Electrode current in lfp #52
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…to allow electrode to contirbute to LFP signal
joseph-tharayil
assigned joseph-tharayil, WeinaJi and jorblancoa and unassigned joseph-tharayil
joseph-tharayil
changed the title
| @@ -227,6 +227,7 @@ A continuous injection of current. | |||
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| amp_start float Mandatory The amount of current initially injected when the stimulus activates. Given in nA. | |||
| amp_end float Optional If given, current is interpolated such that current reaches this value when the stimulus concludes. Otherwise, current stays at amp_start. Given in nA. | |||
| represents_physical_electrode boolean Optional Default is False. If True, the signal will be implemented using a NEURON IClamp mechanism. The IClamp produce an electrode current which is not included in the calculation of extracellular signals, so this option should be used to represent a physical electrode. If the noise signal represents synaptic input, `represents_physical_electrode` should be set to False, in which case the signal will be implemented using a MembraneCurrentSource mechanism, which is identical to IClamp, but produce a membrane current, which is included in the calculation of the extracellular signal. | |||
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If I'm understanding this right, the default value won't be a vanilla IClamp anymore? (what did it used to be in neurodamus @jorblancoa / @WeinaJi / @ferdonline ?). Instead, MembraneCurrentSource is substituted, which uses NONSPECIFIC_CURRENT i instead of ELECTRODE_CURRENT i?
Will this impact how simulations are run, since the default is different?
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Yes, that is correct (the default was previously a vanilla IClamp). This will not have any impact on how simulations are run. It will have an impact on reporting, since now the stimulus current will be included in i_membrane instead of IClamp
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It will have an impact on reporting, since now the stimulus current will be included in i_membrane instead of IClamp
I think we'll need to have broad confirmation that everyone who relies on reporting know about this then, since it's a change that it impacts them. Probably @MWolfR, @romani79 should get their team to comment, @darshanmandge / @anilbey probably need to know, and likely others.
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We just discussed it with @joseph-tharayil. This change does not introduce any issues on bluecellulab side since the voltage traces produces will be identical.
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The changes does not affect any other single cell software. So, it is good from my side.
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Can we move forward with this and the PR in libsonata?
BlueBrain/libsonata#354
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It's been communicated to the circuits and connectomics teams, and no one's raised any objections yet, so I think we can move forward
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It's been communicated to the circuits and connectomics teams,
Great! Can we get an ok on this ticket from them?
I just want to confirm that everyone is aware that we're moving away from a default that has been the standard for many years, to something different.
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Me and the circuit team have not had the opportunity to look into the details of the proposed changes. However, I appreciate that the old setup can be still obtained with represents_physical_electrode:true. If this is the case, I am not contrary to the changes, so you have my green light on that. |
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thanks for getting everyone in the loop, @joseph-tharayil and @jorblancoa; let's do this |
I've added a
represents_physical_electrodekey, which defaults to False, for all of the noise input types. If the key is set to False, then the stimulus should be implemented as either a conductanceSource or a MembraneCurrentSource, both of which are implemented here. In these cases, the current will be a membrane current, which will contribute to the extracellular signalIf the key is set to True, then the stimulus should be implemented as an SEClamp (if a conductance source) or an IClamp (if a current source). The SEClamp and IClamp should not contribute to the extracellular current. This way, the user can specify whether each source individually affects the extracellular signal, rather than having to make an all-or-nothing decision on the IClamp currents