Plastic Arbor: A modern simulation framework for synaptic plasticity—From single synapses to networks of morphological neurons

doi:10.1371/journal.pcbi.1013926

Plastic Arbor: A modern simulation framework for synaptic plasticity—From single synapses to networks of morphological neurons

Fig 2

Classical spike-timing dependent plasticity (STDP), spike-driven homeostasis, and calcium-driven synaptic plasticity in Arbor.

Arbor implementations (in lighter blue) are cross-validated by comparison to Brian 2 (in orange) or a custom simulator. New features of the Arbor core code are highlighted in italic. (A) STDP paradigm where two Poisson spike sources stimulate an excitatory and an inhibitory synapse connecting to a single neuron (spikes shown in blue and red, respectively). The excitatory connection undergoes STDP (results shown in (C)). Image of dice from Karen Arnold/publicdomainpictures.net. (B) STDP paradigm where two regular spike trains, phase-shifted by delay , drive the weight dynamics of a single synapse (results shown in (D)). (C) Strength of the excitatory synapse, subject to STDP, as shown in (A) (goodness of fit between Arbor and Brian 2: , ). (D) Classical STDP curve, obtained as detailed in (B) (, ). (E) Homeostasis with two Poisson spike sources connected to an LIF neuron via current-based delta synapses (results shown in (G–I), averaged over 50 trials). One of these Poisson inputs spikes at a fixed rate and is plastic, while the other spikes at a varying rate and is static. (F) Paradigm of calcium-based, spike-timing- and rate-dependent synaptic plasticity, using the model by Graupner & Brunel [21]. Two regular spike trains, phase-shifted by delay , drive the stochastic weight dynamics of a single synapse (results shown in (J)). (G) Time course of the varying rate of the input in (E). (H) Strength of the plastic synapse, subject to the dynamics given in (E) (, ). (I) Firing rate of the neuron shown in (E) in the presence of homeostatic plasticity dynamics (, ). (J) Calcium-driven synaptic plasticity as shown in (F). Reproduction of the numerical DP curve from Fig 2 of the related paper [21] (the mean is given by the dark dashed line). Every synapse is subject to 60 spike pairs presented at . Arbor results were averaged over 4000 trials, the solid blue line indicates the mean and the shaded region the 95% confidence interval. Quantification of deviation between the mean curves: , . Note that the generation of this plot is now also demonstrated in an Arbor tutorial [38].

doi: https://doi.org/10.1371/journal.pcbi.1013926.g002