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

ciBioBase Vegetation Mapping

We love to show off the accuracy of our submerged vegetation mapping algorithm.  Check out this break in the weeds that was picked up and clearly displayed in the ciBioBase vegetation layer:

The BioBase vegetation layer is automatically generated by powerful cloud computers so you receive an objective output every time.  The white line on the right and red dot on the left show the boat position as a cross section and aerial view of the water column respectively. 

Submerged vegetation is displayed as percent biovolume (BV%) which represents the percent of the water column occupied by plants.  This provides a clear picture of total plant abundance from each trip on the water.  Data can be passively logged because none of our users have to do any of the processing when they get back to the office.  Do what you were already planning to do and our automated system will take care of the rest.

Let us know if you have any questions about how this process works!

Assessing Fish Habitat in Rivers

BioBase is not just a lake vegetation mapping tool, it also can help Fisheries managers and researchers assess, monitor, and simulate fish habitat conditions in large rivers.  We demonstrated this application on a trip to the Mississippi River Pool 2 in St. Paul, MN on 4/27/2012.  Just downstream of the Lock and Dam, we used a Lowrance HDS sounder and the automated processing of BioBase to map the bathymetry of a pool where a range of fish species often congregate (Figure 1).

Figure 1.  Bottom mapping with a Lowrance HDS-5 on Pool 2 of the Mississippi R. just downstream of the Lock and Dam on 4/27/2012.

 

The raw pool elevation on 4/27/2012 was 4.27 feet; still within the range of moderate drought according to the US Drought Monitor but 1.7 feet higher than the most recent low on 12/10/2011. Coincidentally, these drought levels follow historic flood levels just one year earlier (Figure 2). To demonstrate BioBase’s utility as a fish habitat assessment tool, we compared sizes and volumes of our mapped pool under the hydrologic conditions experienced on Pool 2 during the last year.

Figure 2. Hydrograph for the Mississippi River at St. Paul, MN (DNR ID# 20088002; USGS ID# 05331000; Data and figure courtesy of the MN DNR).


On 4/27/2012, we mapped and analyzed a 15-ft pool using the ciBioBase polygon creation tool and determined that the max depth was 17 ft, surface area was 317 m2 and the volume was 1508 m3 (Figure 3).

Figure 3.  Diagnostics of a pool of interest using BioBase’s polygon tool.

In order to reconstruct changes to this pool under the recent low flow on December 10th 2011, we used the Z-depth Offset feature iniBioBase to drop the elevation down 1.7 feet.  In Figure 4, you can see the striking difference this reduction has on the size of this pool and consequently the amount of available fish habitat.  The area on December 10th 2011 was estimated to be 3.1 m2 and volume was 9.4 m3; 100 times smaller in size and 161 times smaller in volume than on 4/27/2012. If we increase the offset by the peak flood elevation on March 30th 2011, the 15-foot hole becomes a 30-foot hole (Figure 5).

 

Figure 4. Polygon overlay in BioBase demonstrating the difference in size and volume of a 15-ft deep hole between the yearly low elevation on 12/10/2011 (pink) and during data collection on 4/27/12 (green).

 

Figure 5. Polygon overlay of drought elevations in 2012 (green and pink) overlain onto simulated peak flood bathymetry on 3/30/2011.
This demonstrates one potential application of BioBase for fish habitat studies in large rivers.  We presented three striking contrasts in fish habitat conditions within one year’s time with data that took 20 minutes to collect and an hour to analyze in BioBase. Different hydrological scenarios can be modeled in BioBase and thus could be used in predictive fisheries habitat models or to reconstruct habitat conditions over some period of time.

Verification of ciBioBase Depth Output

At Contour Innovations we are our own skeptics and constantly perform verification investigations of BioBase output for accuracy. 

As Chief Aquatic Biologist, I’ve been comparing bottom depths sampled with a survey rod with its corresponding depth derived from the automated depth outputs from the BioBase System.  In the figure below depths from Elk Lake (Clearwater Co. MN) are color coded from 1 – 50 ft with blue becoming more intense as depth increases.  The circles are depths recorded with a survey rod while the squares are ciBioBase depths.  Below is one visual representation of the high agreement between true depths and BioBase depths. This visual shows the symbol color agreement demonstrating accuracy in the output! 

True depth data come courtesy of Minnesota Dept. Natural Resources Fisheries Research Biologist Donna Dustin and are copyright of Minnesota DNR.

Ray Valley Joins Contour Innovations as Aquatic Biologist

Please join Contour Innovations in welcoming Ray Valley (RayV@ContourInnovations.com) to our team as Chief Aquatic Biologist. 

Previously employed by the Minnesota Department of Natural Resources as a Senior Research Biologist in the Section of Fisheries, Ray developed aquatic plant mapping protocols with acoustic technology and GIS, researched the link between aquatic plants and fish populations, and most recently chaired the successful launch of a collaborative and comprehensive long-term lake monitoring program called Sustaining Lakes in a Changing Environment (SLICE), Ray holds a B.S. degree in Fisheries from the University of Minnesota and a M.S. degree in Fisheries Ecology from Michigan State.

Ray brings a wide range of expertise to our team specifically related to aquatic vegetation mapping, GIS, and fisheries.   Our team is excited to have his deep technical background in aquatic habitat mapping using acoustics.  “We’ve only scratched the surface of what our platform can do both as a direct output and the benefit our users receive from a collaborative and uniform mapping effort,” said Matt Johnson, CEO of Contour Innovations.  “We will continue to add resources to ensure that Contour Innovations continues to push the boundaries in automated temporal and spatial mapping and Ray brings the expertise to go to the next level.”

Ray will be responsible for aquatic research using the ciBioBase System and providing technical mapping and research support for our empowered customers.    He will also be a keystone piece in designing and evaluating new features and valuable tools provided by the BioBase automated mapping system.  Ray will use his expertise to develop SOPs for and design mapping protocols for our customers’ unique mapping needs and to help maximize time on the water.
Ray has published the following selected list of articles related to submerged aquatic plant mapping and links to fish:

  • Valley, R.D. 2000. Effects of macrophyte structural heterogeneity and fish prey availability on age-0 largemouth bass foraging and growth. M.S. Thesis. Michigan State University, East Lansing.
  • Valley, R.D. and M.T. Bremigan. 2002.  Effects of macrophyte bed architecture on largemouth bass foraging: implications of exotic macrophyte invasions. Transactions of the American Fisheries Society 131(2):234-244
  • Valley, R.D. and M.T. Bremigan. 2002. Effects of selective removal of Eurasian watermilfoil on age-0 largemouth bass piscivory and growth in southern Michigan lakes. Journal of Aquatic Plant Management 40(2):79-87.
  • Valley, R.D., T.K. Cross, and P. Radomski 2004. The role of submersed aquatic vegetation as habitat for fish in Minnesota lakes, including the implications of non-native plant invasions and their management.  MN DNR, Division of Fish and Wildlife, Special Publication No. 160.
  • Valley, R.D., M.T. Drake, and C.S. Anderson. 2005. Evaluation of alternative interpolation techniques for the mapping of remotely-sensed submersed vegetation abundance. Aquatic Botany 81:13-25.
  • Valley, R.D., and M.T. Drake. 2005. Accuracy and precision of hydroacoustic estimates of aquatic vegetation and the repeatability of whole-lake surveys: field tests with a commercial echosounder. MN DNR, Division of Fisheries and Wildlife, Investigational Report No. 527.
  • Valley, R.D., W. Crowell, C. Welling, N. Proux. 2006. Effects of low dose applications of fluridone on submersed aquatic vegetation in a eutrophic Minnesota lake dominated by Eurasian watermilfoil and coontail. Journal of Aquatic Plant Management 44:19-25.
  • Valley, R.D. and M.T. Drake. 2007. What does resilience of a clear-water state in lakes mean for the spatial heterogeneity of macrophyte biovolume? Aquatic Botany 87:307-319.
  • Valley, R.D., M.D. Habrat, E. D. Dibble, and M.T. Drake. 2010. Movement patterns and habitat use of three declining littoral fish species in a north-temperate mesotrophic lake. Hydrobiologia 644:385-399.
  •  Beck, M.W., L. Hatch, B. Vondracek, and R.D. Valley. 2010. Development of a macrophyte-based index of biotic integrity for Minnesota lakes. Ecological Indicators 5:968-979.
  • Heiskary, S and Valley, R.D. In press. Curly-leaf pondweed and interrelationships with water quality. MN DNR Division of Fish and Wildlife, Investigational Report No. 557.
  • Valley, R.D. and Heiskary, S. In preparation. Short-term declines in curly-leaf pondweed across a network of sentinel lakes in Minnesota: potential influences of snow depth and water temperature. To be submitted to Lake and Reservoir Management.

Ray’s most research interests include lake ecology with specific emphasis on the interaction between aquatic plants and water quality regimes. 

He can be contacted at RayV@ContourInnovations.com

Auto Blue Scale Bathymetry Mapping

Contour Innovations (CI) is announcing the addition of a new feature of our BioBase System.  As many of you know, each trip uploaded to your account is processed for depths and plant canopy heights to automatically create maps and output the layered data in your interactive online account.  From now on, depth contours will be displayed in blue scale after launch of our new blue scale image feature.  When loading your vegetation layer, blue scale will disappear but transparent contour lines will display beneath the % biovolume output. 
This feature is great for lake and pond managers that are interested in getting a quick assessment of any sized water body to understand where the deep spots are for diffuser placement and overall management.  We still employ a TIN anlysis for accurately estimating total water volume.  On a pay per upload plan, our customers can get this data quickly for as little as $100 per water body and in as short as 10 minutes.   You collect the data with your low cost Lowrance HDS depth finder, upload it to a secure account from your computer, and the raw sonar is processed in the cloud in minutes.  Images of the blue scale can be exported with ease to be included in management plans (images in this blog are direct exports from the BioBase System).  State agencies are using the System for bathymetric output to update their existing lake maps provided to anglers.    This is just another great feature added to the powerful BioBase System.
To further demonstrate the power of automation and centralization anyone that has already uploaded trips to the BioBase System can now get blue bathymetry for those uploads with little effort.  To try it out, log into your account and click the interactive viewer for any trip.  Using the REPROCESS tab, check “contours” and resend the trip to our servers.  Within minutes you will get an email letting you know that your reprocess has been completed and blue scale will be provided for this trip.  Using an online account there are no software updates or manual processing of older trips.  Let our servers do the work.  That’s what they’re there for.  Anytime we add a new feature to BioBase, anything you’ve already uploaded to your account can be updated.   It’s pretty cool stuff!

Please contact us with any questions at matt@ContourInnovations.com or 715.864.9347.  Pond managers can contact our exclusive partner, Aquatic Eco-Systems (Orlando, FL) at mattr@aquaticeco.com or 407.462.4697.  Let us know what you think!