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change units of compute_current #48

Merged
merged 2 commits into from
Oct 24, 2024
Merged

change units of compute_current #48

merged 2 commits into from
Oct 24, 2024

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huangziwei
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@huangziwei huangziwei commented Oct 23, 2024

To align with jaxleyverse/jaxley#461, compute_current() in all channels now returns current in units of mA/cm^2.

closed #47

@michaeldeistler
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michaeldeistler commented Oct 23, 2024

Thanks Ziwei! I don't think we should have a surface_area parameter though. You can access length and radius from within every channel (via `params["length"]), so you can just compute the surface area directly.

@huangziwei
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hmm.. should it be scaled with the compartment size of our model? I think the conversion factor is the surface area of the cell (or the outer segment of the photoreceptors) that those paper recorded from (and it will vary depends on the species, etc.)...

@michaeldeistler
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If the cell is a point neuron then compartment size and cell size are the same.

If a cell consists of multiple compartments then I would argue that one wants compartment size. (and if the channel exists in all compartments then it will anyways sum up to the cell size)

@huangziwei
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makes sense. now the scale factor is computed with the compartment length and radius.

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Thanks!

@huangziwei huangziwei merged commit 1c9fb3c into main Oct 24, 2024
@michaeldeistler michaeldeistler deleted the units branch October 24, 2024 12:45
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update channel unit conversion
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