  In vivo measurements of muscle architecture (i.e. the spatial arrangement of
muscle fascicles) are routinely included in research and clinical settings to
monitor muscle structure, function and plasticity. However, in most cases such
measurements are performed manually, and more reliable and time-efficient
automated methods are either lacking completely, or are inaccessible to those
without expertise in image analysis. In this work, we propose an ImageJ script
to automate the entire analysis process of muscle architecture in ultrasound
images: Simple Muscle Architecture Analysis (SMA). Images are filtered in the
spatial and frequency domains with built-in commands and external plugins to
highlight aponeuroses and fascicles. Fascicle dominant orientation is then
computed in regions of interest using the OrientationJ plugin. Bland-Altman
plots of analyses performed manually or with SMA indicates that the automated
analysis does not induce any systematic bias and that both methods agree
equally through the range of measurements. Our test results illustrate the
suitability of SMA to analyse images from superficial muscles acquired with a
broad range of ultrasound settings.
