Table 1 Default parameters from Excel file
From: SMASH – semi-automatic muscle analysis using segmentation of histology: a MATLAB application
Default parameters | Default values |
|---|---|
Pixel size (μm/pixel) | 0.645 |
Fiber outline channel (red = 1, green = 2, blue = 3) | 1 |
Nuclei channel (red = 1, green = 2, blue = 3) | 3 |
Fiber type channel (red = 1, green = 2, blue = 3) | 2 |
Object channel (red = 1, green = 2, blue = 3) | 2 |
Segmentation smoothing factor | 5 |
Nuclear smoothing factor | 5 |
Object smoothing factor | 10 |
Minimum fiber area (μm2) | 100 |
Maximum fiber area (μm2) | 5,000 |
Maximum eccentricity | 0.95 |
Minimum convexity | 0.8 |
Nuclear distance from boarder (μm) | 10 |
Minimum nuclear size (μm2) | 5 |
Fiber properties output folder | C:\SMASH\Output |
Fiber type output folder | C:\SMASH\Output |
Central nuclei output folder | C:\ SMASH\Output |
Objects output folder | C:\ SMASH\Output |