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User Documentation for wiring the cortical simulation 2D version
This version of the wiring procedures has retained the same calling conventions as the 1Dversion where possible. The Layer V and Layer II/III Pyramidals and the inhibitory cells areplaced on four coincident 2 dimensional matrices. The orthogonal distances between cells areequal and diagonal distances are calculated as a hypotenuse.
The matrices can be of any size with the X dimension defined as ‘X_DIM’ and the Y dimensionas ‘Y_DIM’ These two parameters are most conveniently defined in the init file before the otherfiles are called. Each cell type’s position is defined by its index within the its respective 2Darray- PL5[X_DIM][Y_DIM], PL2[X_DIM][Y_DIM], IPL2[X_DIM][Y_DIM] andIPL5[X_DIM][Y_DIM] Inhibitory cells, being fewer in number that Pyramidals, use a sparse matrix. The new wiringfunctions for the inhibitory cells do not require a location parameter as the position is definedwithin the matrix array. Feed forward /back functions have been generalized . There are fewer functions than in the 1Dversion. The placement of a FeedX can be anywhere on the coincident matrices and is defined bythe parameters Fsx and Fsy.
There are 5 categories of procedures for wiring the somatosensory cortex simulation remain thesame: 1. Pyramidal to Pyramidal2. Inhibitory to Pyramidal3.Pyramidal to Inhibitory4. Inhibitory to Inhibitory5. Feed-forward and feedback Gaussian distribution
1. Pyramidal to Pyramidal connections
The calling convention for these functions has not changed from the 1D version.
There are 4 Pyramidal to Pyramidal procedures: VtoV( ) -Connects Layer V to Layer V Pyramidals VtoII() -Connects Layer V to Layer II/III Pyramidals IItoII() -Connects Layer II/III to Layer II/III Pyramidals IItoV() -Connects Layer II/III to Layer V Pyramidals this procedure not currently used XtoX( maxW, WSC, seg, rtype, minD, DSC )
maxW - Maximum synaptic weight WSC - weight space constantseg - target segment rtype - receptor type [0=AMPA, 1=NMDA]minD - Minimum delayDSC - delay space constant The target segment (seg) refers to the postsynaptic cell type: Layer V Pyramidal Cells:Apical compartments 0-4Basal 5-7Soma 8 Layer II/III Pyramidal Cells:Apical compartments 0-3Basal 4-6Soma 7 2. Inhibitory to Pyramidal connections
There remain 3 Inhibitory to Pyramidal procedures: IL5toV( ) -Connects Layer V inhibitory cells to Layer V PyramidalsIL2toV( ) -Connects Layer II/III inhibitory cells to Layer V PyramidalsIL2toII( ) -Connects Layer II/II inhibitory cells to Layer II/III Pyramidals The calling convention has changed from the old version:
XtoX(seg, rtype, maxW, WSC, maxP, minD, DSC)
seg - target segment
rtype - receptor type [2=GABAa, 3=GABAb]
maxW - Maximum synaptic weight
WSC - weight space constant
minD - Minimum delay
DSC - delay space constant
3.Pyramidal to Inhibitory connections
There are 3 Pyramidal to Inhibitory procedures IItoIL2() -Connects Layer II/III Pyramidal cells to a single Layer II inhibitory cellVtoIL5() -Connects Layer V Pyramidal cells to a single Layer V inhibitory cellIItoIL5() -Connects Layer II/III Pyramidal cells to a single Layer V inhibitory cell The calling convention has changed from the old version:
XtoX(maxW, WSC, minD, DSC,rtype)
maxW - Maximum synaptic weight
WSC - weight space constant
minD - Minimum delay
DSC - delay space constant
rtype - receptor type [0=AMPA, 1=NMDA]
4. Inhibitory to Inhibitory connections
The calling convention for these functions has not changed from the 1D version.
IL2toIL2( ) -Connect Layer II/III inhibitory cells to themselvesIL5toIL5( ) -Connect Layer V inhibitory cells to themselves XtoX(maxW, WSC, minD, DSC, rtype)
maxW - Maximum synaptic weight WSC - weight space constantminD - Minimum delayDSC - delay space constantrtype - receptor type [2=GABAa, 3=GABAb] Inhibitory cells do not self-inhibit.
5. Feed-forward and feedback connections
The calling convention has changed from the old version and there are fewer
procedures:
The Feed procedures now use a Gaussian distribution for weight and delay. The position of the
Feed is determined by the global variables FSx and Fsy. These are best set in the initialization
file. The FeedX() object used is now a parameter to the procedure.
a. Feed to Pyramidal cells-----
FeedtoII() -feed to Layer II/III pyramidalsFeedtoV() -feed to LayerV pyramidals FeedtoX(seg, rtype, maxW, WSC minD, DSC,fobj)
seg - target segment
rtype - receptor type [0=AMPA,1=NMDA]
maxW - Maximum synaptic weight
WSC - weight space constant
minD - Minimum delay
DSC - delay space constant
fobj - a FeedX object (eg. FF,FF2,FB)
b. Feed to Inhibitory cells--------
FeedtoIL2() -feed to Layer II inhibitory cellsFeedtoIL5() -feed to Layer V inhibitory cells FeedtoX(rtype, maxW, WSC minD, DSC,fobj)
rtype - receptor type [0=AMPA,1=NMDA]
maxW - Maximum synaptic weight
WSC - weight space constant
minD - Minimum delay
DSC - delay space constant
fobj - a FeedX object (eg. FF,FF2,FB)
Uniform Random Distribution
Uniform random distribution functions are implemented and are defined over synaptic weightand delay by a minimum and maximum. The naming convention parallels the Gaussian functionsbut is proceeded by a “U_” ;eg. VtoV( ) becomes U_VtoV( ) .
1. Pyramidal to Pyramidal connections
There are 4 Pyramidal to Pyramidal procedures: U_VtoV( ) -Connects Layer V to Layer V Pyramidals U_VtoII() -Connects Layer V to Layer II/III Pyramidals U_IItoII() -Connects Layer II/III to Layer II/III Pyramidals U_IItoV() -Connects Layer II/III to Layer V Pyramidals The calling convention for these functions has not changed from the 1D version
U_XtoX ( MinW, MaxW , seg, rtype, MinD, MaxD )
minW -Minimum synaptic weightmaxW - Maximum synaptic weight seg - target segment rtype - receptor type [0=AMPA, 1=NMDA]minD - Minimum delaymaxD -Maximum delay 2. Inhibitory to Pyramidal connections
There are 3 Inhibitory to Pyramidal procedures: U_IL5toV( ) -Connects Layer V inhibitory cells to Layer V PyramidalsU_IL2toV( ) -Connects Layer II/III inhibitory cells to Layer V PyramidalsU_IL2toII( ) -Connects Layer II/II inhibitory cells to Layer II/IIIPyramidals The calling convention has changed from the old version:
U_ILxtoX(seg, rtype, MinW, MaxW, MinD, MaxD)
seg - target segment rtype - receptor type [2=GABAa, 3=GABAb]minW -Minimum synaptic weightmaxW - Maximum synaptic weight minD - Minimum delaymaxD -Maximum delay 3.Pyramidal to Inhibitory connections
There are 3 Pyramidal to Inhibitory procedures U_IItoIL2() -Connects Layer II/III Pyramidal cells to a single Layer II inhibitory cellU_VtoIL5() -Connects Layer V Pyramidal cells to a single Layer V inhibitory cellU_IItoIL5() -Connects Layer II/III Pyramidal cells to a single Layer V inhibitory cell The calling convention has changed from the old version:
U_XtoILx(MinW, MaxW, rtype, MinD, MaxD)
MinW -Minimum synaptic weightmaxW - Maximum synaptic weight rtype - receptor type [0=AMPA, 1=NMDA]minD - Minimum delaymaxD -Maximum delay 4. Inhibitory to Inhibitory connections
There are 2 Inhibitory to Inhibitory procedures: U_IL2toIL2( ) -Connect Layer II/III inhibitory cells to themselvesU_IL5toIL5( ) -Connect Layer V inhibitory cells to themselves The calling convention for these functions has not changed from the 1D version.
U_ILxtoILx(MinW. MaxW, MinD, MaxD, rtype )
minW -Minimum synaptic weightmaxW - Maximum synaptic weight minD - Minimum delaymaxD -Maximum delayrtype - receptor type [2=GABAa, 3=GABAb] 5. Feed-forward and feedback connections
The calling convention has changed from the old version and there are fewer
procedures
a. Feed to Pyramidal cells-----
UFeedtoII() -feed to Layer II/III pyramidalsUFeedtoV() -feed to LayerV pyramidals UFeedtoX(seg, rtype, MinW, MaxW, MinD, MaxD,fobj )
seg - target segment rtype - receptor type [0=AMPA,1=NMDA]MinW -Minimum synaptic weightMaxW -Maximum synaptic weightMinD -Minimum delayMaxD -Maximum delayfobj - a FeedX object (eg. FF,FF2,FB) b. Feed to Inhibitory cells--------
UFeedtoIL2() -feed to Layer II inhibitory cellsUFeedtoIL5() -feed to Layer V inhibitory cells UFeedtoX(rtype, MinW, MaxW, MinD, MaxD ,fobj)
rtype - receptor type [0=AMPA,1=NMDA]MinW -Minimum synaptic weightMaxW -Maximum synaptic weightMinD -Minimum delayMaxD -Maximum delayfobj - a FeedX object (eg. FF,FF2,FB)

Source: http://compneurosci.info/SRJ/2D_Wiring.pdf