BioBase Paper Published: Accuracy and Precision of Low-Cost Echosounder and Automated Data Processing Software for Habitat Mapping in a Large River

We are grateful to the aquatic research community who continue to verify and validate Consumer Sonar Technologies (Lowrance) and BioBase automated mapping platform to produce scientifically valid outputs that benefit aquatic conservation.  We are excited to see the recent publication of research out of the University of New Brunswick that evaluated the accuracy and precision of Lowrance and BioBase’s EcoSound depth and vegetation outputs.  The research is published in the open access journal Diversity and can be downloaded here. Below is the abstract

Abstract
The development of consumer hydroacoustic systems continues to advance, enabling the use of low-cost methods for professional mapping purposes. Information describing habitat characteristics produced with a combination of low-cost commercial echosounder (Lowrance HDS) and a cloud-based automated data processing tool (BioBase EcoSound) was tested. The combination frequently underestimated water depth, with a mean absolute error of 0.17 ± 0.13 m (avg ± 1SD). The average EcoSound bottom hardness value was high (0.37–0.5) for all the substrate types found in the study area and could not be used to differentiate between the substrate size classes that varied from silt to bedrock. Overall, the bottom hardness value is not informative in an alluvial river bed setting where the majority of the substrate is composed of hard sands, gravels, and stones. EcoSound separated vegetation presence/absence with 85–100% accuracy and assigned vegetation height (EcoSound biovolume) correctly in 55% of instances but often overestimated it in other instances. It was most accurate when the vegetation canopy was ≤25% or >75% of the water column. Overall, as a low-cost, easy-to-use application EcoSound offers rapid data collection and allows users with no specialized skill requirements to make more detailed bathymetry and vegetation maps than those typically available for many rivers, lakes, and estuaries.

EcoSound vs Manual Measures Vegetation Helminen et al 2019

Portability Options for Your Lowrance

We recently sent out a mailer to our subscribers letting them know about the portability solutions that we have come up with.  Within minutes we received photos and details from many of our customers about how some they have used a little ingenuity to mount their Lowrance units on unique water craft.  Below we have a photo gallery of images that could help you design your own portable setup.  Of primary importance, however, is a mount that minimizes cavitation (air bubbles) directly under the transducer (e.g., surface noise) and maintaining a correct angle on the transducer.  See recent blogs on this topic. The preferable solution is to permanently mount separate transducers following DIY guidance like shown here on each survey craft and just move the Lowrance Elite or HDS display from boat to boat.  But if the job calls for a fully portable mount, we can help!

Continue reading “Portability Options for Your Lowrance”

BioBase Project Propels Jeff Schuckman to Nebraska Game and Parks Employee of the Year!

Lake Yankton, a 332-acre backwater lake on the Nebraska/South Dakota border had a problem. In the summer of 2011, the Missouri River flooded, spilling into the lake a number of undesirable invasive rough fish, including large numbers of carp (silver, bighead, grass, and common), smallmouth buffalo, and gizzard shad. Notorious for stirring up lake bottoms while feeding and spawning — and for overeating zooplankton and aquatic plants — these species degrade water quality and fisheries.  

Overrun by these invasive species, Lake Yankton soon looked like chocolate milk, with a water clarity of only three inches — that’s right, inches, not feet.  So the cavalry was called in to assess the situation and provide a solution. Leading the effort was Nebraska Game and Parks Commission District Fisheries Manager Jeff Schuckman.

Fortunately for Nebraska anglers, this wasn’t Schuckman’s first rodeo. He knew the lake could be rehabilitated with careful application of Rotenone, a common fish-killing chemical. The challenge would be to determine just how much of the chemical was needed, and then purchase and apply just enough to do the job — no more, no less.

Continue reading “BioBase Project Propels Jeff Schuckman to Nebraska Game and Parks Employee of the Year!”

Virtual Eyes to See Aquatic Resources in 3D

One of the biggest challenges to understanding aquatic resources are the optical properties of water and an inability of our human eyes to see the complex world that lurks beneath the surface.  In contrast, when “aeroplanes” (that’s what they were called in the Wright Brother’s days) first took flight in the early 1900’s and pilots figured out how to fix cameras to the belly to take aerial photos, it opened up a new world of exploration for biologists and foresters studying terrestrial landscapes.  The term “landscape” got a whole new meaning.

Continue reading “Virtual Eyes to See Aquatic Resources in 3D”

Color Enhancing your Sonar Log

ciBioBase’s Trip Replay feature that couples bottom depth, aquatic vegetation biovolume, and bottom hardness maps with your actual Sonar Log empowers you with a verification tool that ensures an accurate map in every system you map, every time.  The sonar log also provides users and our Quality Control team helpful information about signal quality and transducer placement that can help both parties diagnose issues.

A little known feature in ciBioBase allows users to reprocess their Lowrance HDS/Elite sonar log at different color and sensitivity settings (Figure 1).

Figure 1. Trip Reprocessing Tab that allows ciBioBase users to reprocess their trips with new edits.  Try reprocessing your sonar log at a higher color (e.g., 240) for “cooling” the colors in your sonar log in ciBioBase and to bring out subtle bottom features.

Sometimes, your Sonar Log may look a little too “hot” making it difficult to distinguish between plants and bottom (Figure 2).

Lowrance, ciBioBase, Sonar Log
Figure 2.  Sonar Log showing colors that may be “too hot” to distinguish between plants and bottom.

Try reprocessing the sonar log at a colorline of 240 (default is 220).  This will bring in “cooler” colors to the sonar log and may help you better distinguish subtle bottom features and gaps in plant beds (Figure 3).

Figure 3.  Sonar Log reprocessed with a colorline of 240.

Alternatively, Lowrance has a powerful free desktop software program called SonarViewer which allows you to replay your Sonar Log with options to dynamically control sensitivity, colorline, zoom, and range (Figure 4).

Figure 4.  SonarViewer is a free download from Lowrance and has a range of tools for enhancing the contrast of bottom features detected by your Lowrance HDS or Elite.

Use SonarViewer to review your files prior to upload to ciBioBase if you suspect possible signal quality issues or are testing different transducer setups for optimal signal quality.  Signal Quality should also be continually monitored by watching your SONAR page on your HDS or Elite while collecting data on the water.  A helpful rule of thumb is that a signal that is clear and crisp to your eyes is most likely clear and crisp to ciBioBase algorithms.

Optimal Percent SAV Biovolume? 50% is a Good Start

At Contour Innovations we’ve long argued the importance of objectively assessing submersed aquatic vegetation (SAV) abundance to better inform management decisions.  Our last blog post discussing a recent controversy over the role of herbicides in indirectly affecting fisheries declines in Wisconsin reinforces why this is so important.  When we talk abundance per se, we need a metric that is quantitative, yet is intuitive.   The percent of the water column taken up by vegetation growth (i.e., percent “biovolume”) represents such a metric and is the primary variable that is mapped in ciBioBase.  Zero means no growth (blue).  100% represents growth all the way to the surface (red; Figure 1).

SAV, Aquatic Vegetation map, Lowrance HDS, Surface growing vegetation
Figure 1. SAV Biovolume map (left), boat tracks (red lines), boat location (red dot), and sonar chart of vegetation growing to the lake surface on Orchard Lake, MN.

Zero is undesirable in lake environments where vegetation growth is natural or where an artificial lake is managed for vegetation-dependent fisheries (e.g., largemouth bass or northern pike).  No vegetation growth can also cause and be an effect of water quality impairments as discussed here).  In contrast, 100% is undesirable from an aquatic recreation standpoint because props get tangled up and it’s difficult to navigate your boat through surface mats of vegetation (Figure 2).

Figure 2. Aquatic Vegetation (100% Biovolume) growing all the way to the water surface on Orchard Lake, MN and impediments to motorized recreation. 

If no plant growth is bad (0%), but plant growth all the way to the surface (100%) is bad, then good MUST be somewhere in between.  Indeed!  From a Fisheries standpoint, 40-60% average biovolume is good because there is habitat for vegetation-dependent species like largemouth bass, bluegill, northern pike, and indicator species like blackchin shiners that are sensitive to vegetation loss (Figure 3).

Figure 3.  Probability of sampling blackchin shiners as a function of increasing SAV % biovolume  in Square Lake, MN (Adapted from Valley et al. 2010 Hydrobiologia 644:385-399)

From a water quality standpoint, 40-60% biovolume is sufficient to anchor sediments and will promoting better water clarity than if nothing was growing.  Finally, 40-60% biovolume means that most growth is below the depth of your outboard prop and thus you generally won’t encounter the situation as seen in Figure 1.

A case study in MN, WI, NC, and FL lakes

CI is currently involved in a collaborative research project where acoustic data with Lowrance HDS was passively collected while conducting point-intercept surveys.  Acoustic data (.sl2 files) were uploaded to ciBioBase and the Biovolume value for each species survey point was extracted from the exported raster grid (“Extract Value From Point” in the Spatial Analyst Toolbox in ArcGIS or see our Point-Intercept on Steroids blog).  Figure 4 displays a wealth of information about the status of plant growth and management in the surveyed lakes.  With on-the-fly data entry for the plant species surveys and uploading of the .sl2 file to ciBioBase, a similar graph could be produced within hours of finishing a survey, and thus facilitating informed and rapid decision making.

Figure 4.  Biovolume at invasive species sample points and native sample points free of invasive species.  Non-vegetated sites are not included in the analysis.  Lakes range from intermediate nutrient levels, Mesotrophic (M), to high nutient levels, eutrophic (E).  Berry, Gibbs, Swan, Wingra, and Round are in WI; Gray’s, Gideon’s, and St. Alban’s Bays are bays of Lake Minnetonka, MN; Waccamaw is NC; Tracy, Kissimmee, Istokpoga are FL lakes.  All MN and WI lakes are infested with Eurasian watermilfoil.  All NC and FL lakes are infested with Hydrilla.  Waccamaw is bog stained and the hydrilla is a recent infestation

Specifically this graph tells us the following:

  1. Invasives grow closer to the surface of lakes than natives and growth seems to be highest in lakes of intermediate productivity (meso-eutrophic)
  2. Natives appear to grow at the 40-60% biovolume level regardless of productivity.
  3. Native growth can be an objective benchmark from which to judge the success of invasive management in non-eradication management regimes.
  4. Aquatic Plant management was successful at bringing down invasive growth to the level of natives in Gray’s Bay of Lake Minnetonka, Kissimmee, and Istokpoga
Something as simple as what is displayed in Figure 4 can bring an objective point of reference to the table when discussing the often controversial nature of aquatic plant management.  With data such as these, discussions by various user and management groups can center on the acceptable level of growth to meet Fisheries, Water Quality, and Invasive Species management goals (which we argue can occur at some intermediate level of plant growth).  Without both species AND abundance data, various factions will continue to take up positions with anecdotal evidence that support their prejudices and the discourse will never get to where it needs to be to tackle these important water resource issues.

GPS Accuracy Test of Lowrance HDS


At BioBase we put Lowrance HDS to the test for GPS precision and accuracy.  We know the importance of accurate maps but also recognize that “consumer-off-the-shelf” doesn’t mean it won’t provide the type of accuracy needed for accurate acoustic mapping.  The question lies more in how precisely accurate we can map aquatic environments with a “survey-grade” versus consumer GPS.  There are a lot of considerations when mapping from the surface of a water body.  Not only the accuracy of the GPS signal itself but the movement of a survey vessel on a liquid surface, wind, number of points surveyed, survey design, depth, acoustic cone degree, etc.  The list goes on because plants grow, you’re usually in a boat and water moves.  But, we can still investigate the precision of the WAAS corrected GPS from Lowrance HDS.  We were happy with our test results . . . but not surprised!

Units Tested:
  • Trimble GeoXH 6000 Series (post processing DGPS correction to 12” accuracy and precision)
  • Lowrance HDS-5 (WAAS-Correction Enabled)
  • Lowrance HDS-7 Gen2Touch (WAAS-Correction Enabled)

 

Methods:
  • Two individuals recording tracks while walking in same footprints, units held at chest level
  • One individual recorded a track with the Trimble Unit while the other held the HDS
  • Process repeated with the Trimble and HDS7 Touch
  • Data collected in a 2-acre soccer field in Minneapolis surrounded by trees
  • GPS Track lines from both units were uploaded to ArcGIS and converted to points
  • Point layers from both units were spatially joined and distance from each HDS track point to the nearest Trimble GPS track point was calculated
  • Conditions: Clear skies and HDOP (Horizontal Dilution of Precision) was less than 3
  • Testing Completed March 14, 2013

 

One glaring item that can be pulled from the chart above is the accuracy of the Trimble unit before DGPS correction.  Published accuracy is much different than actual accuracy.  You can see from the numbers above that the DGPS correction didn’t adjust the Trimble track by much. When compared against the static HDS output, the comparison hardly changes (from an average difference of .71m between the HDS7 Touch and Trimble™ DGPS before correction to .69m after correction and .45m to .83 respectively for the HDS5).  Even after DGPS correction, both HDS units performed extremely well with significantly less than 1m average difference between tracks (.69m for HDS7 Touch and .83 for the HDS5).
At Contour Innovations we’re focused on best and uniform geostatistical models, acoustic processing, number of data points, and other key standard operating/data collection procedures to create good maps.  The average difference shown in the chart above could even be significantly less than the size of your acoustic cone (depending on cone angle and depth).  Spacing of your sample points is also very important.  The Lowrance HDS system records up to 20 pings per second.  The precision and accuracy of a map created from such voluminous data sets is unmatched.  When analyzing this much data during your survey the geostatistical model and spatial references are substantially improved.

 

Geo-statistical algorithms:  No acoustic map is made up of a complete data set.  Data sampling points with less that 100% coverage still require a statistical model of extrapolation or interpolating of neighborhood points.  All aquatic maps are created with some level of geo-statistical model like kriging.  Ensuring accuracy of actual points will help decrease error coefficients of estimated data but more important is the type of geo-statistical model and spacing between data sampling sights.  There is a positive correlation of error coefficient and transect spacing.  We recommend transect spacing of less than 50m and even higher resolution and lower spacing depending on mapping objectives.

 

Geostatistics is a branch of statisticsfocusing on spatial datasets originally developed to predict probability distributions.  A number of simpler interpolation methods/algorithms, such as inverse distance weighting, bilinear interpolation and nearest-neighbor interpolation, were already well known before geostatistics, but it goes beyond the interpolation problem.  Kriging, the model we use, is a group of geostatistical techniques used to interpolate the value at an unobserved location from observations of its value at nearby locations.  This means that as you collect data along a transect, those data can be used to predict unobserved data between points to a statistically significant probability.  A good geostatistical model and the number of sample point are key to a complete and accuracy map!
A couple things to consider that could influence the accuracy and precision of your maps:
  • Pitch, Roll and Yaw – Wave action or other movements of the boat as you take a physical samples
  • Tree Cover – which isn’t as common when mapping open water like lakes
  • Relation of GPS antennae to transducer – Even with 12 inch DGPS accuracy, if you’re standing 3 feet from your transducer your data points will be off.  If you take a core sample and enter the results into a GPS device, your boat could easily have drifted a lot more than your potential error.   With Lowrance HDS we provide an external antennae that can be mounted directly above your transducer so your data collection is happening at the point spot of your GPS signal.
  • Overall Survey Design – The spacing of your transects is key as it relates to the ability to confidently make predictions in unsampled locations with your geo-statistical model. 
  • Speed of Travel – When looking at a wide range of data collection techniques and methods, speed is always the biggest consideration for accuracy and coverage.

 

“Published Accuracy” is much different than actual accuracy.  A lot of this is a guarantee from the manufacturer to be less than a certain error threshold at least 60% of the time and is not a minimum.
Because of this, there’s an opportunity to use scare tactics to discount the power of an off-the-shelf acoustic unit or GPS.  But, as we’ve described here, there’s a lot that goes into making a map!
We were very impressed with the performance of the WAAS corrected Lowrance™ HDS when compared against a system like the differentially corrected Trimble™ unit.  Though, we can’t say we’re surprised!
For more information on getting the best and most accuracy maps please contact one of our fisheries biologists and GIS experts.
Lowrance™ and Trimble™ are registered trademarks of Navico, Inc. and Trimble Navigation Limited respectively.  Neither Company contributed, authorized, or requested this testing.       

Lake Bottom Depth Precision and Accuracy

In an addendum to an earlier post, we continue to evaluate the accuracy and precision of BioBase depth outputs.  Lowrance has been in the depth sounding business since 1957.  They have tight factory calibration standards whereby depth should never be more than 2% different than the actual depth.  Of course then we expect depths to be spot on on hard bottom surfaces where truth can be easily measured.  But what about in mucky bottoms which are common place in many lakes, ponds, backwaters throughout the US and abroad?  With this in mind, in late May of 2012, we traveled to Pool 8 of the Mississippi River near LaCrosse WI to do some testing in a mucky, moderately dense vegetated backwater (Figure 1).  At some point we have to step back and ask, “what is the bottom of a body of water?”

Figure 1.  Vegetation cover and biovolume (% of water column occupied with vegetation) in Pool 8 of the Mississippi R. in LaCrosse WI on 5/29/2012.  Average biovolume was 30% during the survey.

The most difficult aspect of this testing was to get an objective estimate of the true depth.  In other words, where exactly did the plants end and bottom start?  Typically, investigators use a survey rod like that seen in Figure 2 to estimate actual bottom based on where they feel resistance on the survey rod.  Piece of cake over sand.  Not so easy over flocculant silt and muck or vegetative areas.

Figure 2.  Measuring bottom with a survey rod in a mucky Minnesota Lake.  Typically, the survey rod will sink several inches into the bottom before the surveyor feels resistance and judges the depth to the bottom

Many experienced surveyors will tell you that the rod will sink into the muck some distance before you feel resistance.  There is a positive correlation in the distance it sinks and how mucky the bottom is.  So, we went into this investigation expecting deeper rod depths measured than ciBioBase outputs. 

Accurate and precise results in mucky, vegetated bottoms

After 30 points measured with the survey rod, we compared the results with the ciBioBase depths measured in the same location.  We were pleased to see very high precision with a Coefficient of Determination (R^2) of 0.94 and a systematic difference in depth of only 4.9″ (Figure 3).  The depth of 4.9″ was quite possibly the average depth where we first felt resistance of the survey rod.  The upshot here is that ciBioBase depth outputs are highly precise, consistent and accurate even in mucky vegetated bottoms.

Figure 3. Accuracy and precision of ciBioBase depths measured against depths collected with a survey rod in the mucky, vegetated backwaters of Pool 8 of the Mississippi River near LaCrosse, WI.