GUI

Examining connections

The main window shows icons for a population of cells and an icon list (upper left) for all populations. Left-click on the icon list to select which population is displayed in the main window. Right-click on the icon list to select which population is displayed in the connections window. Clicking left/right on one of the icons among the 2D grid of icons in the main window (not in the header) will cause the pre/post synaptic connections with respect to the population in the connections window to be displayed. The display in the connections window can be binarized by pressing b, or normalized to max by pressing m, in the main window. Pressing the same key again will turn off the feature.

If an LGN population is displayed in the connections window, middle clicking an LGN unit in the connections window will show its post-synaptic targets in the main window.

Stimulus mode

• ,. - pressing comma and period scroll forward and backword through video frames of the stimulus.
• > < - less-than and great-than scroll forward and backward through the list of stimuli, if there are multiple stimuli specified in the .stm file.
• s - enters or leaves stimulus mode.

Interactive mode

The basics:

1. Press i to enter interactive mode (you can leave only by exiting the model)

2. Be sure that the desired stimulus has been selected in stimulus mode. You do not have to have stimulus mode turned on, once the desired stimulus has been selected.

3. Verify that some cells are marked (with a dim white highlight) for recording. Cells will be marked based on requested outputs in the response (.rsp) file. You can mark cells in the GUI by clicking on them, then pressing f, then highlighting the desired output options, and using ESC (escape key) to quit.

4. Note, the spacebar is used to clear all requested output.

5. Press r to run the selected stimulus on the model.

Monitor Window

Limitations

The monitor window currently shows output and does not accept input. The window can be resized with the mouse, but will not refresh properly until the next stimulus is run by pressing r in the main window.

Response file parameters

• gui_flag - 0-do not activate GUI, 1-activate GUI.
• gui_win_x - x location of main window (pix)
• gui_win_y - y location of main window (pix)
• gui_win_w - width of gui main window (pix)
• gui_win_h - height of gui main window (pix)
• gui_win2_x - x location of connection window (pix)
• gui_win2_y - y location of connection window (pix)
• gui_win2_w - width of gui connection window (pix)
• gui_win2_h - height of gui connection window (pix)
• gui_colormapflag - 0-start w/o colormap, 1-w/ colormap
• gui_stim_frame - [0] initial frame index of stimulus (this is the frame that will appear first when entering stimulus mode)
• gui_stim_num - [0] initial stimulus number in stimulus mode

  Response Monitor

• mon_flag - whether to show the monitor window (0 or 1)
• mon_stim_flag - show visual stimulus in monitor window (0 or 1)
• mon_t - temporal epoch (sec), use -1 for default time period
• mon_dt - update monitor plot this often (sec)
• mon_winw - monitor window width (pixels)
• mon_winh - monitor window height (pixels)
• mon_mV_y0 - y-axis lower bound for mV (-90)
• mon_mV_y1 - y-axis upper bound for mV (-20)
• mon_nS_y0 - y-axis lower bound for nS (-20)
• mon_nS_y1 - y-axis upper bound for nS ( 40)

  Statistics (mean, SD) for plots

• mon_stat_t0 - start of window for statistics (sec)
• mon_stat_tn - duration of window for statistics (sec), 0=off

• mon_presyn_layer_to_cell in exs 8 8 0 spikes  # Monitor spikes from 'in' layer
  

Population Icons

• circle
• square
• polygon
  • nside [number_of_sides]
• stellate
  • npoint [number_of_points]
• cs - Center/Surround, used for LGN

  <icon>
    shape circle
    r 0.4
    g 0.4
    b 0.8
  </icon>

  <icon>
    shape stellate
    r 0.0
    g 0.8
    b 0.2
    npoint 5
  </icon>

Population size and geometry

<geometry>
  xn  16           # Number of cells in x-dimension [Area xn?]
  yn  16           # Number of cells in y-dimension [Area yn?]
  zn   4           # Number of cells in z-dimension [1]
  x0   8           # Origin w.r.t. Area origin [0]
  y0   8           # Origin w.r.t. Area origin [0]
  xf   1.0         # Scaling w.r.t. Area (or stimulus grid?) [1.0]
  yf   1.0         # Scaling w.r.t. Area (or stimulus grid?) [1.0]
  oddxoff 0.0      # x-offset of odd row numbers [0.0] (grid units)
</geometry>

An <area> is defined as follows,

<area>
  name  v1           # Name to identify this area [exit]
  xn    16           # Size of area in x-dimension [exit]
  yn    16           # Size of area in y-dimension [exit]
  x0     8           # Origin w.r.t. stimulus grid [exit]
  y0     8           # Origin w.r.t. stimulus grid [exit]
  xf     1.0         # Scaling w.r.t. stimulus grid [1.0]
  yf     1.0         # Scaling w.r.t. stimulus grid [1.0]
  umx   59.0 (um)    # micons per Area grid unit [0.0]
  umy   59.0 (um)    # micons per Area grid unit [umx]
</area>

xn      16           # (pix) Size of stimulus in x-dimension [exit]
yn      16           # (pix) Size of stimulus in y-dimension [exit]
sscale   0.04        # (deg/pix) spatial scaling of stimulus grid [exit]

Maps

Orienation. The following parameters govern the orientation map. Default values are specified in parentheses. Note, the phase shifts below refer to some fraction of a full cycle (0 to 360 deg), and the unit of deg here does not refer to the 0-180 degree orientation scale. [This can be confusing, and perhaps a range of 0.0 to 1.0 should be used instead.]

<map>
  name   orimap       # Name to identify this map [exit]
  type   ori          # Type of map, determines the orientation pattern [exit]
  ncol_x   2          # Number of orientation columns along x-axis [2]
  ncol_y   2          # Number of orientation columns along y-axis [ncol_x]
  phase_x  0.0        # (0-360 deg) shift pinwheels along x-axis [0.0]
  phase_y  0.0        # (0-360 deg) shift pinwheels along y-axis [0.0]
  phase_p  0.0        # (0-360 deg) rotate ori around pinwheel [0.0]
</map>

Direction. Currently, the orientation map sets a value that is interpreted as a direction, but only covers directions from 0-180. When forming direction selective (DS) cells, the direction can be changed by using a flag parameter, as follows:

  map_dir_flag  ori    # "ori", "ori_invert", "ori_alt_z", ...

• ori - use the orientation map value for the reference direction
• ori_invert - add 180 deg to the orientation map value
• ori_alt_z - alternate between ori and ori+180 for z=0, 1, ... This allows the construction of multiple sheets of cells with opponent directions, consistent with the underlying orientation map.

<map>
  name odmap          # Name to identify this map [exit]
  type ocdom          # Type of map [exit]
  ncol_x   4          # Number of OD columns in X-direction
  phase_x  1.0        # (0-360 deg) Phase of OD map on X-axis
</map>

<map>
  name rfxmap         # Name to identify this map [exit]
  type rfx            # Type of map
  ncol_x   4          # Number of OD columns in X-direction
  phase_x  1.0        # Phase of OD map on X-axis (deg)
</map>

Cell Attributes

• ori - orientation, 0..180.0
• dir - direction, 0..360.0 (this is stored as 'ori', but can be referred to as 'dir' when the relevant values go from 0..360)
• ori_cv - circular variance of orientation 0..1
• phase - phase of spatial RF, 0..360.0
• ocdom - Ocular dominance, -1.0 (left) to 1.0 (right)
• rfx, rfy - position of center of RF on LGN/stimulus grid (xn by yn)
• cx, cy - cortical location in microns

• attr_ori_derive_from_pop [pop_name] - to compute the ori from the ori values of all synaptic inputs from the named population, weighted by the synaptic weights.
• attr_dir_derive_from_pop [pop_name] - to compute the ori as a direction value (0..360) from the ori values and synaptic interactions (e.g. as DS02 with negative phase shift will add 180 to the input ori values).

Customize

Examples:

• Delete all synapses where the specified pre-synaptic unit is involved in a synaptic interaction as index 0 and where the post-syn unit is in the specified layer.

  <customize>
    type        synapse_delete         # Delete synapses between units
    unit_pre    exs_11_11_0            # Pre-synaptic unit
    layer_post  ds                     # Post-synaptic layer name
    si_index    0                      # Synaptic interaction index
  </customize>
  
  
  

• Adjust all synapses between the specified pre-synaptic unit and the post-synaptic layer. Currently, if there is a synaptic interaction, the weight only gets adjusted if the pre-syn unit has cell index 0.

  <customize>
    type        synapse_adjust         # Adjust synaptic weight
    unit_pre    exs_11_11_0            # Pre-synaptic unit
    layer_post  ds                     # Post-synaptic layer name
    syn_weight  6.23                   # Synaptic weight
  </customize>
  
  
  

• Add a synapse between the specified pre-synaptic unit and the post-synaptic unit. (Layers not impl'd yet).

  <customize>
    type        synapse_add            # Add a synapse
    unit_pre    exs_11_11_0            # Pre-synaptic unit
    unit_post   ds_0_0_0               # Post-synaptic unit
    syn_weight  6.23                   # Synaptic weight
    syn_tdelay  0.0                    # Time delay (s), axon transit time
    syn_type    1                      # Synaptic type, 1-ex, 2-in
  </customize>
  
  
  

Below is old way - does not work with .moo files

• CUSTOMIZE unit ex_9_8_0 synapse_delete from_layer in

  deletes all synapses to the target unit (ex_9_8_0) from the named layer (in).

• CUSTOMIZE unit ex_9_8_0 synapse_copy layer_to_unit in ex_8_8_0

  copy to the target unit (ex_9_8_0) all synapses from the named layer (in) to the source unit (ex_8_8_0).

• CUSTOMIZE unit ex_8_8_0 set_param bg_rate_x 100.0

  set the parameter named "bg_rate_x" to the value (100.0) for the target unit (ex_8_8_0).

• CUSTOMIZE unit ex_8_8_0 bg_corr_ex 0.90 ex_9_8_0
• CUSTOMIZE unit ex_8_8_0 bg_corr_in 0.90 ex_9_8_0

  cause there to be 90% of shared spikes in the excitatory (first line) or inhibitory (second line) background inputs for ex_8_8_0 and ex_9_8_0. Both lines can be used together to correlate both ex and in background spike inputs. The fraction of identical spikes, here 0.9, may vary from 0 to 1.0.

• CUSTOMIZE unit ex_8_8_0 style ds01

  Customize this unit according to a pre-defined style.

Response output

• spikes - spike times
• vm - Vm for soma (mV)
• vd - Vm for dendrite (mV)
• gad - Adaptation conductance (nS)
• in_gi - Total inhibitory conductance from population "in"
• in_ii - Current from population "in"
• ex_gx - Total excitatory conductance from population "ex"
• ex_ix - Current from intrcortical excitatory synapses, including "..._bg_rate_x".
• lgn_ga - AMPA conductance from LGN, same as gx for inh cells
• lgn_ia - AMPA current from LGN (nA)
• lgn_gn - NMDA conductance from LGN (Not for inhib cells)
• lgn_gx - Total excitatory g from LGN = lgn_ga + lgn_gn

• lgn_gain - (a + b*gsum) signal which will divide original lgn_ga and lgn_gn (thus, lgn_gx).

  for LGN cells:

• vm - sampling at 1000.0 (Don't know if other values work)
• gx - sampling at 500.0 (Don't know if other values work)
• gi - sampling at 500.0 (Don't know if other values work)

  save_pop_unit_as_ex_8_8  s 1000.0  ex 8 8 0  spikes

  save_pop_unit_as_ex_8_8_vm  f 1000.0  ex 8 8 0  vm

• si_mask - mask values for a synaptic interaction, such as si_ds02

• si_mask1 - mask values for a synaptic interaction, using 'symmask'
• si_mask2 - mask values for a synaptic interaction, using 'symmask'

  save_pop_syn_as_syn0  f 1000.0  ex 8 8 0  ds 0 0 0  si_mask

Cortical unit function

The pre-computed (PC) inputs (from ON and OFF LGN cells) include the scale, bias, and noise for 'ifc_ex_' params. The IFC params for inhibitory scale, bias, and noise are currently not used, however, perhaps the bias and the noise could be used to form a PC inhibitory conductance?

The PC inputs are combined with the dynamic (D) inputs in the 'pop_util_deriv_01' routine.

Some excitatory units will have two compartments. The transfer resistance is set to be 15.4 nS = 65 MOhm (Larkum et al. 2004, Cerebral Cortex, used 65 MOhm).

• ifc_ex_g_tran - (0 default) transfer conductance. If > 0, there will be a dendritic compartment, and NMDA can be used. If 0, then there will be no dendritic compartment, and no NMDA can be used.

• AMPA - EPSC is given by the following parameters for alpha functions:
  • pop_ex_psc_tau_ex - onto ex cells
  • pop_ex_psc_amp_ex - This will set the amplitude of the AMPA conductance, and that for NMDA will be scaled according to 'nmda_frac'.

• NMDA - (from Lauritzen et al., 2001; see also Carmignoto and Vicini 1992; Lester et al. 1990). Channels were 35.5% open at spike threshold, 52.5mV (Krukowski and Miller, 2001). Used 90% NMDA integrated current (Krukowski and Miller, 2001).

  To model the NMDA unitary conductance shape of Lauritzen et al. (2001), three alpha-functions are summed (see 'COMPARE_ALPHA_DBL_EXP' in 'test0.c'). The parameters are:

  • nmda_alpha_1 - 0.09 (time to peak = 1/alpha msec)
  • nmda_alpha_2 - 0.025
  • nmda_amp_2 - 0.8
  • nmda_alpha_3 - 0.008
  • nmda_amp_3 - 0.1

  The shape of this function is then scaled so that the fraction of integrated current (Krukowski and Miller, 2001, used 90%), NMDA/AMPA, is 'nmda_frac' for a cell clamped at the spike threshold. A separate value, 'lgn_nmda_frac' specifies the fraction for thalamocortical synapses.

  Apparently, increasing 'lgn_nmda_frac' adds to the NMDA input but keeps the same amount of AMPA input (as opposed to trying to keep the total excitatory conductance equal while only adjusting the relative fraction). Thus, changing the NMDA fraction from say 80% to 0 will reduce the total amount of excitatory input.

  The voltage dependence of the NMDA is given by Jahr and Stevens (1990) Equation 4a, whereas their Eqn 4c does not seem to be a very good approximation.

• LEAKAGE
• ADAPTATION

Thomson and Deuchars, 1994 - cite Salt and Herring (1991) for the idea that LGN->CTX_E is non-NMDA. Has this been overturned?

Background input rates

• pop_ex_bg_ex_rate [rate] - (0.0 default) - spikes/sec arriving via the "ex" conductance
• pop_ex_bg_ex_amp [amp] - (1.0 default) - EPSG amplitude relative to pop_ex_psc_amp_ex
• pop_ex_bg_in_rate [rate] - (0.0 default) - spikes/sec arriving via the "in" conductance
• pop_ex_bg_in_amp [amp] - (1.0 default) - EPSG amplitude relative to pop_ex_psc_amp_in

Spike transmission

    DOE(t) = amp [ e^(-t/tau_f) - e^(-t/tau_r) ].

    ALPHA(t) = amp * a*t*e * e^(-a*t),

When a spike is discharged in the population model, it is added to the input lists of post-synaptic cells with a 1.0 ms delay. The spike is represented in the list as a floating point value of 1.0 for full strength. Synaptic depression is applied by reducing the value that is added to the list.

See Boudreau and Ferster (2005) for cat synaptic depression.

Synaptic Depression

See Boudreau and Ferster (2005) for recent data?

The following parameters govern synaptic depression, which is separate for LGN-to-CTX and CTX-to-CTX:

Cortex to Cortex

• *** WARNING: these params control *all* intracortical transmission
• ctx2ctx_ex_sdf - Efficacy immediate following a spike
• ctx2ctx_ex_sdtau - (ms) time constant of recovery from depression

  LGN to Cortex

• lgn2ctx_sdf - Efficacy following a spike at the synapse
  • 1.0 - no depression
  • 0.0 - full depression
• lgn2ctx_sdtau - Time course of exponential recovery towards full efficacy (1.0)

Synaptic Interaction

si_ds02

• dt - time to peak of mask function
• masktype - 1-sinusoid, 2-maxwell function
• ph_shift - phase shift between spatial RFs of u0 and u1 (90.0 deg)
• ph_dev - phase deviation around phase shift (5.0 deg)

si_nonlin

• nonlin - ['mask'] or 'mult' or 'symmask', the latter symmetrical mask causes each cell in the pair to set a mask for the spikes of the other.
• dt - [must specify] Peak interaction time (s) or SD for Gaussian
• masktype - [must specify] 1-sinusoid (down up down), 2-maxwell function (dt is peak), 3-sine positive lobe only, 4-half Gaussian, (dt is SD), 5-alpha function (dt is peak).
• mask_comp - ['prod'] to mulitply by mask, 'prod1m' to multiply by 1-mask.
• mask_amp - [1.0] mask amplitude. At its peak, the mask would take this value.

multiply

An example of using this nonlinearity is as follows:

  <mech>
    name       pair1        # Name, to be referred to by an <input>
    type       multiply     # Multiply the two conductance traces
  <>

  <input>
    type            lgn_pair   # Create pairs of LGN inputs
    receptor        lgn_ex     # Mechanism for post-syn. conductance
    pair_mech       pair1      # Name of mechanism for paired computation
    pop_origin_1    lgn_a      # Population of origin of LGN inputs [lgn]
    pop_layer_z_1   -1         # z-Layer within population (-1 all z)
    pop_origin_2    lgn_b      # Population of origin of LGN inputs [lgn]
    pop_layer_z_2   -1         # z-Layer within population (-1 all z)

    offset_direction       0.0  (deg) # Offset direction (deg)
    offset_distance        0.25 (deg) # Offset distance (deg of visual angle)
    offset_jitter_para     0.0  (deg) # Jitter parallel to offset vector
    offset_jitter_orth     0.0  (deg) # Jitter orthogonal to offset vector
    offset_jitter_seed  1121          # Randomization seed

    <distrib>
      type   rf_center      # Distribution depends on RF center location
      form   Gaussian       # 'Gaussian', ...
      cdist      0.1  (deg) # critical distance (SD for Gaussian)
      minw       0.05       # suppress connections with lower weight
      normw     50.0        # normalize total weights to this; 0.0 no norm.
      n         10          # Number of inputs
      seed    1777          # Randomization seed
    </distrib>
  </input>

divide

  y = g1 / (a + b*g2)

where 'g1' is the conductance from "pop_origin_1". An example of using this nonlinearity is as follows:

  <mech>
    name       pair1        # Name, to be referred to by an <input>
    type       divide       # Divide the two conductance traces
    div_a      1.0          # 'a' additive constant, to avoid division by zero
    div_b      1.0          # 'b' multiplicative constant
  <>

  <input>
    type            lgn_pair   # Create pairs of LGN inputs
    receptor        lgn_ex     # Mechanism for post-syn. conductance
    pair_mech       pair1      # Name of mechanism for paired computation
    pop_origin_1    lgn_a      # Population of origin of LGN inputs [lgn]
    pop_layer_z_1   -1         # z-Layer within population (-1 all z)
    pop_origin_2    lgn_b      # Population of origin of LGN inputs [lgn]
    pop_layer_z_2   -1         # z-Layer within population (-1 all z)

    offset_direction       0.0  (deg) # Offset direction (deg)
    offset_distance        0.25 (deg) # Offset distance (deg of visual angle)
    offset_jitter_para     0.0  (deg) # Jitter parallel to offset vector
    offset_jitter_orth     0.0  (deg) # Jitter orthogonal to offset vector
    offset_jitter_seed  1121          # Randomization seed

    <distrib>
      type   rf_center      # Distribution depends on RF center location
      form   Gaussian       # 'Gaussian', ...
      cdist      0.1  (deg) # critical distance (SD for Gaussian)
      minw       0.05       # suppress connections with lower weight
      normw     50.0        # normalize total weights to this; 0.0 no norm.
      n         10          # Number of inputs
      seed    1777          # Randomization seed
    </distrib>
  </input>

Afferent Gain Control

S(t) = gain_ca + gain_cb * h(t), 

          n
  h(t) = SUM wi [ri(t) - rH] / rMax
         i=1

In practice, The signal h(t) has been observed to have a value of about 0.04 for a grating of SF 1 cyc/deg and TF 8 Hz for the Dog.0.0 model. The value 0.04 indicates about 4% of maximal theoretical LGN activation on average across the gain field. The theoretical r_Max is probably never achieved.

To smooth the signal, S(t), it is convolved with a one-sided decaying exponential with time constant gain_tau.

<input>
  type lgn_on_off
   ...
  gainflag   1      # 1-Apply gain control, 0-none
  gain_tau   0.020  # Exponential convolution, time constant (s)
  gain_ca    1.0    # Additive constant
  gain_cb   14.0    # Multiplicative constant (0.0=no gain control)
   ...
  sd_orth    0.125  # (deg) Gaussian SD for Gabor RF orthog to ori
  sd_par     0.215  # (deg) Gaussian SD for Gabor RF parallel to ori
   ...
</input>

LGN

Mesh Interface

To prepare, and receive information

• mod_mesh_rgc_01_prep() - Prepare the retina mesh model
• mod_mesh_get_mm_mosaic_cn() - get number of cones in mosaic
• mod_mesh_ptr_mm_mosaic_cx() - get pointer to list of cone x-coords
• mod_mesh_ptr_mm_mosaic_cy() - get pointer to list of cone y-coords
• mod_mesh_ptr_mm_mosaic_cid() - get ptr. to cone ID: 0,1,2 (S,M,L)
• mod_mesh_ptr_mm_mosaic_dens_deg() - get cone density, per deg^2.
• mod_mesh_ptr_mm_mosaic_degpmm() - get deg/mm on retina.

On each trial, to get responses

• mod_mesh_compute_diff_all() - Run mesh model on stimulus, compute P-H difference at all loci
• mod_mesh_get_spikes_2d_flag() - Return spikes for each unit that is flagged in the indicator array

Connectivity - <input>

• regular - inputs between cortical populations

• lgn_on_off - inputs from LGN population
  (See section below on LGN to CTX).

• bg - background spikes
  • ex_rate [rate] - (0.0 default) - spikes/sec arriving via the "ex" conductance
  • ex_amp [amp] - (1.0 default) - EPSG amplitude relative to pop_ex_psc_amp_ex
  • in_rate [rate] - (0.0 default) - spikes/sec arriving via the "in" conductance
  • in_amp [amp] - (1.0 default) - EPSG amplitude relative to pop_ex_psc_amp_in

  Example

    <input>
      type       bg     # Background input spikes
      ex_rate   100.0   # spikes/s
      ex_amp      4.0   # relative to _psc_amp_ex
      in_rate   200.0   # spikes/s
      in_amp      2.0   # relative to _psc_amp_in
    </input>
  

Writing and Reading from files

Some input types can have associated connectivity files (.conn), which allow connection patterns to be stored to be read later. This is configured using the top-level parameters:

• mod_conn_rw - "read", "write", or "none" (default)
• mod_conn_dir_r - directory path prefix for file_read
• mod_conn_dir_w - directory path prefix for file_write

In addition to setting these top-level values, the following must be used within any relevant model inputs:

  <input>
    type    regular
    ...
    file_write conn/local/e2i.conn   # Writes only if 'mod_conn_rw' is "write"
    file_read  conn/global/e2i.conn  # Reads only if 'mod_conn_rw' is "read"
    ...
  </input>

Connectivity - LGN to CTX

mod_conn_gabor_02

• Create a 2D Gabor function, called p.
• Take the absolute value of p
• Scale p to have a maximum value of 1.
• Call the routine mod_conn_meth_02, sending p
  Make a set, G, of all grid points for which p is greater than eps (a small probability value). Choose at random with replacement from G the specified number of inputs. If any input is chosen more times than allowed (specified by ..._maxrep), then disregard this input, and choose another in its place.

Gabor function params

• sf 1.00 # (cyc/deg) SF
• sd_orth 0.25 # (deg) Gaussian SD for Gabor RF, orthog to ori
• sd_par 0.43 # (deg) Gaussian SD for Gabor RF, parallel to ori
• phseed 6577 # for chosing phase (random in 1 of 4 phases)
• seed 1777 # for chosing DOG sampling
• nsamp 200 # number of samples to select as inputs
• maxrep 1 # number of times any one connection can be sampled
• eps 0.05 # no connections where profile < this frac of max
• balance 1 # 0-do not balance ON/OFF, 1-balance ON/OFF

• cell_condition all # "all", "0", "1", "2" ... E.g., cone type

Gabor function params - phase

• phtype 0 # 0-constant for all in z-axis, 1-regular steps
• ph0 x # initial phase (phtype 1)
• phstep x # step by this phase (phtype 1)

Connectivity - CTX I to E (and E-E, and I-I)

Parameters

• conn_i2e_algorithm - values are listed below (0 is default)
  • 0 (mod_conn_corr_on_off) - pointwise correlation
  • 1 (mod_conn_corr_on_off_01) - convolve sampling points (1's for ON, and -1's for OFF) with the center Gaussian of the DOG to create masks for both E and I RFs. The correlation metric is the sum of the products of the RF masks. The distribution of all negative values is formed. The values are scaled so that the mean plus 2 SDs is set to have weight 1. Any higher values are set to 1. Any values lower than conn_i2e_minw are set to 0.

• conn_i2e_minw - Do not make synaptic connections if the weight would be below this value. This can significantly lower the number of I->E contacts, and may speed up the model.
• conn_i2e_prob - Of the set of valid weights, choose connections with this probability (Default 1.0).
• conn_i2e_seed - Randomization seed for i2e connections, used only when conn_i2e_prob < 1.0 (Default 1880).

• conn_e2e_algorithm - (-1 default, no connections) 1=connections
• conn_e2e_... - See parameters above for conn_i2e_...

• conn_e2i_algorithm - (-1 default, no connections) 1=connections
• conn_e2i_... - See parameters above for conn_i2e_...

Connectivity - "distrib"

NOTE there appears to be an inconsistency in the placement of the file parameter, because it appears for some 'distrib' types below, but not for 'ori_dist' (where it apparently appears in the 'input' object. This should be resolved.

ori_dist

• cdist - (um) SD of Gaussian weighting function (max is 1) in orientation. Set to any negative value for SD infinity (i.e., no distance constraint). [-1.0 default]
• cori - (deg) SD of Gaussian weighting function (max is 1) in cortical distance. Set to any negative value for SD infinity (i.e., no orientation constraint). [-1.0 default]

• ori_mean_flag
  • 0 - [default] orientation of the post-syn cell is the reference
  • 1 - add an offset to the orientation of the post-syn cell
  • 2 - use a fixed, absolute orientation as the reference
• cori_offset - (deg) used only if ori_mean_flag is 1
• cori_mu - (deg) used only if ori_mean_flag is 2

• minw - (0..1) make no synapses with weights below this threshold [0.0 default]
• normw - (synapses) Normalize the total of all weights to this number of synapses [0.0, default, no normalization]
• prob - () probability of making a connection [1.0 default]
• seed - (non-zero int) randomization seed for applying 'prob' [23138 default]
• self - (0/1) 0-disallow connection to self [1 default]

corr_lgn

• file - (file name) read inputs from file, ignoring parameters here. Comment this out to disable.

• algorithm - (0,1,...) strategy for picking random connections. Only '1' works now. [1 default]
• minw - (0..1) make no synapses with weights below this threshold [0.0 default]
• cdist - (um) Cutoff distance - no synapses beyond this distance; ignored if less than or equal to zero [0 default].
• prob - () probability of making a connection [1.0 default]
• seed - (non-zero int) randomization seed for applying 'prob' [23138 default]
• corr_sign - (1) sign of correlation: 1-positive, -1-negative [1 default].
• normw - (synapses) Normalize the total of all weights to this number of synapses [0.0, default, no normalization]

gabor_mask

• file - (file name) read inputs from file, ignoring parameters here. Comment this out to disable.
• mask_pre_pop - name of LGN layer, e.g., 'rgc' or 'lgn' [exit]

• sf - (cyc/deg) [exit]
• sd_orth - (deg) [exit]
• sd_par - (deg) [exit]

• cdist - () [exit]
• minw - () [exit]
• seed - () [exit]
• prob - () [exit]
• normw - () [exit]

binoc_mask

• file - (file name) read inputs from file, ignoring parameters here. Comment this out to disable.

• disp_x - (pix) [0.0]
• disp_y - (pix) [0.0]

• sf - (cyc/deg) [exit]
• sd_orth - (deg) [exit]
• sd_par - (deg) [exit]

• cdist - () [exit]
• minw - () [exit]
• seed - () [exit]
• prob - () [exit]
• normw - () [exit]

Models of this type