Project by: Nina Zhang
Selected cell model: neuronal model 626170421 from allen SDK database.
my_sim directory and sim.ipynb simulates various intracellular current injections on model 626170421. Currents tested are as follows: 40 pA, 70 pA, 80 pA, 90 pA, 120 pA. Membrane potential and calcium concentration were recorded and graphed.
task2_analysis.ipynb analyzes the graphs that were gathered from the experimentation of the first simulation (my_sim)
my_sim02 directory and sim2.ipynb simulates and generates an extracellular spike waveform data set. The input for the external stimuli were provided from neuropixel_electrode_1um.csv. Membrane potential and calcium concentration were recorded and graphed.
sim2_task4.ipynb is a continuation of the second simulation (my_sim02), and is an analysis on the extracellular AP waveform. It extracts features such as the amplitude, half-width, and EAP.
task3_4_analysis.ipynb analyzes the graphs and data that were gathered from the experimentation of the second simulation (my_sim02)
stretch.ipynb is the stretch goal. The animation is saved as somatic_v_dynamics.mp4. With matplotlib and its animation feature, I created an animation of a current injection with these following parameters:
amp = 0.09 nA
delay = 200 ms
duration of current = 300 ms
total simulation = 500 ms
stretch_analysis.ipynb is the analysis of the stretch goal from stretch.ipynb and its output, somatic_v_dynamics.mp4. It's best to play the animation at 2x speed.
images holds the graphs for the various experiments. 626170421 is the files from the original download of the allen SDK database.