Defining types of seafloor substrate and relating them to the distribution of fish and invertebrates is an important but difficult goal. An examination of the processing steps
of a commercial acoustics analyzing software program, as well as the data values produced by the proprietary first echo measurements, revealed potential benef its and drawbacks for distinguishing acoustically distinct seafloor substrates. The positive aspects were convenient processing
steps such as gain adjustment, accurate bottom picking, ease of bad data exclusion, and the ability to average
across successive pings in order to increase the signal-to-noise ratio. A noteworthy drawback with the processing
was the potential for accidental inclusion of a second echo as if it were part of the first echo. Detailed
examination of the echogram measurements quantified the amount of collinearity, revealed the lack of standardization (subtraction of mean, division by standard deviation) before principal components analysis (PCA),
and showed correlations of individual echogram measurements with depth and seafloor slope. Despite the facility of the software, these previously unknown processing pitfalls and echogram measurement characteristics may have created data artifacts that generated user-derived substrate classifications, rather than actual seafloor substrate types
