Code: Select all
ASSIGNED {
ik (mA/cm2)
...}
Code: Select all
vector_current.record(&soma.ik(.5))
Code: Select all
ASSIGNED {
ik (mA/cm2)
...}
Code: Select all
vector_current.record(&soma.ik(.5))
Then your voltage clamp will only control membrane potential in the near vicinity of the clamp electrode, and the current that the clamp collects will be contaminated with cable charging artifact, and confounded by the facts that membrane is not isopotential, and the clamp won't be capturing all of the membrane current. But maybe you're not interested in the current recorded by the clamp.manyi wrote:I want to fit some data from voltage clamp experiments. Now I have a multi-compartment model
Use SEClamp, not VClamp. Seeand use VClamp(0.5)
So you are recording the potassium current density associated with the node at the middle of soma--something that can't be done in real life. OK, that's one of the strengths of computational modeling.In my code,Code: Select all
vector_current.record(&soma.ik(.5))
mA/cm2, as you will discover from the first FAQ list item that I mentioned.I got a reasonable trace of the recorded current, but what is the unit of the values in vector_current?
Sorry to dash your expectations, butActually I expect to obtain something with current unit ampere, not per unit area, in order to compare the current that the soma electrode see in experiments.
Given any patch of membrane, NEURON can tell you the current carried by any named ion through that patch of membrane. It is simplymanyi wrote:we want a realistic model with multiple channels and their interactions
. . .
Is it possible to get the current in nA of ion x at the soma with all accumulated artefacts of space clamp errors, like doing a real recording of what the electrode actually see?
Yes! Do you have any reference or suggestion for me?The current recorded by a voltage clamp attached to the soma reflects contributions from all membrane currents throughout the entire cell, subject to filtering (signal loss) due to the properties of the membrane and cytoplasm that separates the clamp electrode from any given patch of membrane. Do you want to know what portion of that clamp current is attributable to sodium current throughout the cell? Is that what you're asking?
Can't be done. Period. Not by NEURON, not by any pharmacological manipulation, not by any experimental or theoretical or computational approach.manyi wrote:Yes! Do you have any reference or suggestion for me?Do you want to know what portion of that clamp current is attributable to sodium current throughout the cell? Is that what you're asking?
I agree.manyi wrote:I think we understand different things by "... what portion of that clamp current is attributable to sodium current..."
And this assumes good space clamp.I understand that in a typical experimental voltage-clamp characterization of an ion channel, the current is isolated by applying a specific drug and subtracting current post-drug from current pre-drug.
True of any wet-lab (i.e. real) experiment.In an (slice) experiment you cannot block all ion channels of a neuron and record only one specific remaining ion channel (you may be able to record a subset of K+ currents, but it is not possible to really block all other conductances).
That is a difference between what is possible in a computational experiment on a model and what is possible in a wet-lab experiment.Therefore the difference between the model and the experiment is that you can insert only on ion channel in the model and read the variable i of a SEClamp object at the soma (in unit of nA, right?).
soma.ix would be the density of the current carried by the "x ion" in the compartment that contains the middle of the soma. For example, soma.ina would be the density of the transmembrane sodium current at the middle of the soma. This is discoverable in NEURON, but not in a real experiment unless na is the only charge carrier (and you'd still have to subtract the capacitive membrane current).Alternatively we can read the variable of any sub-compartment by e.g. soma.ix (in mA/cm2), which is also difficult experimentally (because the area is only determined with large errors).
The procedure would be identical for wet-lab or computational experiment:Hence, to have a situation we can compare model to experiment, we would need to read the variable i of the SEClamp, but for selected ion
channel mechanisms (stim.ix). This is possible experimentally by drug-subtraction, is it really not possible in NEURON?