# Single cell injection of discrete square current pulse(s) **URL:** \ **Category:** Support\ **Created:** [6 October 2024 21:41 UTC](https://brian.discourse.group/t/single-cell-injection-of-discrete-square-current-pulse-s/1298 "2024-10-06T21:41:02Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![MitchG\_HunterCollege](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/mitchg_huntercollege/32/865_2.png) [@MitchG\_HunterCollege](https://brian.discourse.group/u/MitchG_HunterCollege)\ **Post date:** [6 October 2024 21:41 UTC](https://brian.discourse.group/t/single-cell-injection-of-discrete-square-current-pulse-s/1298/1 "2024-10-06T21:41:02Z")
Hello, Marcel. I am working with a network of synaptically interconnected excitatory PYR neurons and inhibitory PVN neurons. A small tonic external current Iapp is being injected into all PYR cells to drive network activity. What I wish to do now is inject a brief strong pulse of current into one PYR cell of the network. I tried coding this by making Iapp variable time-dependent in one of the cells. This naïve effort gave syntax errors. Can you suggest a solution? Unfortunately, the guide on input stimuli ([Input stimuli — Brian 2 2.7.1 documentation](https://brian2.readthedocs.io/en/stable/user/input.html)) did not seem to offer a clear answer to my problem. * * * Here is some of the code. I have removed some components (incl. synaptic currents) here to focus on the problem at hand. ```auto N1 = 5000 *# number of PYR neurons in network* eqs_pyr = """ Iapp : amp k = (int(v=vt) * khigh) : siemens/volt dv/dt = (k*(v-vr)*(v-vt)+Iapp)/C_pyr : volt """ reset = ''' v = c ''' PYR = NeuronGroup(N1, model=eqs_pyr, reset=reset, threshold='v >= vpeak', method = 'euler') #create one cell, PYR1, into which a current pulse can be applied** PYR1 = PYR[:4999] PYR2 = PYR[1:] ``` I would like to add Ipulse to the PYR eqs to give ```auto eqs_pyr = """ Iapp : amp Ipulse : amp k = (int(v=vt) * khigh) : siemens/volt dv/dt = (k*(v-vr)*(v-vt)+Iapp + Ipulse)/C_pyr : volt """ ``` So how do I, e.g., step `Ipulse` up from 0 during, e.g., a 20 msec window in the middle of the run in PYR1 only? Alternatively, do built-in Brian2 functions offer a method for current-clamp pulse injection? ---
**Author:** ![mstimberg](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/mstimberg/32/11_2.png) [@mstimberg](https://brian.discourse.group/u/mstimberg)\ **Post date:** [7 October 2024 08:33 UTC](https://brian.discourse.group/t/single-cell-injection-of-discrete-square-current-pulse-s/1298/2 "2024-10-07T08:33:21Z")
Hi @MitchG_HunterCollege. In general, I’d say there are three general approaches to inject a pulse current (in the below example: 20ms injection of 1nA after 100ms): 1. A `TimedArray`: ```auto Iapp = TimedArray([0, 0, 0, 0, 0, 1, 0]*nA, dt=20*ms) # for times beyond the end of the array, the last value is used eqs_pyr = """ Iapp : amp k = (int(v=vt) * khigh) : siemens/volt dv/dt = (k*(v-vr)*(v-vt)+Iapp + Ipulse(t))/C_pyr : volt """ ``` 1. A time-dependent equation: ```auto eqs_pyr = """ Iapp : amp Ipulse = int(t>=100*ms and t < 120*ms)*1*nA : amp k = (int(v=vt) * khigh) : siemens/volt dv/dt = (k*(v-vr)*(v-vt)+Iapp + Ipulse)/C_pyr : volt """ ``` 1. Multiple run calls ```auto eqs_pyr = """ Iapp : amp Ipulse : amp k = (int(v=vt) * khigh) : siemens/volt dv/dt = (k*(v-vr)*(v-vt)+Iapp + Ipulse)/C_pyr : volt """ # ... run(100*ms) PYR.Ipulse = 1*nA run(20*ms) PYR.Ipulse = 0*nA run(remaining_time) ``` If you want to inject the current only in a subset of neurons, there are again a few options: For variant 3 from above, you simply just set the current for the respective neuron, i.e. `PYR1.Ipulse = 1*nA` instead of `PYR1.Ipulse` (note that in your example code, both `PYR1` and `PYR2` have 4999 neurons – but I guess this was a typo). For all variants, you can introduce a new variable that decides whether a neuron should receive input. E.g. for variant 2 this would look like this: ```auto eqs_pyr = """ Iapp : amp receives_pulse : boolean (constant) Ipulse = int(receives_pulse) * int(t>=100*ms and t < 120*ms) * 1*nA: amp k = (int(v=vt) * khigh) : siemens/volt dv/dt = (k*(v-vr)*(v-vt)+Iapp + Ipulse)/C_pyr : volt """ # ... PYR1.receives_pulse = True ``` For variant 1, you can have different inputs for different cells – this could be useful for complex inputs (different inputs to different neurons at different times), here it is a bit unnecessarily complex, since the input is zero for most cells: ```auto inputs = np.zeros((7, 5000))*nA # input for most neurons is zero inputs[5][3675] = 1*nA # neuron 3675 receives a current pulse Iapp = TimedArray(inputs, dt=20*ms) # for times beyond the end of the array, the last value is used eqs_pyr = """ Iapp : amp k = (int(v=vt) * khigh) : siemens/volt dv/dt = (k*(v-vr)*(v-vt)+Iapp + Ipulse(t, i))/C_pyr : volt """ ``` Hope that clears things up and gives you a few options for more complex inputs 😊