Mitral cell model used in the paper: Functional structure of the mitral cell dendritic tuft in the rat olfactory bulb. Djurisic, M., Popovic, M., Carnevale, N., and Zecevic, D. Journal of Neuroscience 28:4057-4068, 2008. Questions about how to use this code should be addressed to email@example.com na.mod and kd.mod are identical to the files used in the mitral cell model by Shen, G.Y., Chen, W. R., Midtgaard, J., Shepherd, G.M., and Hines, M.L. (1999) Computational Analysis of Action Potential Initiation in Mitral Cell Soma and Dendrites Based on Dual Patch Recordings. Journal of Neurophysiology 82:3006 These files will generate the data that were used to produce Supplemental Figure 2 of Djurisic et al. (retrograde spike invasion of the tuft with passive or active membrane). First, be sure to compile the mod files with mknrndll or nrnivmodl. After that, the easiest way to proceed is to use NEURON to load mosinit.hoc This will bring up a panel with buttons labeled "Passive tuft" and "Active tuft". Clicking on one of these brings up a model with passive or active tuft membrane, runs a simulation, and displays graphs that show: --Peak spike amplitude throughout the tuft as a function of distance from the tuft origin. For example when the "Passive tuft" button is clicked on one of the graphs shows part of the data in Supplemental Figure 2: --Normalized peak spike amplitude throughout the tuft. --Distribution of peak spike amplitude throughtout the tuft. In this graph, each compartment in the tuft is represented by a vertical blue line with x coordinate that is the peak spike amplitude in that compartment, and height that is 10 x the normalized surface area of that compartment (normalized by dividing compartment area by the total area of the tuft). The black curve is 10 x the smoothed probability of peak spike amplitude, calculated by convolving a Gaussian with Dirac delta functions whose x axis offsets and amplitudes are the spike peak amplitudes and the normalized surface areas of each compartment, respectively. In other words, this is 10 x the peak spike amplitude probability function. --Cumulative membrane area vs. peak spike amplitude. This is the peak spike amplitude distribution function, calculated by integrating the Dirac delta functions (there are so many of them that no smoothing was necessary). For any point on this curve, the y coordinate is the fraction of tuft membrane area in which the spike peak was <= the x coordinate. The horizontal dotted lines at y = 0.1, 0.5, and 0.9 intersect this curve at the 10th, 50th, and 90th percentiles. The x coordinates of these intersections are the peak spike amplitudes that correspond to these percentiles. For the model with passive membrane there is also a small panel with radio buttons that allow changing the values of cm and/or Rm, and running simulations to see how these perturbations alter the results. Running a simluation produces four output files, whose names and contents are: parameters.dat Parameters of the model cell, number of segments (compartments) in the tuft, and the experimental condition. areas.dat Surface areas of all segments (compartments) in the tuft, printed tab separated in the same order as the segments in the tuft SectionList (see * below). Imagine the following loop: for each section in tuft for each compartment in this section, starting at its proximal end, print the area of this compartment vpeak.dat Peak depolarizations in all segments (compartments) in the tuft, printed tab separated in the same order as the segments in the tuft SectionList (see * below). Imagine the following loop: for each section in tuft for each compartment in this section, starting at its proximal end, print the peak depolarization of this compartment results.dat Mean, minimum, maximum, variance and standard deviation of the peak depolarizations in the tuft, printed tab separated. *--This statement forsec tuft print secname() prints out, in sequence, the names of the sections in the tuft SectionList.