BioBase EcoSound Vegetation and Bottom Hardness Algorithms Improved

Aquatic vegetation mapping with downscan sonar

Sonar technology continues to improve bringing anglers and aquatic managers better, more clear pictures of the underwater environment on which they are so intently focused. Launched in 2011, BioBase’s EcoSound technology was the first cloud aquatic mapping system designed to process sonar logs from off-the-shelf Lowrance® sonar and create maps of bathymetry, aquatic vegetation biovolume, and bottom hardness for aquatic resource professionals. Today, BioBase is the leading cloud software solution for automated lake and coastal seagrass mapping.

Between 2011 and 2014, the algorithm underwent five major revisions. The bottom hardness algorithm has undergone two major revisions, with the last one in 2014.  Thus, our code base was due for an overhaul in order to maintain performance and compatibility with newer generation Lowrance and Simrad sonar. This refactoring effort was also an opportunity for us to improve the vegetation and bottom hardness algorithms. Many of these improvements also carry over sister consumer technology C-MAP Genesis, which uses many of the same algorithms and backend processing architecture

Algorithms are signal and transducer “agnostic”

Previously, accurate EcoSound (and Genesis) outputs required users to log the 200 kHz channel on 500W Lowrance transducers as the algorithm was tightly tuned to this frequency and power level. New methods use signal smoothing methods to extract features (e.g., first and second echoes, vegetation features) and are less dependent on the precise backscatter of a particular Lowrance echosounder and transducer. This improvement opens up compatibility with a greater range of higher powered Airmar transducers (Figure 1).  EcoSound compatibility remains exclusive to Lowrance and Simrad echosounders (.slg, .sl2, and .sl3 file formats)

Figure 1. Airmar TM260. One of many narrow-beam 1 kW transducers compatible with Lowrance and Simrad and now EcoSound. EcoSound compatibility remains exclusive to Lowrance and Simrad echosounders (.slg, .sl2, and .sl3 file formats)

Better target separation between face of transducer and vegetation growing near the surface

High energy environments (e.g., shallow water, high turbulence, active photosynthesis by plants, cavitation (airbubbles) around the transducer due to suboptimal installation are a challenge for mapping aquatic vegetation. To the algorithm, “noise” can look a lot like vegetation and vice versa. Although the previous algorithm did have some sensitivity knobs we could turn, there was a tendency for the algorithm to mistake noise for aquatic plant growth and overestimate biovolume in some places (Figure 2a and 2b).

Figure 2a. Aquatic vegetation delineation with the previous algorithm showing overestimates of biovolume (BV) in shallow environments with modest aquatic plant growth.
Figure 2b. The new EcoSound algorithm has enhanced noise filtering abilities generating more accurate predictions of near-surface aquatic plant growth. Note: the system does not map every plant stem but uses a formula for preserving a certain density of points, typically a point every meter.

EcoSound is now Downscan compatible!

One of the biggest advancements in off-the-shelf sonar technology is side and down imaging, or scanning sonar, which can generate high definition images of bottom features. Although the 200 kHz primary channel is still the default channel for creating vegetation maps with EcoSound, users can choose to reprocess their trips with downscan (455 of 800 kHz) if they have a downscan compatible transducer and logged their files as .sl2 or .sl3 file formats (.slg is primary sonar only). Downscan has a narrow (2.5 degrees fore-aft) scanning beam 47 degrees wide, and sometimes can generate better images of bottom than the 22 degree flashlight-like broadband beam of the Primary 200 kHz channel.

Figure 3. Vegetation mapping outputs from the 455 kHz Downscan sonar channel

Preliminary tests showed both channels performed well in detecting the top of vegetation growth in most cases. However, accuracy of outputs will depend on a variety of environmental conditions such as depth, water clarity, transducer install, vegetation density, etc. We recommend that users run their own tests, reprocessing a sample of trips with both channels comparing the maps with the sonar viewer and field observations, to know which channel will produce the best outputs for their use cases. Fortunately, both primary and downscan channels are logged together in the .sl2 and .sl3 file format and users can select which channel All depth measures come from the primary channel since numerous tests have determined that the 200 kHz channel is the best channel offered for tracking depth through vegetation. We don’t recommend recording 50, 83, or CHIRP Primary frequencies as they are not suitable frequencies for mapping vegetation and are thus, not supported.

More sensitive and accurate bottom hardness

Similar to previous versions of the algorithm, hardness is determined by the characteristics of the second (false) echo. If it’s strong, usually the bottom is hard. If it’s absent or weak, usually the bottom is soft. Values remain along a continuum between 0 (soft) and 0.5 (hard). The new algorithm is more accurate and sensitive than the old algorithm over a broader range of depths. The new algorithm is able to discriminate between a broader range of composition types (e.g., really soft mud, clay, soft sand, hard sand, gravel, boulder) than the previous algorithm (Figure 4.). Efforts were made to maintain consistency between old and new methods but a different equation was used with the new algorithm, so users may find differences in values and colors between old and new maps. Users should always do field checks of hardness to calibrate EcoSound outputs with field observations.

Figure 4. Comparisons of hardness between the old and new algorithms. Note that sandy areas in this lake were mapped as the hardest substrates (deep orange – left). Now, sand is mapped as a medium hard substrate, reserving the deepest orange colors and values for rock. Also, muddy bottoms generate values at the lower end of the scale (off white or light tan) compared with the previous algorithm (tan)

Bulk Editing Tools

Although EcoSound is more “turn-key” than ever, users may still encounter bad soundings, difficult to map environments (extremely shallow, high energy/noisy underwater environment), or situations where debris on the bottom might be mistaken for vegetation. Map outputs can be reviewed and small or large areas can be edited through our new bulk editing tool (see “Modify Coordinates” button in uploaded EcoSound trips (feature not available for merges, Figures 5-9).

Figure 5. Bottom of a Florida lake where organic bottom debris (Detritus) forms a layer that visually looks like vegetation (green dots). Investigators can reclassify vegetation along stretches-in this case the yellow box-to a desired value based on field observations.
Figure 6. Using the Modify Coordinates feature, biovolume was reclassified to zero along the stretch identified in Figure 5.
Figure 7. After reprocessing, map and data layers are updated with biovolumes reclassified to zero. Records are flagged as “Modified” for data stewardship protocols.
Figure 8. Sometimes, extremely dense vegetation growth can obscure what Lowrance records as bottom.
Figure 9. With the Modify Coordinates tool, you can correct erroneous depths seen in Figure 8.

Advanced Default Processing Preferences

Users can now adjust processing settings at the account level like depth offsets, buffer, grid cell, min/max depth of vegetation detection, sonar processing channel, etc. so that every trip uploaded has your custom settings (Figure 10)! You can still change settings on a trip by trip basis as well. Read more about it here.

Figure 10. Adjust default processing preferences in My Account in your BioBase Account.

To inquire about other BioBase features or plans, send a message to info.biobase@navico.com. BioBase EcoSound is free to all Environmental Agencies, Non-profits, and Universities engaged in water or fisheries research or management. Special conditions apply. Learn more here – https://www.biobasemaps.com/Plans.

Author: biobasemaps

BioBase is a cloud platform for the automated mapping of aquatic habitats (lakes, rivers, ponds, coasts). Standard algorithms process sonar datafiles (EcoSound) and high resolution satellite imagery (EcoSat). Depth and vegetation maps and data reports are rapidly created and stored in a private cloud account for analysis, and sharing. This blog highlights a range of internal and external research, frequently asked questions, feature descriptions and highlights, tips and tricks, and photo galleries.

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