Soma size in Cell Types SDK

Technical
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Hey there –

I’m interested in looking for correlations between soma size and input resistance. I’m familiar with working with the AllenSDK for the Cell Types data and how to get the pre-computed metrics for the electrophysiology of the cell. I’m less familiar with the morphology side of things. :slight_smile:

Is there a computed soma size (e.g., diameter, surface area) in any of the SDK tools for the Cell Types data? I see by using morphology = ctc.get_reconstruction(cell_id), in “morphology.soma” there is “radius” but my understanding from the documentation is that this is the radius of the node (?)

I see on the API there is usefully a tag “soma-surface” (which seems to be surface area in µm) but I was hoping to get it through the SDK if possible and thought I’d ask.

Thanks!
Ashley

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Hi Ashley. We are doing all new neuron morphology development in a new repo, aptly named neuron_morphology.

This function will calculate soma surface:

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Just to follow on to Wayne’s answer - the SWCs that we use to represent morphologies do just represent the soma as a sphere (unlike some other morphology file formats that have a more detailed soma outline or surface), so all you actually need to calculate the surface area is the radius of the soma node. You can see in the function Wayne linked that it’s just using that value in the formula for the surface area of a sphere.

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Gotcha! So the radius of the node in the SWC is informative! That’s useful and definitely simplifies things. I’ll stick with 4 x pi x r^2. :slight_smile: Thank you!

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This is great to know about, thanks!