Evaluation

Evaluation of SLI Profiles

SLIXLineplotParameterGenerator allows the evaluation of individual SLI profiles (txt-files with a list of intensity values): For each SLI profile, the maximum, minimum, number of prominent peaks, corrected peak positions, fiber direction angles, and average peak prominence are computed and stored in a text file. The user has the option to generate a plot of the SLI profile that shows the profile together with the peak positions before/after correction. The corrected peak positions are determined by calculating the geometric center of the peak tip, improving the accuracy of the determined peak positions in discretized SLI profiles. If not defined otherwise, the peak tip height corresponds to 6% of the total signal amplitude (for derivation, see Menzel et al. (2020), Appx. B).

SLIXLineplotParameterGenerator -i [INPUT-TXT-FILES] -o [OUTPUT-FOLDER] [[parameters]]

Required Arguments

Argument	Function
-i, --input	Input text files, describing the SLI profiles (list of intensity values).
-o, --output	Output folder used to store the characteristics of the SLI profiles in a txt-file (Max, Min, Num_Peaks, Peak_Pos, Directions, Prominence). Will be created if not existing.

Optional Arguments

Argument	Function
--smoothing	Smoothing of SLI profiles before evaluation. The smoothing is performed using a Savitzky-Golay filter with 45 sampling points and a second order polynomial. (Designed for measurements with < 5° steps to reduce the impact of irrelevant details in the fiber structure, cf. orange vs. black curve in Figure 1c in the paper.)
--with_plots	Generates plots (png-files) showing the SLI profiles and the determined peak positions (orange dots: before correction; green crosses: after correction).
--target_peak_height	Change peak tip height used for correcting the peak positions. (Default: 6% of total signal amplitude). Only recommended for experienced users!

Example

The following example demonstrates the evaluation of two SLI profiles, which can be found in the "examples" folder of the SLIX repository:

SLIXLinePlotParameterGenerator -i examples/*.txt -o output --with_plots

The resulting plot and txt-file are shown below, exemplary for one of the SLI profiles (90-Stack-1647-1234.txt):

Max: 119.0
Min: 68.0
Num_Peaks: 4
Peak_Pos: [2.5935516 7.723009 14.294096 20.10292]
Directions: [143.3426513671875 61.305511474609375 -1.0]
Prominence: 0.27323946356773376

The plot shows the SLI profile derived from a stack of 24 images. The x-axis displays the number of images, the y-axis the measured light intensity [a.u.]. To detect peaks at the outer boundaries, the profile was extended taking the 360° periodicity of the signal into account; the red line indicates the boundary. The orange dots are the original peak positions, the green crosses indicate the corrected peak positions, taking the discretization of the profile into account.

The txt-file lists the maximum and minimum intensity values in the SLI profile, the number of prominent peaks (i.e. peaks with a prominence above 8% of the total signal amplitude), the corrected peak positions (on the x-axis), the direction angles of the nerve fibers (in degrees, derived from the mid-positions between peak pairs), and the average prominence of the peaks normalized by the average of the signal.