

    Do you have any plan of starting an ongoing list of tools useful for neuroscientist outside the lab? I am a Master’s student and I feel that such a list would be very helpful for beginners to help them analyse or automatise the analysis of their data (Matlab, GraphPrism), create nice figures (besides Illustrator I really have no clue of what I can use), organise their references, write nice looking papers or reports (latex), create nice presentations (I am really stuck with PowerPoint and I hate it) or really just a nice tasks organiser or a blog/website reader for a 30 minute morning update with the world. I know it might be a bit of work but I think that it would be easier with some kind of community involvement (like a shout out on twitter).

    If such an initiative already exists then pleease share it with the world, I think it would make the lives of some many people waay easier (especially beginners like me),


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