| home | user guide | examples | reference | changelog | resources |
A population of _CMLINK(channel, KSChannel, kinetic scheme channels). The population may be defined either by the absolute number of channels, or by the channel density. In the latter case, the actual number of channels in a given context depends on the membrane area of the component to which the population is attached. The same channel model can be interpreted in two ways: either stochastically (by setting the _TT(stochastic) flag) or in the continuous limit.
A connection of specified conductance. It may only be used between _CMLINK(cell, IntegratorCompartment, integrator compartments). Optionally, the wire may be rectifying in the direction of the arrow, in which case the target compartment is influenced by the source, but not the converse.
Parameters are as for the SynapsePopulation, except for those relationg to LTD and normalization that are not present in the populations. ThenormalizeWeights flag causes weights to be normalized across a population of synapses. That is, the total starting weight is recorded, and then the weight modification rules proceed for the weight variable G, as they would without modification. But the conductance that is actually applied is scaled up by the ratio of the initial total weight to the current total weight. This has the effect that the total effective weight of the population remains constant. Note that this is not exactly equivalent to changing all weights to maintain a fixed total whenever any single weight changes. The difference lies in the application of the saturation factor G_max, but diifferences can probably safely be ignired. The synapse definition supports two further forms of depression that are independent of the Spike Timing Dependent Potentiation and Depression that are used in the SynapsePopulation. These are depression caused by pre-synaptic events, irrespective of post-synaptic activity (afferentSpikeDepression - ASD), and depression from post-synaptic events, irrespective of pre-synaptic activity (BSD for Backpropagating Spike Depression). In either case, the depression is only applied if the corresponding boolean flag is set. TheXSDFactor (where X isA orB ) determines the magnitude of the depression. The weight is divided by exp(XSDFactor). This has the effect that if the depression factor is zero, the weight doesn't change. If it is very large, the weight is reduced to zero in one go, and intermediate values cause intermediate levels of depression. Of particular interest, small values of the depression factor affect the weight roughly linearly, so for example, a deression factor of 0.01 would cause a weakening of 1 % for each presynaptic spike. When spikes arrive in rapid succession, it is not always appropriate to have the same net depression as if the same number of spikes arrived slowly (without any postsynaptic spikes in either case). This can be achieved by setting a non-zerorechargeTime . This is the timescale on which the ability for depression to take place recovers. That is, it does not influence the weieght, just whether another spike is able to cause as much depression as its predecessor. Mathematically, the depression caused by a spike that follows its predecessor by time tau is (1 - exp(-tau/rechargeTime)) times the depression caused by the predecessor. The underlying model that this corresponds to is one where depression is caused by a pool of some active agent. A first spike converts the whole pool to another form, from which it cannot cause any further depression. The pool recovers on the timescale given by therechargeTime .
A box for capturing compound cell objects. See the _CMLINK(assembly, CaptureBox, capture box) for details. The only extra feature of this component is that once captured the compound is called a _CMLINK(network,Neuron,Neuron) so it can be used in populations of neurons.
Instances of _CMLINK(cell, MultiLinearCell, MultiLinearCell) can be built from scratch or imported. The editor allows the structure to be rotated and scaled, points to be added or removed, sections to be marked for later use, and connections between points to be changed. New cells have just two points. To extend the structure, press the middle mouse button on a point (or left button with the ALT or SHIFT key held down) and drag out a new segment. To move a point use the left mouse button and to change its radius the right button (or left with the CTRL or META key), dragging up or down to with the mouse button down. To delete a point and all its descendents, drag the point off the window to the left or right. To delete a point but leave its descendents attached to its parent, drag it off the window to the bottom. To divide a segment in half, click on the blue proto-point at its center.
A bi-exponential conductance response function. This response runction is reset whenever a new event arrives. That is, all memory of previous events is lost and the response starts again from the beginning. For a response which persists independent of further spikes, use the _CMLINK(cell,CumulativeResponseFunction,CumulativeResponseFunction). When a spike arrives on the input port, an conductance change is triggered in the attached membrane with the given _TT(riseTime), _TT(fallTime), maximal conductance (_TT(conductance)), reversal potential, _TT(Erev) and total _TT(duration). For a smooth profile, the duration should be several times the decay time. If the decay time is set to be smaller than the rise time it will be ignored and an alpha function (x * exp(-x/tau)) will be used. This is the limiting form of a bi-exponential as the decay time approaches the rise time from above. Any number of response functions may be applied to the same component.
Like a SynapsePopulation, except that the parameters are taken from a separate SynapseType object.
passive electrical properties for BranchedCell objects Passive properties for BranchedCell objects. The fields are the membrane capacitance _TT(C-mem) in micro-farads/cm_POW(2), cytoplasmic resistivity _TT(R-cyt) in Ohm cm, A dimensionless area scale factor to account for folds or spines by increasing the effective area, the persistent conductance _TT(G-pers) in nS per square micron and the reversal potential _TT(E-pers) of this conductance in mV.
A bi-exponential conductance response function which is NOT reset when a second event arrives. In this resopect it differes from the _CMLINK(cell, SpikeResponseFunction, SpikeResponseFunction) which is reset. When a spike arrives on the input port, an conductance change is triggered in the attached membrane with the given _TT(riseTime), _TT(fallTime), maximal conductance (_TT(conductance)), reversal potential, _TT(Erev) and total _TT(duration). For a smooth profile, the duration should be several times the decay time. If the decay time is set to be smaller than the rise time it will be ignored and an alpha function (x * exp(-x/tau)) will be used. This is the limiting form of a bi-exponential as the decay time approaches the rise time from above. If the _TT(saturates) flag is set, then the single synapses can saturate under repeated stimulation. For computational convenience, this is not implemented by imposing the maximal conductance, but rather by specifying a _TT(saturationFactor) indicating what fraction of the post-synaptic receptors are involved in transmission of a single event. Another event occurring immediately would be scaled down by (1 - saturationFactor). The available receptors are assumed to recover at the same rate as the decay of the synaptic conductance (_TT(fallTime)). Thus, a saturation factor of zero means that conductances sum indefinitely. A saturation factor of 1 means that two spikes in rapid succession have the same effect as a single spike.
A spike generator which produces a spike whenever the input exceeds a given threshold. After generating a spike, no spike can be produced for a period _TT(refractoryPeriod). If the input is continuously above threshold, then a series of spikes will be produced at this interval. Typically, when used with an _CMLINK(cell, IntegratorCompartment, integrator compartment) the spike output will be connected to the reset port of the compartment, or to a _CMLINK(cell, SpikeResponseFunction, response function) or the compartment will include membrane channels which generate a spike waveform. (or any combination of the above).
A conductance clamp which can be applied to any component accepting conductance input. Like other conductance providers, the clamp should be attached with an _CMLINK(link, InsertionArrow, insertion arrow). If the inputs are not specified, then the _TT(defaultConductance) and _TT(defaultPotential) are applied. If vector inputs are provided on one or both input ports, then these override the defaults.
A variable size population of synapses. This component is a population rather than a single synapse, in that one synapse element is created for each different index on incoming spikes. The individual synapses then evolve according to the properties of the population to which they belong. These include the reversal potential,Erev , initial conductance,G_0 , rise time, fall time and duration as for _CMLINK(cell, SpikeResponseFunction), spike response functions). If thevoltageDependent flag is set, then the conductance caused by a single synapse gated on the post-synaptic potential with equivalent gating chargez and half-open potentialVhalf . If thesaturates flag is set, then the single synapses can saturate under repeated stimulation. For computational convenience, this is not implemented by imposing the maximal conductance, but rather by specifying asaturationFactor indicating what fraction of the post-synaptic receptors are involved in transmission of a single event. Another event occurring immediately would be scaled down by (1 - saturationFactor). The available receptors are assumed to recover at the same rate as the decay of the synaptic conductance (fallTime ). Thus, a saturation factor of zero means that conductances sum indefinitely. A saturation factor of 1 means that two spikes in rapid succession have the same effect as a single spike. If specified, the _CMLINK(standard, Profile, profile) set in theG_ModRule selector is used to implement spike time dependent synaptic plasticity using the arrival times of spikes on theafferent andback propagating ports. The profile is interpreted as a percentage modification to be applied as a function of the time between afferent and back-propagating spikes. Thus, the positive part of the profile is used for the cases when the back-propagating spike follows an afferent spike; the negative part for the case when a back-propagating spike precedes an afferent spike. When several spikes occur on one port between spikes on the other, only the first and last are used for conductance modification. That is, the modification rule only takes effect for pre followed by post or post followed by pre sequences, not for pre followed by pre or post followed by post sequences. The conductance modification saturates atG_max , the exact behavior being given by the following code fragment: _SCODE double trel = backPropSpikeTime - afferentSpikeTime; _BR double delta = 0.01 * G_ModProf.valueAt(trel); _BR double f = -1 + 2/(1+ Math.exp(-delta)); _BR if (f _GT 0) conductance + = f * (G_Max - conductance);_BR if (f _LT 0) conductance + = f * conductance;_BR _ECODE
A detailed cell morphology specification, similar to that procuded by Neurolucida or manipulated by the program Cvapp.
An isopotential compartment with a capacitance and membrane potential. It has an intrinsic leak to _TT(restPotential) which can be specified either as the total membrane resistance (by setting the _TT(leak) option to set resistance ) or indirectly throught the time constant (with the set time constant option). In the second case, the leak is adjusted so that it gives the desired time constant, whatever the capacitance of the cell is. Whenever a spike is received on the reset port, the potential is set to zero for a period _TT(spikeWidth) and then to _TT(resetPotential). The compartment accepts any number of conductance providing components which include _CMLINK(cell,SpikeResponseFunction, spike response functions), _CMLINK(cell,ChannelPopulation, membrane channels), _CMLINK(network, ConductanceProjection, conductance projections) and _CMLINK(cell,SynapsePopulation, synapse populations). Compartments can be connected together with _CMLINK(cell,ResistiveWire, resistive wires) to produce multi-compartmental cells. Such cells may also be constructed by starting with a _CMLINK(cell,MultiLinearCell, geometry specification). (dec 01 - not ready yet).