Monday, April 29, 2013

Mapping Ponds with BioBase

As an addendum to our blog series on rapid, portable applications we wanted to experiment with a "thru-hull" mount of the 83/200 khz Lowrance HDS transducer on a kayak for mapping storm water retention ponds in an urban area of Minnesota (City of Maple Grove).  Electrician putty (sold as "Duct Seal") available for a few dollars at the neighborhood hardware store worked as a perfect medium for this application.  Follow the series of pictures and captions to see how this worked!
Electrician putty or "Duct Seal" available at most hardware stores can be used for shoot "thru-hull' applications on kayaks or canoes

Figure 2. A 83/200 Lowrance skimmer transducer secured to the hull of a polyethylene kayak by duct seal putty. Care should be taken to remove all air bubbles from the mold before pressing in the transducer
James Johnson from Freshwater Scientific Services LLC ( gets his Lowrance HDS-5 all set to log data. 
Tracks showing a concentric circle approach toward mapping ponds smaller than 10 acres.  This one is 3 acres located in an urban area of Minnesota near Minneapolis (Maple Grove).  Data took 30-min to collect
Blue-scale bathymetric output created after 10-minutes of data processing time by Contour Innovations servers after upload.  Map was produced by 1,000 passively acquired GPS and bottom points.  All map outputs (e.g., water volume or hardness - next picture) can be analyzed in your private ciBioBase online account or exported to GIS for more sophisticated data analyses and layering
Bottom hardness automated output automatically created along with bathymetric and aquatic vegetation layers  in ciBioBase.  Areas that are maroon represent hard areas that remained from the original construction of the pond.  Soft areas are represented by the lighter brown colors and represent sand deltas from parking lot runoff.  Hardness and bathymetric outputs can be used to assess whether storm water retention ponds require maintenance and where specifically to focus efforts

Friday, April 19, 2013

New ciBioBase Website and Mapping Dashboard

At Contour Innovations, ease of use, organization, and user experience are top priorities.  We recognized that our old site wasn't the best it could be, so over the last few months the website and dashboard have been rebuilt from scratch.  We've listened to all the questions our customers had and attempted to incorporate all of these into the new dashboard.   The result is a sleek, user friendly dashboard with a great user experience.  It's fast and has the features to sort, organize, and use the important data you upload to your account for automated processing.  Now you can maximize your BioBase experience!

New features include:
  • Tagging - You are now able to add descriptive tags to each of your trips for better sorting
  • Improved Search Capabilities - search all categories generally by user last name, lakes, and even tags
  • Collapsing Trip Organization by Lake - Trips are categorized by lake in the dashboard and only loaded when you want them
  • Trip Track Quick View - Each trip in the dashboard provides a snapshot of where your track is on the water body for quickly identifying a survey area
  • Sort by Date - Trips can be filtered by date range so you're only looking at the trips you want to see
  • Advanced Searching - This feature will allow you to sort by a specific category like file name, tags or water bodies
  • Support Tab - Many of the methods that we blog about are now available as PDFs and step-by-step Powerpoint documents in your account
  • Trip Support Request - Quick boxes within each trip allow you to communicate your questions directly to QC experts for a specific file or merge
  • Overall cleaner look for a better user experience!

This dashboard should be much easier to use and was designed so the things you are looking for are right where they should be.  We're always interested in hearing from you so please log into your account and check out!  Let us know what you think and if you have questions about any of the new, powerful features

Thursday, April 11, 2013

Detect Change in Your Lake Before it's Too Late!

Citizens all over the globe love their lakes and go to great lengths and spend lots of money to protect and manage them.  In the US, the Environmental Protection Agency supports a multitude of State, Local, and citizen efforts to monitor water quality in lakes and has implemented a rigorous National Lakes Assessment.  Despite these efforts, lakes across the nation continue to be impacted from runoff pollution and invasive species proliferation under our noses. How does this happen?

Unfortunately, despite well-intentioned efforts to monitor various lake parameters, established monitoring methods such as water sampling from the middle of the lake or presence/absence surveys of aquatic plants often do not change significantly until there has been a fundamental shift in a lake’s ecology.  We blogged about this concept in more depth last year.

The risks of not monitoring sensitive indicators are high.  First, once a lake has “tipped” into a new regime, it’s difficult if not impossible to restore the lake to its original condition.  Second, a lot of money is on the table for either watershed protection/restoration or lake management (e.g., herbicide or other remediation costs).   This reality demands that citizens and lake managers monitor lake parameters that respond quickly to environmental change and lake management interventions such that environmental or economic costs are kept minimal.

Aquatic plant abundance in lakes is responsive to change, frequency of occurrence is not

We discussed an interesting case study near the end of our Point-Intercept on Steroids blog last October about a moderately nutrient-polluted lake in Minnesota infested with non-native Eurasian watermilfoil.  A whole-lake herbicide treatment was applied to target and kill the Eurasian watermilfoil.  Unfortunately, there was little else growing in the lake that was not vulnerable to the herbicide.  The herbicide wiped out almost all submersed vegetation.  This had negative effects on the water clarity and fish habitat in the lake.  In glacial lakes, aquatic plants are often critical components of healthy lakes.

The fact that the herbicide “wiped out almost all vegetation” would have been nothing more than the desperate cries of a Fisheries manager or a concerned citizen who saw it “with their own eyes” if it was not for a hydroacoustic assessment of plant abundance that occurred before and two years following the treatment (Valley et al. 2006; Figure 1).  Concurrently occurring rake surveys of frequency of occurrence, although important for determining what species were growing at the time, did not detect the almost complete loss of submersed vegetation in the lake (Figure 1).  Figure 2 demonstrates why rake frequency surveys are so insensitive to changes in abundance.  To put it concisely, rake surveys are not abundance surveys, they are species occurrence surveys.  Large changes to the lake must occur before change is reflected in species frequency data.
Figure 1.  Frequency of occurrence of all plants estimated using the point-intercept method (numbers above bars) in a eutrophic Minnesota lake (Schutz)  treated with a whole-lake herbicide in June 2002.  The bars represent the whole-lake biovolume of aquatic vegetation in Schutz and a nearby reference lake (Auburn).   Average biovolume declined from 35% in 2002 before the treatment to 1.5% the year following the treatment.  Biovolume was assessed over the entire waterbody and more closely reflects the true changes in abundance than percent frequency or any other adaptation that uses qualitative estimations of abundance (e.g., abundance on a scale of 0-3).  Figure adapted from Valley et al. 2006
Figure 2.  Two drastically different environments that get the same data value (present) if a rake picks up the sprig in panel B.  Weighting by a rank (e.g., A = "3" or Abundant and B = "1" or Sparse) is only moderately more informative about true abundance since no quantitative judgement can be made by the ranks

Passive logging of acoustics by citizens to rapidly detect change in lakes

Lowrance HDS log up to 20 data points (pings) per second.  A GPS report of your location is automatically logged approximately every second.  Spend a couple of hours driving back and forth on your lake (like you may already do normally) and now you have a full system map incorporating 144,000 data points on plant abundance on a lake all summarized nicely in a map and summarized statistical reports (Figure 3).  By repeating this process multiple times throughout the year with other lake citizens (see our wisdom of the crowd blog) over several years, you will measure the “heartbeat” of your lake and begin to notice when an irregular rhythm shows up and what might be causing it.

Figure 3.  Sample output of vegetation abundance (red = vegetation near the surface, green = vegetation near the bottom, blue = no vegetation) and GPS tracks in a 235 acre Minnesota Lake.  Bathymetry, vegetation, and bottom hardness maps were created by simply logging acoustic data from Lowrance HDS, driving back and forth for 3 hours, and then uploading the data to ciBioBase
Infrequent plant species rake surveys or water sample monitoring in the middle of the lake will not give you the heartbeat of the lake; only a snapshot of the current conditions and whether your “patient” is in critical condition.  ciBioBase is your tool for good preventative lake health care.

Literature Cited

Valley, R. D., W. Crowell, C. H. Welling, and N. Proulx. 2006. Effects of a low-dose fluridone treatment on submersed aquatic vegetation in a eutrophic Minnesota lake dominated by Eurasian watermilfoil and coontail. Journal of Aquatic Plant Management 44:19–25.

Monday, April 8, 2013

Guest Blog: ciBioBase and Arctic charr habitat in Windermere, U.K.

By Dr. Ian J. Winfield and Joey van Rijn

The Arctic charr (Salvelinus alpinus) is well appreciated as an important fisheries species in many northern areas of the world.  In addition, it is equally important to evolutionary biologists because of this species’ frequent development of ‘morphs’ or 'types' and their bearing on our understanding of mechanisms of speciation (Figure 1).  In the U.K., this fascinating fish is also recognised as having great nature conservation value.
Figure 1.  A female (top) and male (bottom) Arctic charr from Windermere, U.K.  Photo courtesy of the Center for Ecology and Hydrology)
Windermere is England’s largest lake and has been at the forefront of several areas of Arctic charr research for many decades, with the notable exception of studies of their spawning grounds (Figure 2).  Despite their long appreciated significance for the coexistence of autumn- and spring-spawning Arctic charr types, local spawning grounds have not been studied in any detail since their original brief description in the 1960s.  At that time, laborious and spatially-limited direct observations by divers showed that spawning requires the availability of gravel or other hard bottom habitat.  New information on these critical areas is needed by ecologists and evolutionary biologists and, more urgently, by fisheries and conservation organisations responsible for the management of Windermere.

Figure 2.  Breathtaking view of Windermere's north basin; home to several spawning populations of Arctic charr.  Photo courtesy of Dr. Ian Winfield.
We are currently using the newly developed bottom hardness capability of ciBioBase to survey and characterise the spawning grounds of Arctic charr in Windermere.  Limited underwater video is being used for ground-truthing, but the combination of a Lowrance HDS-5 sounder with ciBioBase is allowing us to investigate the known spawning grounds with unprecedented speed (Figure 3).  For the first time, we have been able to document in detail the bathymetry and bottom features of a long-monitored (for spawning fish) spawning ground just north of the island of North Thompson Holme in the lake’s north basin.  ciBioBase is also enabling us to examine other known spawning grounds in Windermere and to expand our coverage to other potential areas previously unstudied.
Figure 3. An example ciBioBase output of bottom composition on and around the Arctic charr spawning ground of North Thompson Holme in the north basin of Windermere
The rapidity of the field component of hydroacoustic surveys is well known.  ciBioBase now offers us a similarly fast method of hydroacoustic data analysis for key environmental characteristics in relation to the spawning of Arctic charr.  This new approach helps us to dramatically increase our return on investment and also allows us to review results within hours of coming off the water, leading in some cases to us adapting our field plans on the basis of initial results.

Dr. Ian J Winfield is a Freshwater Ecologist at the Centre for Ecology & Hydrology in Lancaster, U.K.  He has over 30 years of research experience in fish and fisheries ecology, hydroacoustics, and lake ecosystem assessment and management.  Dr. Winfield sits on several regional, national and international advisory boards and is the current President of the Fisheries Society of the British Isles (FSBI).

Joey van Rijn is an undergraduate student currently following a BSc. degree course in Applied Biology at the University of Applied sciences, HAS Den Bosch, in the Netherlands. He is experienced in ecological and particularly phenological research including work on temperature-induced differences between urban and rural areas in the timing of blossoming and leaf unfolding in shrubs.  He has also been involved with the development of fish ways for standing waters in the Netherlands. Joey is currently undertaking a research internship at the Centre for Ecology & Hydrology in Lancaster, U.K., where his research mainly focuses on using hydroacoustics to investigate Arctic charr spawning grounds in Windermere.

Thursday, April 4, 2013

GPS Accuracy Test of Lowrance HDS

At Contour Innovations 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)

  • 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 statistics focusing 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.