Analysis of Dendrite/Axon Exit Position

by Album Shen

Categorizes the exit position of primary dendrites and axon from the soma into 10 vertical locations.

Data needed:

Scaling information used to construct neurites model
Scaling information of the image (pixel to um conversion)
Lowest and highest slice in which cell body appears

Parameters:

['PA.py', input, x_d, y_d, z_d, x_s, y_s, z_s, s_l, s_h]
input: .swc file to be read; results will be output to the filename plus the extension '_output.txt'
scale_default: refers to the scaling used when plotting the neurites in NeuronStudio
scale_actual: refers to the actual scaling of the images
s_l: lowest slice in which the cell body appears
s_h: highest slice in which the cell body appears

Assumptions about neurites file:

Soma is indexed with integer label n = '1', and neuronal type T = '1')
Axon is labeled with neuronal type T = '2'
All dendritic ends are labeled with neuronal type T = '6'
There is a single point of origin (one soma with T = '1')

DO ONE OF THE FOLLOWING BEFORE USING:

Uncomment line below "# Sample run" to allow for manual entry of input filename and pertinent scales directly into the script. Script can be run using "python P10.py" at the command line or simply clicking to execute.
Uncomment line below "# Running through command line" to run by passing parameters through command line.