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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