Click here to Download # # Ret_Mesh.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 64 # width yn 64 # 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 #--------------------------------------.--------------------------------------# # # # RGC # # # #-----------------------------------------------------------------------------# <pop> name rgc type retina0_gc0 # Layer type 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 sig1 0.1 # For Display Only - no effect on mesh model sig2 0.2 # For Display Only - no effect on mesh model 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 (stim pix) for summing BP signals # Instead of the above, can use 'sum_bp_dist_deg' 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 <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> #file mosaic01.txt # Read from file 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' 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>