Repository for the article:
S. Romeni, G. Valle, A. Mazzoni, and S. Micera. Tutorial: A computational framework for the design and optimization of peripheral neural interfaces. Nature Protocols, 2020
Code by Simone Romeni, Ph.D. Assistant at Bertarelli Foundation Chair in Translational NeuroEngineering, Center for Neuroprosthetics and Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Function classification
- Fascicle shape simplification:
- main functions:
poly2ell.m,poly2circ.m; - auxiliary functions:
equivellipses.m; - external functions:
minboundrect.m.
- main functions:
- Fibre and fascicle packing:
- main functions:
msg_packing.m,aci_packing.m; - auxiliary functions:
activate_centers.m,assign_diameters.m
- main functions:
- FEM modelling:
- main function:
fem_gui.m; - auxiliary functions:
assign_materials.m,generate_circfasc.m,generate_ec.m,generate_electrode.m,generate_ellfasc.m,generate_materials.m,generate_outernerve.m,interface_nervelec.m.
- main function:
Main function docstrings
- Fascicle shape simplification:
poly2ell.mApproximate polyshape fascicles with elliptical fascicles;poly2circ.mApproximate polyshape fascicles with circular fascicles.
- Fibre and fascicle packing:
msg_packing.mMulti-scale Square Grid packing of circular objects in a multiregion;aci_packing.mA-priori Check for Intersections packing of circular objects in a circular region.
Fascicle representation conventions
- Polylinear fascicles are represented by an N-cell array, where N is the number of fascicles, whose elements are Knx2 arrays, where Kn is the number of points defining fascicle n and the columns represent x and y coordinates of the points, respectively.
- Elliptical fascicles are represented by an array with shape Nx5, where N is the number of fascicles and the columns represent: x and y coordinates of the center, x and y half-axis lengths, orientation of the x axis.
- Circular fascicles are represented by an array with shape Nx3, where N is the number of fascicles and the columns represent: x and y coordinates of the center, radius of the fascicle.