PyFibers: An open-source NEURON-Python package to simulate responses of model nerve fibers to electrical stimulation
Fig 9
Replication of published responses for the MRG fiber model.
Data in black were provided by the original authors [17], and data in purple and green are from the MRG-discrete and MRG-interpolation PyFibers implementations, respectively. All fibers were 21 nodes long and except for panel A, all data are for 10 μm diameter fibers. We used an anodic rectangular pulse for intracellular stimulation (panels A-C) and a monopolar rectangular pulse delivered by a cathodic point current source in an anisotropic medium (sigma(x,y,z) = {1/12, 1/12, 1/3} [S/m], where z is along the axis of the fiber (panels D-E). The stimulation pulse began at t = 0 and lasted for 0.1 ms, except for panel C where we evaluated pairs of pulses (1 ms duration each) and panel D where we evaluated different pulse widths. A) Conduction velocity across fiber diameters, calculated using action potential times from fiber(0.25) to fiber(0.75) after intracellular stimulation at fiber[1]. B) Action potential time course, recorded at the center node (fiber(0.5)) after an intracellular stimulus at fiber[1]. C) Recovery cycle for intracellular stimulation delivered at the center node (fiber(0.5)). We first determined activation threshold (Ith) for a single pulse with 1 ms duration. We then simulated a pair of pulses: one at t1 = 1 ms and Ith, and a second at t2 = 1 ms + interpulse interval; we determined the activation threshold for the second pulse and its difference relative to Ith. D) Strength-duration response for electrode-fiber distances from 100 to 500 μm and longitudinal alignment at (1) the center node, (2) shifted by ¼ of the internodal length, (3) shifted by ½ of the internodal length. For the MRG-discrete implementation, we matched the point current source position to the original publication; the z-position was assigned relative to the start of the fiber. The MRG-interpolation implementation has slightly different ultrastructure, including positions of the nodes of Ranvier; therefore, we altered the longitudinal coordinates of the point current sources to maintain the same position with respect to the center node of Ranvier. E) Current-distance response for point sources with electrode-fiber distances from 109 to 953 μm and longitudinal alignment from −563 to +549 μm (with respect to the center node).