时域波形图matlab代码+仿真结果和运行方法.zip

# FourLayerRetinalModel-Esler2017 Code to simulate epiretinal stimulation of the retina using a four-layer model. The code in this repository was used to conduct the analysis presented in: * Minimizing activation of overlying axons with epiretinal stimulation: The role of fiber orientation and electrode configuration Esler TB, Kerr RR, Tahayori B, Grayden DB, Meffin H, et al. (2018) Minimizing activation of overlying axons with epiretinal stimulation: The role of fiber orientation and electrode configuration. PLOS ONE 13(3): e0193598. https://doi.org/10.1371/journal.pone.0193598 ## Quick Start 1. Download repository to a machine with MATLAB installed. 2. Navigate to folder containing repository, and open `Code` folder. 3. Type `AnyElecConfig_RotatedNeurite` to run a simulation using 4 electrodes which displays the induced membrane potential for neurites at various locations and with various orientations (this generates a similar figure to Fig. 6 in the above paper). ## Code files ### CellComp4Layer_Ve_f_Plane.m *CellComp4Layer_Ve_f_Plane* returns the electric field in the Fourier domain due to epiretinal stimulation with point or disk electrodes in a plane in the x-z dimensions (where y is in the direction normal to the surface of the retina, toward the electrode). The retina is modelled using a 4-layer description, including Insulator, Vitreous, Nerve Fibre Layer, and the Ganglion Cell Layer (+ others). The insulator layer is modelled using a no-current boundary condition within the vitreous (see diagram below for geometry). All units are S.I. _____________________________________________________ 1.Insulator _____________________________________________________ [|||] [|||] [|||] Electrodes (at layer boundary) 2.Vitreous _____________________________________________________ 3.Nerve fibre layer _____________________________________________________ 4.'Other' cell layer (incl. GCL) _____________________________________________________ The extracellular potential for the NFL is calculated using a modified version of the self-consistent, linear, sub-threshold model presented in: * B. Tahayori, H. Meffin, E.N. Sergeev, I.M.Y. Mareels, A.N. Burkitt, and D.N. Grayden (2014), "Modelling extracellular electrical stimulation: IV. Effect of the cellular composition of neural tissue on its spatio-temporal filtering properties", J. Neural Eng. 11. This script was used to conduct the analysis presented in: * Minimizing activation of overlying axons with epiretinal stimulation: The role of fiber orientation and electrode configuration Esler TB, Kerr RR, Tahayori B, Grayden DB, Meffin H, et al. (2018) Minimizing activation of overlying axons with epiretinal stimulation: The role of fiber orientation and electrode configuration. PLOS ONE 13(3): e0193598. https://doi.org/10.1371/journal.pone.0193598 #### Inputs | Input | Description | |---|---| | Xi, Yi and Zi | x-, y-, and z- coordinates of the point source electrodes. (m) | | I_M, I_D | Stimulation amplitude and duration for each electrode. (A, s) | | z_max, x_max, t_max | z-, x- and time-extent of the simulation. (m, m, s) | | d_z, d_x, d_t | z , x and t step sizes. (m, m, s) | | h_F | Nerve fibre layer thickness (m) | | Ya | Depth below the retina surface at which we want to calculate extracellular potential. (m) | | rot | Coordinate rotation for a fibre which is rotated w.r.t. the fibre bindle (only set to a nonzero value if the output will be used to calculate the membrane potential of a rotated fiber). (rad) | | Ri | Radius of disk for each electrode (set to 0 for point source). (m) | #### Outputs | Output | Description | | --- | ---| | Ve_L_f | The calculated longitudinal extracellular potential for a full plane in the Fourier domain. This is equal to the extracellular potential itself. (V) | | Ve_T_#_f | The calculated transverse extracellular potential in the #-direction for a full plane in the Fourier domain. (V) | | neur_eq | The transformation matrix for converting the longitudinal extracellular potential into longitudinal membrane potential. Multiplying Ve_L_f by this pointwise will give the membrane potential in the x, z, and t Fourier domain. | #### Example usage Xi = 0e-6; Yi = 200e-6; Zi = 0e-6; I_M = -50e-6; I_D = 200e-6; x_max = 2000e-6; z_max = 2000e-6; t_max = 600e-6; d_x = 10e-6; d_z = 10e-6; d_t = 4e-6; h_F = 100e-6; Ri = 50e-6; Ya = -10e-6; [Ve_L_f, Ve_T_X_f, Ve_T_Y_f, Ve_T_Z_f, n_e] = CellComp4Layer_Ve_f_Plane(... Xi, Yi, Zi, I_M, I_D, ... % Electrode parameters x_max, z_max, t_max, d_x, d_z, d_t, ... % Spatial sampling h_F, Ya, rot, Ri); % Simulation geometry A further example can be found in *AnyElecConfig_RotatedNeurite_4L*. ### CellComp3Layer_Ve_f_Plane.m NOTE: Identical in implementation to CellComp3Layer_Ve_f_Plane but with a 3-layer model instead of 4, to simulate stimulation where no insulator is used. *CellComp3Layer_Ve_f_Plane* returns the electric field in the Fourier domain due to epiretinal stimulation with point or disk electrodes in a plane in the x-z dimensions (where y is in the direction normal to the surface of the retina, toward the electrode). The retina is modelled using a 3-layer description, including Vitreous, Nerve Fibre Layer, and the Ganglion Cell Layer (+ others) (see diagram below for geometry). All units are S.I. [|||] [|||] [|||] Electrodes (at layer boundary) 2.Vitreous _____________________________________________________ 3.Nerve fibre layer _____________________________________________________ 4.'Other' cell layer (incl. GCL) _____________________________________________________ The extracellular potential for the NFL is calculated using a modified version of the self-consistent, linear, sub-threshold model presented in: * B. Tahayori, H. Meffin, E.N. Sergeev, I.M.Y. Mareels, A.N. Burkitt, and D.N. Grayden (2014), "Modelling extracellular electrical stimulation: IV. Effect of the cellular composition of neural tissue on its spatio-temporal filtering properties", J. Neural Eng. 11. This script was used to conduct the analysis presented in: * Minimizing activation of overlying axons with epiretinal stimulation: The role of fiber orientation and electrode configuration Esler TB, Kerr RR, Tahayori B, Grayden DB, Meffin H, et al. (2018) Minimizing activation of overlying axons with epiretinal stimulation: The role of fiber orientation and electrode configuration. PLOS ONE 13(3): e0193598. https://doi.org/10.1371/journal.pone.0193598 #### Inputs | Input | Description | |---|---| | Xi, Yi and Zi | x-, y-, and z- coordinates of the point source electrodes. (m) | | I_M, I_D | Stimulation amplitude and duration for each electrode. (A, s) | | z_max, x_max, t_max | z-, x- and time-extent of the simulation. (m, m, s) | | d_z, d_x, d_t | z , x and t step sizes. (m, m, s) | | h_F | Nerve fibre layer thickness (m) | | Ya | Depth below the retina surface at which we want to calculate extracellular potential. (m) | | rot | Coordinate rotation for a fibre which is rotated w.r.t. the fibre bindle (only set to a nonzero value if the output will be used to calculate the membrane potential of a rotated fiber). (rad) | | Ri | Radius of disk for each electrode (set to 0 for point source). (m) | #### Outputs | Output | Description | | --- | ---| | Ve_L_f | The calculated longitudinal extracellular potential for a full plane in the Fourier domain. This is equal to the extracellular potential itself. (V) | | Ve_T_#_f | The calculated transverse extracellular potential in the #-direction for a full plane in the Fourier domain. (V) | | neur_eq | The transformation matrix for converting the lon