.. currentmodule:: brian2

.. Kremer_et_al_2011_barrel_cortex:

Example: Kremer_et_al_2011_barrel_cortex
========================================


        .. only:: html

            .. |launchbinder| image:: http://mybinder.org/badge.svg
            .. _launchbinder: https://mybinder.org/v2/gh/brian-team/brian2-binder/master?filepath=examples/frompapers/Kremer_et_al_2011_barrel_cortex.ipynb

            .. note::
               You can launch an interactive, editable version of this
               example without installing any local files
               using the Binder service (although note that at some times this
               may be slow or fail to open): |launchbinder|_

        

Late Emergence of the Whisker Direction Selectivity Map in the Rat Barrel Cortex.
Kremer Y, Leger JF, Goodman DF, Brette R, Bourdieu L (2011).
J Neurosci 31(29):10689-700.

Development of direction maps with pinwheels in the barrel cortex.
Whiskers are deflected with random moving bars.

N.B.: network construction can be long.

::

    from brian2 import *
    import time
    
    t1 = time.time()
    
    # PARAMETERS
    # Neuron numbers
    M4, M23exc, M23inh = 22, 25, 12  # size of each barrel (in neurons)
    N4, N23exc, N23inh = M4**2, M23exc**2, M23inh**2  # neurons per barrel
    barrelarraysize = 5  # Choose 3 or 4 if memory error
    Nbarrels = barrelarraysize**2
    # Stimulation
    stim_change_time = 5*ms
    Fmax = .5/stim_change_time # maximum firing rate in layer 4 (.5 spike / stimulation)
    # Neuron parameters
    taum, taue, taui = 10*ms, 2*ms, 25*ms
    El = -70*mV
    Vt, vt_inc, tauvt = -55*mV, 2*mV, 50*ms  # adaptive threshold
    # STDP
    taup, taud = 5*ms, 25*ms
    Ap, Ad= .05, -.04
    # EPSPs/IPSPs
    EPSP, IPSP = 1*mV, -1*mV
    EPSC = EPSP * (taue/taum)**(taum/(taue-taum))
    IPSC = IPSP * (taui/taum)**(taum/(taui-taum))
    Ap, Ad = Ap*EPSC, Ad*EPSC
    
    # Layer 4, models the input stimulus
    eqs_layer4 = '''
    rate = int(is_active)*clip(cos(direction - selectivity), 0, inf)*Fmax: Hz
    is_active = abs((barrel_x + 0.5 - bar_x) * cos(direction) + (barrel_y + 0.5 - bar_y) * sin(direction)) < 0.5: boolean
    barrel_x : integer # The x index of the barrel
    barrel_y : integer # The y index of the barrel
    selectivity : 1
    # Stimulus parameters (same for all neurons)
    bar_x = cos(direction)*(t - stim_start_time)/(5*ms) + stim_start_x : 1 (shared)
    bar_y = sin(direction)*(t - stim_start_time)/(5*ms) + stim_start_y : 1 (shared)
    direction : 1 (shared) # direction of the current stimulus
    stim_start_time : second (shared) # start time of the current stimulus
    stim_start_x : 1 (shared) # start position of the stimulus
    stim_start_y : 1 (shared) # start position of the stimulus
    '''
    layer4 = NeuronGroup(N4*Nbarrels, eqs_layer4, threshold='rand() < rate*dt',
                         method='euler', name='layer4')
    layer4.barrel_x = '(i // N4) % barrelarraysize + 0.5'
    layer4.barrel_y = 'i // (barrelarraysize*N4) + 0.5'
    layer4.selectivity = '(i%N4)/(1.0*N4)*2*pi'  # for each barrel, selectivity between 0 and 2*pi
    
    stimradius = (11+1)*.5
    
    # Chose a new randomly oriented bar every 60ms
    runner_code = '''
    direction = rand()*2*pi
    stim_start_x = barrelarraysize / 2.0 - cos(direction)*stimradius
    stim_start_y = barrelarraysize / 2.0 - sin(direction)*stimradius
    stim_start_time = t
    '''
    layer4.run_regularly(runner_code, dt=60*ms, when='start')
    
    # Layer 2/3
    # Model: IF with adaptive threshold
    eqs_layer23 = '''
    dv/dt=(ge+gi+El-v)/taum : volt
    dge/dt=-ge/taue : volt
    dgi/dt=-gi/taui : volt
    dvt/dt=(Vt-vt)/tauvt : volt # adaptation
    barrel_idx : integer
    x : 1  # in "barrel width" units
    y : 1  # in "barrel width" units
    '''
    layer23 = NeuronGroup(Nbarrels*(N23exc+N23inh), eqs_layer23,
                          threshold='v>vt', reset='v = El; vt += vt_inc',
                          refractory=2*ms, method='euler', name='layer23')
    layer23.v = El
    layer23.vt = Vt
    
    # Subgroups for excitatory and inhibitory neurons in layer 2/3
    layer23exc = layer23[:Nbarrels*N23exc]
    layer23inh = layer23[Nbarrels*N23exc:]
    
    # Layer 2/3 excitatory
    # The units for x and y are the width/height of a single barrel
    layer23exc.x = '(i % (barrelarraysize*M23exc)) * (1.0/M23exc)'
    layer23exc.y = '(i // (barrelarraysize*M23exc)) * (1.0/M23exc)'
    layer23exc.barrel_idx = 'floor(x) + floor(y)*barrelarraysize'
    
    # Layer 2/3 inhibitory
    layer23inh.x = 'i % (barrelarraysize*M23inh) * (1.0/M23inh)'
    layer23inh.y = 'i // (barrelarraysize*M23inh) * (1.0/M23inh)'
    layer23inh.barrel_idx = 'floor(x) + floor(y)*barrelarraysize'
    
    print("Building synapses, please wait...")
    # Feedforward connections (plastic)
    feedforward = Synapses(layer4, layer23exc,
                           model='''w:volt
                                    dA_source/dt = -A_source/taup : volt (event-driven)
                                    dA_target/dt = -A_target/taud : volt (event-driven)''',
                           on_pre='''ge+=w
                                  A_source += Ap
                                  w = clip(w+A_target, 0*volt, EPSC)''',
                           on_post='''
                                  A_target += Ad
                                  w = clip(w+A_source, 0*volt, EPSC)''',
                           name='feedforward')
    # Connect neurons in the same barrel with 50% probability
    feedforward.connect('(barrel_x_pre + barrelarraysize*barrel_y_pre) == barrel_idx_post',
                        p=0.5)
    feedforward.w = EPSC*.5
    
    print('excitatory lateral')
    # Excitatory lateral connections
    recurrent_exc = Synapses(layer23exc, layer23, model='w:volt', on_pre='ge+=w',
                             name='recurrent_exc')
    recurrent_exc.connect(p='.15*exp(-.5*(((x_pre-x_post)/.4)**2+((y_pre-y_post)/.4)**2))')
    recurrent_exc.w['j<Nbarrels*N23exc'] = EPSC*.3 # excitatory->excitatory
    recurrent_exc.w['j>=Nbarrels*N23exc'] = EPSC # excitatory->inhibitory
    
    
    # Inhibitory lateral connections
    print('inhibitory lateral')
    recurrent_inh = Synapses(layer23inh, layer23exc, on_pre='gi+=IPSC',
                             name='recurrent_inh')
    recurrent_inh.connect(p='exp(-.5*(((x_pre-x_post)/.2)**2+((y_pre-y_post)/.2)**2))')
    
    if get_device().__class__.__name__=='RuntimeDevice':
        print('Total number of connections')
        print('feedforward: %d' % len(feedforward))
        print('recurrent exc: %d' % len(recurrent_exc))
        print('recurrent inh: %d' % len(recurrent_inh))
    
        t2 = time.time()
        print("Construction time: %.1fs" % (t2 - t1))
    
    run(5*second, report='text')
    
    # Calculate the preferred direction of each cell in layer23 by doing a
    # vector average of the selectivity of the projecting layer4 cells, weighted
    # by the synaptic weight.
    _r = bincount(feedforward.j,
                  weights=feedforward.w * cos(feedforward.selectivity_pre)/feedforward.N_incoming,
                  minlength=len(layer23exc))
    _i = bincount(feedforward.j,
                  weights=feedforward.w * sin(feedforward.selectivity_pre)/feedforward.N_incoming,
                  minlength=len(layer23exc))
    selectivity_exc = (arctan2(_r, _i) % (2*pi))*180./pi
    
    
    scatter(layer23.x[:Nbarrels*N23exc], layer23.y[:Nbarrels*N23exc],
            c=selectivity_exc[:Nbarrels*N23exc],
            edgecolors='none', marker='s', cmap='hsv')
    vlines(np.arange(barrelarraysize), 0, barrelarraysize, 'k')
    hlines(np.arange(barrelarraysize), 0, barrelarraysize, 'k')
    clim(0, 360)
    colorbar()
    show()
    

.. image:: ../resources/examples_images/frompapers.Kremer_et_al_2011_barrel_cortex.1.png