6.1 Generating Spikes

Author: Michael Beyeler

6.1.1 Generating Poisson Spikes

6.1.1.1 The PoissonRate Object

The PoissonRate class allows a user create spike trains whose inter-spike interval follows a Poisson process. The object can then be linked to a spike generator group (created via CARLsim::createSpikeGeneratorGroup) by calling CARLsim::setSpikeRate.

The easiest way to initialize a PoissonRate object is via the following:

int nNeur = 50; // # neurons

PoissonRate poissRate(nNeur);

This will generate a mean rate vector for 50 neurons. By default, these rates will be allocated on CPU. An optional second argument to the constructor allows allocation on GPU instead (onGPU=true). This allows the minimization of memory transfers when CARLsim is run in GPU_MODE:

int nNeur = 50;                                       // # neurons
bool onGPU = true;                                    // whether to allocate on GPU (true) or CPU (false)
PoissonRate poissRate(nNeur, onGPU);

6.1.1.2 Setting Mean Firing Rates

At first, all the rates will be initialized to zero. The user then has several options to assign non-zero rates:

// set all rates to 10 Hz
poissRate.setRates(10.0f);
 
// set rates according to some vector
std::vector<float> someVector;
for (int neurId=0; neurId<nNeur; neurId++)
    someVector.push_back(neurId*2.0f);
poissRate.setRates(someVector);
 
// set rate of each neuron
for (int neurId=0; neurId<nNeur; neurId++)
    poissRate.setRate(neurId, neurId*2.0f);

6.1.1.3 Retrieving Mean Firing Rates

The mean firing rates can then be queried via the following getter functions:

std::vector<float> rates = poissRate.getRates(); // get all rates in a vector

float someRate = poissRate.getRate(17); // get rate of neuron with ID=17

6.1.1.4 Integrating PoissonRate with a CARLsim Simulation

Finally, a PoissonRate object can be linked to a spike generator group (created via CARLsim::createSpikeGeneratorGroup) by calling CARLsim::setSpikeRate. For this to work, the number of neurons for the PoissonRate object must be the same as for the spike generator group.

CARLsim sim("MyNet",GPU_MODE,0,42);                   // run simulation in GPU_MODE
// configure network
int nNeur = 10;                                       // # neurons in group
int g0 = sim.createSpikeGeneratorGroup("grpPoiss", nNeur, EXCITATORY_NEURON);
// ...
sim.setupNetwork();
 
// setup PoissonRate object
PoissonRate poissRate(nNeur, true);                   // allocate on GPU for minimal memory copies
poissRate.setRates(13.0f);                            // set all rates to 13 Hz
 
// apply to neuron group g0
// nNeur of PoissonRate must match that of createSpikeGeneratorGroup
sim.setSpikeRate(g0, &poissRate);
 
// run network
// g0 will now produce Poisson spike trains with mean rate = 13 Hz
sim.runNetwork(1,0);
 
// note that spike rates will still be 13 Hz in subsequent runs ...
sim.runNetwork(0,500);
 
// ... until you reset the rates
poissRate.setRates(0.0f);
sim.setSpikeRate(g0, &poissRate);                     // need to call setSpikeRate again
sim.runNetwork(0,10);                                 // no more input spikes

Note: This method can only be applied to SpikeGenerator groups.

Attention: CARLsim::setSpikeRate will not take over ownership of PoissonRate. In other words, if you allocate the PoissonRate object on the heap, you are responsible for correctly deallocating it.; Make sure to reset spike rate after use (i.e., for the next call to CARLsim::runNetwork), otherwise the rate will keep getting applied to the group.; You cannot use the same PoissonRate object for multiple spikeGenerators. Each PoissonRate objects can only be used for a single SpikeGenerator object at a time.

6.1.2 Periodically Generating Spikes

A PeriodicSpikeGenerator can be used to generate spike trains of a given mean firing rate with a constant inter-spike-interval (ISI) that is equal to 1/rate.

A PeriodicSpikeGenerator is instantiated as follows:

float rate = 10.0f;
bool spikeAtZero = false;
PeriodicSpikeGenerator PSG(rate, spikeAtZero);

Here, the firing rate of the Spike Generator is 10 Hz (rate), which leads to an ISI of 100ms. Thus, the PeriodicSpikeGenerator will schedule spike for each neuron in the group it is applied to at t=100ms, t=200ms, t=300ms, etc. If the flag spikeAtZero is set to true, an additional spike will be scheduled at t=0.

In order for a PeriodicSpikeGenerator to be associated with a SpikeGenerator group, CARLsim::setSpikeGenerator must be called on the group in CONFIG_STATE:

#include <carlsim.h>
 
// configure network
CARLsim sim("PSG example",CPU_MODE,USER);
int g0 = sim.createSpikeGeneratorGroup("input", 10, EXCITATORY_NEURON);
// etc.
 
// create periodic spike gen
PeriodicSpikeGenerator PSG(50.0f, true);
 
// associate group g0 with PSG
sim.setSpikeGenerator(g0, &PSG);
 
sim.setupNetwork();
// etc.

Since: v3.0

6.1.3 Generating Spikes from a Vector

A SpikeGeneratorFromVector can be used to schedule exact spike times (ms) from a vector. Note that currently the only option is to specify a single vector of spike times, which will apply to all neurons in the group. In the future, it should be possible to specify a vector of spike times for each neuron in the group.

A SpikeGeneratorFromVector is instantiated as follows:

std::vector<int> spikeTimes = {2, 14, 100, 1353};

SpikeGeneratorFromVector SGV(spikeTimes);

In order for a SpikeGeneratorFromVector to be associated with a SpikeGenerator group, CARLsim::setSpikeGenerator must be called on the group in CONFIG_STATE:

#include <carlsim.h>
 
// configure network
CARLsim sim("SGV example",CPU_MODE,USER);
int g0 = sim.createSpikeGeneratorGroup("input", 10, EXCITATORY_NEURON);
// etc.
 
// create spike gen from vector
std::vector<int> spikeTimes = {2, 14, 100, 1353};
SpikeGeneratorFromVector SGV(spikeTimes);
 
// associate group g0 with PSG
sim.setSpikeGenerator(g0, &SGV);
 
sim.setupNetwork();
// etc.

Attention: Currently the vector of spike times will apply to all neurons in the group. However, in a near-future release it should be possible to specify a vector of spike times for each neuron in the group.

Since: v3.0

6.1.4 Generating Spikes from File

A SpikeGeneratorFromFile can be used to schedule exact spike times (ms) from a spike file binary that was previously created with a SpikeMonitor. This makes it possible to repeatedely apply pre-recorded spike times to the same network (or a different network with the same amount of neurons in the associated group).

A SpikeGeneratorFromFile is instantiated as follows:

SpikeGeneratorFromFile SGF("results/spk_input.dat");

where the string "results/spk_input.dat" points to a spike file previously created with a SpikeMonitor.

In order for a SpikeGeneratorFromFile to be associated with a SpikeGenerator group, CARLsim::setSpikeGenerator must be called on the group in CONFIG_STATE:

#include <carlsim.h>
 
// configure network
CARLsim sim("SGF example",CPU_MODE,USER);
int g0 = sim.createSpikeGeneratorGroup("input", 10, EXCITATORY_NEURON);
// etc.
 
// create spike gen from file
SpikeGeneratorFromFile SGF("results/spk_input.dat");
 
// associate group g0 with SGF
sim.setSpikeGenerator(g0, &SGF);
 
sim.setupNetwork();
// etc.

Note: The current implementation might be relatively slow for large networks and long simulations. However, a near-future release will take care of this issue.

Since: v3.0

6.1.5 Generating Custom Spikes

For more fine-grained control over spike generation, individual spike times can be specified per neuron in each group. This is accomplished by using a callback mechanism, which is called at each time step, to specify whether a neuron has fired or not.

In order to specify spike times, a new class is defined that derives from the SpikeGenerator class:

class MySpikes : public SpikeGenerator {
    // etc.
}

The user must then define a SpikeGenerator::nextSpikeTime method. The following is a simple example that generates a spike every 100ms for each neuron in the group.

unsigned int nextSpikeTime(CARLsim* sim, int grpId, int nid, unsigned int currentTime, 
        unsigned int lastScheduledSpikeTime) {
        return (lastScheduledSpikeTime + 100);
}

In order for a custom SpikeGenerator to be associated with a SpikeGenerator group, CARLsim::setSpikeGenerator must be called on the group in CONFIG_STATE:

#include <carlsim.h>
 
// configure network
CARLsim sim("custom SG example",CPU_MODE,USER);
int g0 = sim.createSpikeGeneratorGroup("input", 10, EXCITATORY_NEURON);
// etc.
 
// create custom spike generator
MySpikes CSG;
 
// associate group g0 with CSG
sim.setSpikeGenerator(g0, &CSG);
 
sim.setupNetwork();
// etc.

Since: v2.0

6.2 Generating Current

Author: Michael Beyeler

CARLsim::setExternalCurrent can be used to inject currents, specified on a per-neuron basis, into the soma of each neuron in a group, at each timestep of the simulation (every millisecond). For this, a float vector of current amounts (mA) is specified, one element per neuron in the group.

Note that once CARLsim::setExternalCurrent is called, the specified amount of current will be injected every timestep, until the user calls CARLsim::setExternalCurrent again with updated values (e.g., with value zero).

To input different currents into a neuron over time, the idea is to run short periods of CARLsim::runNetwork and subsequently calling CARLsim::setExternalCurrent with updated current values.

For example, the following code snippet injects 5mA for 50ms into the soma of every neuron in the group:

#include <carlsim.h>
CARLsim sim("Current Injection",CPU_MODE,USER);
int g0 = sim.createGroup("input", 10, EXCITATORY_NEURON);
// etc.
 
sim.setupNetwork();
 
std::vector<float> current(10, 5.0f);
snn.setExternalCurrent(g0, current);
snn.runNetwork(0,50);

Note that in the case where the same current applies to every neuron, it is sufficient to pass a single float value:

// the following statement ...
sim.setExternalCurrent(g0, 5.0f);
// ... is equivalent to:
std::vector<float> current(10, 5.0f);
sim.setExternalCurrent(g0, current);

After stimulation, the idea is to reset the external current to zero:

// apply current for 10ms
sim.setExternalCurrent(g0, 5.0f);
sim.runNetwork(0,10);
 
// then reset current
sim.setExternalCurrent(g0, 0.0f);
sim.runNetwork(1,0);
// etc.

Note: This method cannot be applied to SpikeGenerator groups.; If all neurons in the group should receive the same amount of current, you can use the convenience function setExternalCurrent(int grpId, float current).

Attention: Make sure to reset current after use (i.e., for the next call to runNetwork), otherwise the current will keep getting applied to the group.

Since: v3.0

6.3 Visual Stimulus Toolbox

Author: Michael Beyeler

The VisualStimulus utility consists of a MATLAB Toolbox that allows for the generation of 2D visual stimuli such as sinusoidal gratings, plaids, and random dot fields as well as some C++ CARLsim plug-in code. The MATLAB class allows to mix-and-match stimuli of different types, on a frame-by-frame basis. Stimuli can also be confined to visual aperture and combined with noise. Frames can then be dumped to a binary file, so that they can be reloaded later on.

Usage example: The following MATLAB code snippet creates a 32x32 pixel grayscale stimulus that consists of a sinusoidal grating (first ten frames), followed by a blank frame (delay period), followed by a plaid stimulus (next ten frames), confined to a circular aperture. The resulting stimulus is first plotted in figure axes, then recorded to AVI, and finally stored as a binary with a default name depending on the stimulus type, such as "inpGratingPlaid_gray_32x32x21.dat".

>> VS = VisualStimulus(32,32);
>> VS.addSinGrating; % add 10 frames of a sinusoidal grating
>> VS.addBlankFrames; % blank frame for delay period
>> VS.addPlaid; % add 10 frames of a plaid stimulus
>> VS.addApertureToExistingFrames; % confine frames to aperture
>> VS.displayFrames; % plot them!
>> VS.recordMovie; % record an AVI movie
>> VS.saveToFile; % store the created stimulus to binary

CARLsim provides plug-in code to interface the generated binary files with SpikeGenerator groups. This allows the user to create sophisticated visual stimuli in MATLAB, and interface them to a spiking network on a frame-by-frame basis. The class VisualStimulus reads frames from binary, and returns either the raw character array or a PoissonRate object with the same size as number of pixels in a stimulus frame.

A VisualStimulus is instantiated as follows:

VisualStimulus VS("inpGratingPlaid_gray_32x32x21.dat");

int videoLength = VS.getStimulusLength();

where the string "inpGratingPlaid_gray_32x32x21.dat" references the created file mentioned above. The number of frames can be retrieved with VisualStimulus::getStimulusLength.

It is then straightforward to interface the recorded stimulus with a CARLsim simulation by making use of VisualStimulus::readFrame, which, whenever called, reads the next unread frame and returns it either as a raw character array or as a PoissonRate object.

#include <carlsim.h>
CARLsim sim("VisualStimulus Example",CPU_MODE,USER);
int g0 = sim.createSpikeGeneratorGroup("VSinput", Grid3D(32,32,1), EXCITATORY_NEURON);
// etc.
sim.setupNetwork();
 
for (int i=0; i<videoLength; i++) {
    PoissonRate * rates = VS.readFrame(50.0f); // grayscale value 255 will be mapped to 50 Hz
    sim.setSpikeRate(g0, rates); // for this to work, there must be 32x32=1024 neurons in g0
    sim.runNetwork(1,0); // run the network
}

The following figures shows a number of different stimulus frames created with the MATLAB Visual Stimulus toolbox. The Toolbox provides methods to compose stimuli made of sinusoidal gratings, bars, dots, noise, and custom frames. Apertures can be rectangular or circular. Noise can be white, Gaussian, Poissonian, salt & pepper, or speckle. Random dots can exhibit translatory motion, rotations, expansions, contractions, and mixtures of those types.

VisualStimulus Toolbox examples: sinusoidal gratings, plaids, random dot fields, confined to apertures, with added noise.

Note: Currently only grayscale stimuli are supported. However, a near-future release will add support for RGB stimuli.

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