Analyses

Simulations can be analyzed using SimTracker. A variety of analysis options are available, and users can add additional options if they wish (when using SimTracker via MATLAB scripts). Most analyses are performed on specific, defined simulations. However, users can choose to perform the same analysis on multiple simulations at once, and users can also design their own custom analyses that use any simulation data from all executed simulations in the repository.

Standard Analyses

When results from an executed simulation are uploaded to SimTracker, several standard analyses scripts become available. These scripts generate figures or tables to characterize the behavior of the network or individual cells. Multiple display or analyses options are available for several of the analyses:

Spike Raster: Which cells spiked and when separate: the spikes of each cell type grouped separately pyremph: separate with pyramidal cell type emphasized interspersed: all celltypes plotted together spikedist: histogram by type of firing rate of each cell phasepre: phases of each spike individual: separate figure for each type rasthist: histogram of spikes by time, per type pyrpos: pyramidal spikes by time and position Firing Rates: Firing rates of cells all: include all cells in calculation subset: include only firing cells in calculation Local Field Potential (LFP): Calculated LFP analog Membrane Potential (MP): Average, by type, or heat map of computed MP [blank]:potential of each recorded cell (very long load time) [gid]:recording if cell with given gid average|avg:the average MP of all recorded cells pyr:average MP of all recorded pyramidal cells (3 character code for each cell type) type: average MP of all recorded cells, by cell type Spectral Analysis: Spectral analysis of SDF, spike times, LFP, or MP by average, type, or heatmap, using Pwelch, periodogram, or FFT analysis method: pwelch|gram|fft property to analyze: sdf|spikes|lfp|mp organization: type|all|{gid}|{type} ex: 3920 for {gid} or sca for {type} output: 2d|heatmap|table normalization desired: norm Spectrogram: Spectral analysis as a function of time of spike times, LFP, or MP by average, type, or heatmap property to analyze: spikes|lfp|mp organization: type|all|{gid}|{type} ex: 3920 for {gid} or sca for {type} Phases & Modulation: Activity of each cell type as a function of oscillation phase hist: histogram of spike times compass: phase and modulation of spike times wave: phase on an LFP wave table: table of phases and modulations mod: modulation level {Hz}: frequency of oscillation of interest, in Hz {activity}: which network property to analyze - spikes|lfp|mp|avglfp Cell Type Activity Table: Gid range and cell numbers for each cell type Cell Type Spectral Activity Graphs: Break down of cell type activity Connectivity: Connection matrix, convergence, divergence, and axonal distributions for network matrix: total number of connections convdiv: convergence & divergence weights: synaptic weights axondist: axonal distributions for recorded cells grade: desired v. actual connections Cell Positions: 3D position of each cell in network, using (hopefully) the same algorithm as the model code Memory Usage: Memory used during simulation by host 0 Show results in: KB|MB|GB Run Time: Time required to run each part of simulation Single Cell MP, LFP & Inputs: Single recorded cell’s potentials and synaptic inputs with time gid Single Cell Spike Train: Spike times of a single cell gid

Custom Analyses

Custom analyses for a specific model can be created as MATLAB *.m files and placed in the customout directory within the model code folder. SimTracker will list any files in that directory in a submenu within SimTracker when that repository is active.