Click here to Download # # ELC_V1_Simp.0.moo # mod_type pop sscale 0.02 # degr/pix (this is different from stim) tscale 0.002 # sec/frame xn 128 # x size yn 128 # y size tn 1024 # t size <area> name v1 # Area name x0 58.0 # Origin wrt stim grid y0 58.0 # xn 12 # width yn 12 # height umx 64.0 (um) # microns per Area grid unit (for now, Area = Stim grid) </area> <area> name stim # Area name x0 0.0 # Origin wrt stim grid y0 0.0 # xn 128 # width yn 128 # height umx 1.0 (um) # microns per Area grid unit (for now, Area = Stim grid) </area> <map> name orimap # ID for reference type ori # Type of map ncol_x 1.5 # Number of ori columns in X-direction phase_x 45.0 (deg) # Phase of pinwheel centers along x-axis, 0-360 phase_y 45.0 (deg) # Phase of pinwheel centers along y-axis, 0-360 phase_p 315.0 (deg) # Phase of color around pinwheel center, 0-360 </map> model_noise_seed 231965 # Controls trial seed mod_trial_reset 1 # reset state between stimuli, default 1 #--------------------------------------.--------------------------------------# # # # IN_RG # # # #-----------------------------------------------------------------------------# <pop> name in_rg area v1 <icon> shape circle r 0.4 g 0.4 b 0.8 </icon> map_ori orimap # Set orientations using the named map <geometry> zn 4 </geometry> <mech> name ex type psg_alpha # Mechanism type tau 0.003 # (s) Tau for excit PSC amp 1.0 # (nS) Amplitude for excit PSC syntype 1 # 1-excit, 2-inhib <> <mech> name in type psg_alpha # Mechanism type tau 0.004 # (s) Tau for inhib PSC amp 4.0 # (nS) Amplitude for inhib PSC syntype 2 # 1-excit, 2-inhib <> <mech> name lgn_ex type psg_doe # Mechanism type ### EPSG from LGN to cortex, Diff Of Exp tau_r 1.0 # (ms) rise time constant tau_f 4.0 # (ms) fall time constant amp 1.0 # (nS) amplitude sdf 1.0 # () synaptic depression, ampl after spike sdtau 99.0 # (ms) synaptic depression, recovery time constant <> <input> type bg # Background input spikes ex_rate 0.0 # spikes/s ex_amp 1.0 # relative to _psc_amp_ex in_rate 0.0 # spikes/s in_amp 6.0 # relative to _psc_amp_in </input> <input> # Ex layer input connections (from LGN) name lgn type lgn_on_off receptor lgn_ex pop_origin rgc sf 2.00 # (cyc/deg) Spatial frequency 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 phseed 485401 # for chosing phase (random in 1 of 4 phases) seed 1777 # for chosing DOG sampling nsamp 30 # () number of samples to select as inputs maxrep 1 # number of times any one connection can be sampled eps 0.03 # no connections where profile < this frac of max cell_condition 1 # "all", "0"-S, "1"-M, "2"-L phtype 1 # 0-const, 1-regular phase steps, 4-regular quads ph0 0.0 # (degr) initial phase phstep 90.0 # (degr) phase step balance 0 # Balance the # of ON and OFF connections </input> <input> # Ex layer input connections (from LGN) name lgn type lgn_on_off receptor lgn_ex pop_origin rgc sf 2.00 # (cyc/deg) Spatial frequency 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 phseed 485401 # for chosing phase (random in 1 of 4 phases) seed 1777 # for chosing DOG sampling nsamp 30 # () number of samples to select as inputs maxrep 1 # number of times any one connection can be sampled eps 0.03 # no connections where profile < this frac of max cell_condition 2 # "all", "0"-S, "1"-M, "2"-L phtype 1 # 0-const, 1-regular phase steps, 4-regular quads ph0 180.0 # (degr) initial phase phstep 90.0 # (degr) phase step balance 0 # Balance the # of ON and OFF connections </input> <spike_gen> type ifc # Conductance driven integrate and fire v_spike 10.0 # (mV) Spike height v_th_x -52.5 # (mV) Spike threshold v_reset_x -57.8 # (mV) Spike reset voltage tau_r_ad 1.00 # (ms) Adaptation rise time tau_f_ad 80.0 # (ms) Adaptation fall time gbar_ad 0.0 # (nS) Adaptation conductance v_ex 0.0 # (mV) Excitatory reversal v_in -70.0 # (mV) Inhibitory reversal v_ad -90.0 # (mV) Adaptation reversal v_leak_x -81.6 # (mV) Leakage reversal g_leak_x 18.0 # (nS) Leakage conductance c_x 214.0 # (pF) Membrane capacitance trefr_x 1.5 # (ms) Refractory period gx_scale 1.3 # () Scale excit g, before adding bias gx_bias 7.0 # (nS) Constant added to g, after any scaling <gx_noise> type gfg # gfg = Gaussian filtered Gaussian noise mean 0.0 (nS) # mean sd 4.0 (nS) # standard deviation tsd 2.0 (ms) # temporal SD <> grect 1 # half-wave rectify gx, gi after adding noise </spike_gen> </pop> #--------------------------------------.--------------------------------------# # # # IN # # # #-----------------------------------------------------------------------------# <pop> name in area v1 <icon> shape circle r 0.0 g 0.0 b 1.0 </icon> map_ori orimap # Set orientations using the named map <geometry> zn 2 </geometry> <mech> # Incoming excitatory spikes name ex type psg_alpha # Mechanism type tau 0.003 # (s) Tau for excit PSC amp 1.0 # (nS) Amplitude for excit PSC syntype 1 # 1-excit, 2-inhib <> <mech> # Incoming inhibitory spikes name in type psg_alpha # Mechanism type tau 0.004 # (s) Tau for inhib PSC amp 4.0 # (nS) Amplitude for inhib PSC syntype 2 # 1-excit, 2-inhib <> <mech> name lgn_ex type psg_doe # Mechanism type ### EPSG from LGN to cortex, Diff Of Exp tau_r 1.0 # (ms) rise time constant tau_f 4.0 # (ms) fall time constant amp 1.0 # (nS) amplitude sdf 1.0 # () synaptic depression, ampl after spike sdtau 99.0 # (ms) synaptic depression, recovery time constant <> <input> type bg # Background input spikes ex_rate 0.0 # spikes/s ex_amp 1.0 # relative to _psc_amp_ex in_rate 200.0 # spikes/s in_amp 4.0 # relative to _psc_amp_in </input> <input> # Ex layer input connections (from LGN) name lgn type lgn_on_off receptor lgn_ex pop_origin rgc sf 2.00 # (cyc/deg) Spatial frequency 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 phseed 485401 # for chosing phase (random in 1 of 4 phases) seed 1777 # for chosing DOG sampling nsamp 30 # () number of samples to select as inputs maxrep 1 # number of times any one connection can be sampled eps 0.03 # no connections where profile < this frac of max cell_condition 1 # "all", "0"-S, "1"-M, "2"-L phtype 1 # 0-const, 1-regular phase steps, 4-regular quads ph0 0.0 # (degr) initial phase phstep 90.0 # (degr) phase step balance 0 # Balance the # of ON and OFF connections </input> <input> # Ex layer input connections (from LGN) name lgn type lgn_on_off receptor lgn_ex pop_origin rgc sf 2.00 # (cyc/deg) Spatial frequency 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 phseed 485401 # for chosing phase (random in 1 of 4 phases) seed 1777 # for chosing DOG sampling nsamp 30 # () number of samples to select as inputs maxrep 1 # number of times any one connection can be sampled eps 0.03 # no connections where profile < this frac of max cell_condition 2 # "all", "0"-S, "1"-M, "2"-L phtype 1 # 0-const, 1-regular phase steps, 4-regular quads ph0 0.0 # (degr) initial phase phstep 90.0 # (degr) phase step balance 0 # Balance the # of ON and OFF connections </input> <spike_gen> type ifc # Conductance driven integrate and fire v_spike 10.0 # (mV) Spike height v_th_x -52.5 # (mV) Spike threshold v_reset_x -56.5 # (mV) Spike reset voltage tau_r_ad 1.00 # (ms) Adaptation rise time tau_f_ad 83.3 # (ms) Adaptation fall time gbar_ad 0.0 # (nS) Adaptation conductance v_ex 0.0 # (mV) Excitatory reversal v_in -70.0 # (mV) Inhibitory reversal v_ad -90.0 # (mV) Adaptation reversal v_leak_x -73.6 # (mV) Leakage reversal g_leak_x 25.0 # (nS) Leakage conductance c_x 500.0 # (pF) Membrane capacitance trefr_x 2.5 # (ms) Refractory period gx_scale 4.0 # () Scale excit g, before adding bias gx_bias 0.0 # (nS) Constant added to g, after any scaling <gx_noise> type gfg # gfg = Gaussian filtered Gaussian noise mean 0.0 (nS) # mean sd 2.0 (nS) # standard deviation tsd 1.0 (ms) # temporal SD <> grect 1 # half-wave rectify gx, gi after adding noise </spike_gen> </pop> #--------------------------------------.--------------------------------------# # # # EX_RG # # # #-----------------------------------------------------------------------------# <pop> name ex_rg area v1 <icon> shape stellate r 0.8 g 0.0 b 0.2 npoint 5 </icon> map_ori orimap # Set orientations using the named map <geometry> zn 4 </geometry> <mech> # Incoming excitatory spikes name ex type psg_alpha # Mechanism type tau 0.003 # (s) Tau for excit PSC amp 1.0 # (nS) Amplitude for excit PSC syntype 1 # 1-excit, 2-inhib <> <mech> # Incoming inhibitory spikes name in type psg_alpha # Mechanism type tau 0.004 # (s) Tau for inhib PSC amp 4.0 # (nS) Amplitude for inhib PSC syntype 2 # 1-excit, 2-inhib <> <mech> name lgn_ex type psg_doe # Mechanism type ### EPSG from LGN to cortex, Diff Of Exp tau_r 1.0 # (ms) rise time constant tau_f 4.0 # (ms) fall time constant amp 1.0 # (nS) amplitude sdf 1.0 # () synaptic depression, ampl after spike sdtau 99.0 # (ms) synaptic depression, recovery time constant <> <input> type bg # Background input spikes ex_rate 0.0 # spikes/s ex_amp 1.0 # relative to _psc_amp_ex in_rate 0.0 # spikes/s in_amp 6.0 # relative to _psc_amp_in </input> <input> # Ex layer input connections (from LGN) name lgn type lgn_on_off receptor lgn_ex pop_origin rgc sf 2.00 # (cyc/deg) Spatial frequency 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 phseed 485401 # for chosing phase (random in 1 of 4 phases) seed 1777 # for chosing DOG sampling nsamp 30 # () number of samples to select as inputs maxrep 1 # number of times any one connection can be sampled eps 0.03 # no connections where profile < this frac of max cell_condition 1 # "all", "0"-S, "1"-M, "2"-L phtype 1 # 0-const, 1-regular phase steps, 4-regular quads ph0 0.0 # (degr) initial phase phstep 90.0 # (degr) phase step balance 0 # Balance the # of ON and OFF connections </input> <input> # Ex layer input connections (from LGN) name lgn type lgn_on_off receptor lgn_ex pop_origin rgc sf 2.00 # (cyc/deg) Spatial frequency 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 phseed 485401 # for chosing phase (random in 1 of 4 phases) seed 1777 # for chosing DOG sampling nsamp 30 # () number of samples to select as inputs maxrep 1 # number of times any one connection can be sampled eps 0.03 # no connections where profile < this frac of max cell_condition 2 # "all", "0"-S, "1"-M, "2"-L phtype 1 # 0-const, 1-regular phase steps, 4-regular quads ph0 180.0 # (degr) initial phase phstep 90.0 # (degr) phase step balance 0 # Balance the # of ON and OFF connections </input> <input> ### i2e inputs type regular # pop_origin in_rg # Where it comes from receptor in # Where it lands <distrib> type corr_lgn # Correlation lgn_pname rgc # pop name for LGN corr_sign -1 # 1-correlated, -1-anticorrelated algorithm 1 # run new picking algorithm, 0 calls old minw 0.5 # minimum weight cdist 500.0 (um) # Cutoff distance (probably need to mult x 2 amp) normw 10.0 # Based on cell center </distrib> </input> ## ## LUM suppression ## <input> type regular # pop_origin in # Where it comes from receptor in # Where it lands <distrib> type ori_dist cdist 58.0 # (um) crit connection distance (SD) cori 30.0 # (degr) crit orientation difference (SD) ori_mean_flag 0 # 0-self, 1-offset, 2-fixed absolute [0] cori_offset 0 # Only used if 'ori_mean_flag' is 1 minw 0.05 # () suppress connections with lower weight normw 30.0 # () normalize weights to this many unitary seed 32510 # Randomization seed for probabilistic sampling prob 1.00 </distrib> </input> <spike_gen> type ifc # Conductance driven integrate and fire v_spike 10.0 # (mV) Spike height v_th_x -52.5 # (mV) Spike threshold v_reset_x -56.5 # (mV) Spike reset voltage tau_r_ad 1.00 # (ms) Adaptation rise time tau_f_ad 83.3 # (ms) Adaptation fall time gbar_ad 0.0 # (nS) Adaptation conductance v_ex 0.0 # (mV) Excitatory reversal v_in -70.0 # (mV) Inhibitory reversal v_ad -90.0 # (mV) Adaptation reversal v_leak_x -73.6 # (mV) Leakage reversal g_leak_x 25.0 # (nS) Leakage conductance c_x 500.0 # (pF) Membrane capacitance trefr_x 2.5 # (ms) Refractory period gx_scale 4.0 # () Scale excit g, before adding bias gx_bias 0.0 # (nS) Constant added to g, after any scaling <gx_noise> type gfg # gfg = Gaussian filtered Gaussian noise mean 0.0 (nS) # mean sd 2.0 (nS) # standard deviation tsd 1.0 (ms) # temporal SD <> grect 1 # half-wave rectify gx, gi after adding noise </spike_gen> </pop> #--------------------------------------.--------------------------------------# # # # RGC # # # #-----------------------------------------------------------------------------# <pop> name rgc type retina0_gc0 # Layer type # area retina area stim <icon> shape circle r 0.7 g 0.7 b 0.7 </icon> <geometry> type irregular # Locations will be irregular source retina0 # Locations to be received from retina mosaic # xn,yn are inherited from stim grid zn 2 # Two sheets, 0-off, 1-on </geometry> binocular 0 # 0-monocular, 1-binocular attrib_conetype 012SML # Set cell attrib 'conetype' (012SML for future) sig1 0.05 # For Display, and RF template for anti-corr i2e connections, sig2 0.2 # but no effect on retina mesh processing. amp1 1 # For Display Only - no effect on mesh model amp2 0.2 # For Display Only - no effect on mesh model <input> ### this is needed to build the BP to RGC synapses name bp type mesh_bp_to_rgc receptor ex pop_origin bipolar </input> sum_bp_distrib 0 # 0-Gaussian, 1-uniform sum_bp_dist 0.10 # Distance (in stimulus pixels) for summing BP signals sum_bp_minw 0.10 # Minimum weight (rel to 1) to include in sum sum_bp_normw 0.3 # Total weight of all BP inputs sum_bp_ccode 111 # Cone code: 111-SML, 010-M only, 011-L+M, ... spike_dump_xi -1 # RGC index, set to -1 to avoid dump spike_dump_zi 1 # 0-OFF, 1-ON <spike_gen> type poisson # Spike generation algorithm offset0 0.0 # Added *before* scaling [0.0] scale 4.0 # Multiplying factor [1.0] offset 0.0 # Added *after* scaling [0.0] toffset 0.020 (s) # Time offset (delay) added to spikes [0.0] </spike_gen> </pop> #--------------------------------------.--------------------------------------# # # # BIPOLAR # # # #-----------------------------------------------------------------------------# <pop> name bipolar type virtual # This is not a layer for computation run_flag 0 # Do not simulate this pop, inherit from mesh model area stim # Coordinate reference is stimulus grid # WYETH - this should be default??? <icon> shape circle r 1.0 g 1.0 b 0.0 </icon> <geometry> type irregular # Locations will be irregular source retina0 # Locations to be received from retina mosaic # xn,yn are inherited from stim grid zn 2 # Two sheets, 0-off, 1-on </geometry> <response> data_id photo # Identifier for .rsp file source retina0 # Source of data within model sampling 500.0 # (samples/s) </response> <response> data_id horiz # Identifier for .rsp file source retina0 # Source of data within model sampling 500.0 # (samples/s) </response> <response> data_id diff # Identifier for .rsp file source retina0 # Source of data within model sampling 500.0 # (samples/s) </response> </pop> #--------------------------------------.--------------------------------------# # # # RETINA0 # # # #-----------------------------------------------------------------------------# <retina0> stim_auto_center_mi -1 # Center stimulus on this mosaic index [-1 ignore] stim_override 0 # 0-no override, 1-stimulus ignored and replaced stim_override_binary all # 0,L,M,S,all,none - set to 1, all others to 0 stim_override_delay 1 # 0-full override, 1-override at tn/2, zero before stim_override_zero_ci -1 # Set this ci to zero always, -1 to deactivate # PHOTORECEPTORS photo_delta 0 # 1-Override photo filter with delta-function mod_mesh_photo_m1 0.020 # Maxwell kernel, 1/2wid = 1.5*m1 (s) mod_mesh_photo_m2 0.040 # Maxwell kernel, 1/2wid = 1.5*m2 (s) mod_mesh_photo_a2 0.70 # Maxwell kernel, amplitude of m2 relative to m1 cone_mosaic_flag 1 # [0] Color mosaic (0-cartesian, 1-mosaic) <cone_mosaic> arrangement RegJit # "Spiral", "RegJit" custom_cid_file null # Reset ConeID's from named file ("null" to ignore) gui 0 # Show GUI for cone mosaic [1] ecc 5.0 # (degr) Eccentricity, for density [-1.0 ignore] degpermm 5.34 # degrees per mm on retina ncone 6600 # number of cones to create (extra discarded) seed_loc 1777 # randomization of cone locations noise 0.3 # amplitude of spatial noise, 0..1 seed_col 1977 # randomization of cone color (L,M,S) - Red Center lm_ratio 1.0 # L:M cone ratio prob_s 0.0 # S cone probability L_rgb 0.0085 0.0271 0.0059 # L cone sensitivity to R G B M_rgb 0.0035 0.0281 0.0086 # M cone sensitivity to R G B S_rgb 0.0009 0.0024 0.0237 # S cone sensitivity to R G B out_id 0 # mosaic index for dump (GUI shows indices) </cone_mosaic> # QUANTAL NOISE noise_factor 0.0 # Quantal noise scaling factor # HORIZONTAL MESH mesh_type 1 # Use a hexagonal mesh [0-cartesian] # # The following values are interpreted differently when mesh_type = 1 # mesh_gh 1.80 # Difference fraction per small time step mesh_gp 0.064 # Time from 1 to 1/e, if 'gh' is 0.0 mesh_dt 0.02 # Time increment (time units); Must be <= 1.0 # BIPOLAR DIFF mesh_whc 1.0 # Weight of HC signal in diff. (1.0 is balanced) # GAIN CONTROL mesh_gain_hp_flag 0 # Apply the gain-controlled HP filtering (0) mesh_lp_tau 0.004 # (s) 1/alpha for LP-filter of 'diff' (0-none) mesh_gsig_mean 0.6 # gain1 value which maps to 0.5 * lp mesh_gsig_slope 10.0 # slope of sigmoid at gsig_mean mesh_gain_inhib_g2 0 # (0) 1-apply 'gain2' as 'gti' for IFC spike-gen mesh_lp2_tau 0.050 # (s) 1/alpha for LPfilter of 'gain2' (0-no LP) # ADAPTATION ad1_tau 20.0 # (s) Adaptation tau, Stim-Horiz difference [0.0] ad1_amp 1.0 # Adaptation ampl [0.0], set < 1 to weaken ad1_t0 0.020 # (s) Time to set ad1 reference # ON/OFF mesh_off_flag 0 # 0/1 = ON/OFF cell [0], negate before IFC # DUMPING OUTPUT mesh_3d_dump_file null # Flag to write 3D data, "null" mesh_display_type hc # "hc" default, also "diff" mesh_dump_all 0 # Write intermediate responses to dump file (0) mesh_dump_prep 0 # Write fixed traces to a dump file (0) mesh_dump_slice_t -1.0 # Time for slice [-1 for none] mesh_dump_slice_x 0.0 # x-position for slice (deg) mesh_dump_hex 0 # Dump traces for hex mesh (should unify w/ above) # # New way of dumping, should make the above conform to this. # mesh_dump_type null # 'val_v_dist', 'mosaic_coord' mesh_dump_file zz.dist.pl # File name mesh_dump_cid 608 # Reference cone ID for dump mesh_dump_tsec -1.0 # Time reference (s), -1.0 for max time </retina0>