Tuesday, December 16, 2014

Need a Custom Map? We'll make you one!

BioBase's primary strength is an automated map creation engine designed to take thousands raw of data signals from your Lowrance and rapidly summarize them into informative maps.  These maps have helped aquatic resource professionals throughout the globe make more informed aquatic management decisions.

But BioBase also creates maps that are rather pleasing to the eye and many have asked how they might be able to create customized digital or print maps for their clients.  We offer two solutions that will help you create professional quality maps. First, as ESRI Silver Partners we offer basic support of viewing and analyzing BioBase data in ArcGIS and have produced several do-it-yourself tutorials that are available in your BioBase Support & Resources.  Second, we offer GIS Services to BioBase customers who lack expertise in GIS or the proper software licenses.  Below we present a gallery of images from these projects.  Identities and locations of projects have been changed or omitted to protect the privacy of the customers.

We'll create a map for you!
Navico offers custom GIS services where interested customers fill out an order form specifying their needs.  Navico GIS staff will transfer the appropriate BioBase data to ArcMap 10.x and any ancillary GIS shapefiles (e.g., sampling waypoints or other points of interest) and produce a custom-sized, high resolution digital map that you can have printed online or at a local print shop.  Email us at info.biobase@navico.com to get print and pricing details.
Multiple BioBase maps can be combined into one map and exported as any image format and custom sized.  Send us your logo and we'll add it to the map.
Request transparency to the image to show floating leaf vegetation in the aerial imagery. 
Send us points of interest to add to the map.  In this case, navigation hazards in front of a land owner's property
Send us sediment depth point data and if sufficient, we'll interpolate and create a sediment depth map (left) and pare it with other BioBase maps (in this case aquatic vegetation biovolume).
Would you like to add water body statistics? We'll add full lake summaries or summaries by depth.  You tell us the contour interval and units.
An example where a customer desired to simulate the pond depth at a significantly higher water elevation than when mapped with BioBase. Customer used survey-grade GPS to generate precise land elevation data while walking along the soon-to-be-inundated shore.  Customer submitted these point elevation data to Navico along with a high-water shoreline for incorporation into the lake map.

If you have any custom mapping or presentation needs with your BioBase data contact us today at info.biobase@navico.com and we'll provide you with an order form and generate a quote and delivery timeline for your map.

Thursday, November 20, 2014

Aquatic Mapping Strategies

Producing professional-quality aquatic maps has never been easier with Lowrance and BioBase mapping technologies, but there are several strategies that can help you optimize your time on the water and produce the best possible map output:

Make Sure Your Transducer is Aligned Correctly
An angled transducer is the most common oversight of users and has been the subject of blogs in 2013 and more recently in 2014 (Figure 1).

Figure 1. Example of a misaligned skimmer transducer and effects on the sonar signal.  For good BioBase outputs, your Lowrance transducer should be aligned parallel with the ground (inset).
A misaligned transducer will result in weak return signals over flat bottoms or slopes where the beam is pointed away from the slope (Figure 1).  In contrast, if the beam is pointed toward the slope, the signal return will be much stronger than normal (Figure 2).  A misaligned transducer can result inaccurate bathymetry, aquatic vegetation, and bottom hardness outputs.

Figure 2.  Example BioBase output where a transom mounted transducer was slanted downward.  In this case, with the boat moving from SW to NE along shore, signal strength is much more diminished on the downslope than on the upslope where the signal is more direct.
Make Sure Your GPS is Aligned With Your Transducer
A second common oversight is large horizontal separation between the GPS receiver (X,Y position) and the transducer (Z position).  This is especially problematic on console-steer boats where the Lowrance Display with an internal GPS may be a good 5 ft (1.5 m) from the transducer.  This means the location of the mapped depth will be 5 ft off in one direction and another 5 ft off in the other direction if the surveyor is doing back-and-forth passes (Figure 3).  A misaligned GPS will result in local imprecision and a "crinkly" looking contour map, but should not affect lake-wide statistics.
Figure 3. Result of a misaligned GPS. In this instance, the surveyor was using the GPS position from the internal antenna in the Lowrance HDS display that was 7 ft away from the transducer where the depths were being recorded.  This positional bias was doubled as a result of the back and forth transect passes (red lines).
BioBase users have two "first party" external GPS antenna solutions which can be mounted right over the transducer and communicate with your Lowrance or Simrad Display.  The Point-1 GPS is a low-cost solution that suits most user needs (Figure 4).  Although the published horizontal accuracy is 5-m, users may expect much better than this, especially in open water.  In 2013, in tests with a differentially corrected Trimble GeoXH 6000, we found differences compared with the internal Lowrance HDS antenna (which uses similar technology as Point-1) to be less than 1-m.  Still, if the user requires more rigorous horizontal positional standards, they can opt for a Simrad HS60 DGPS (Figure 4).  Lowrance and Simrad also support any NMEA 2000 compatible third-party GPS receivers.  Thus with the appropriate NMEA settings and connections, users can stream positions from a wide-range of stand-alone receivers that they may already have as part of other survey work.
Figure 4. Users can align their GPS position with depths by using an external GPS antenna.  Point-1 GPS (left) is the lowest cost and most popular option.  The Simrad HS60 ensures higher reliability of 1m GPS accuracy with its capability of differential correction.  Both antenna are NMEA2000 compatible.

Design and travel transects in a way that maximizes coverage of the features you want to map
A question anyone who desires to make a quality map must address is what is the minimum amount of coverage needed.  BioBase uses the broadband, down-looking 200 kHz signal that collects "point" samples (actually bundled samples from a rapid-firing, 10-20 ping-per-second transducer) directly below your boat (see more about this here here).  Kriging interpolation is a geostatistical way that BioBase employs to predict depth, vegetation, or hardness in unsampled locations.  The more closely spaced the samples (or boat passes), the better the predictions between passes.  You need fewer passes for simple bowl-shaped shallow lakes than convoluted, deep lakes with complex bottom topography.  Same goes for homogeneous vs patchy vegetated or hard bottoms.  Here are some simple transect designs that BioBase users have found successful for creating good bottom maps:
Figure 5.  Parallel to shore design in a flooded reservoir bay.  Note the precision of the internal-GPS track which never crossed structures or shore ensuring confidence in the accuracy of resultant contours.
Figure 6.  Concentric circle transects may be the best data collection approach in small ponds or bays (the pond pictured is 3 acres; 1.2 ha).  In a small boat, kayak, or canoe, the user starts logging as they travel close to shore slowly working their way to the middle of the pond.  This design typically results in smooth bathymetric contours.
Figure 7.  Traveling parallel to the longest shoreline is an effective way of mapping large lakes (the lake pictured is 250 acres; 101 ha). Adding a single trip around shore may enhance the precision and accuracy of nearshore habitats which are often patchy. This approach can be used simultaneously with other lake sampling like aquatic plant point-intercept sampling.  
Figure 8.  Back and forth passes over an experimental plot on Lake Tohopekaliga, Florida USA.  This approach to mapping invasive aquatic plant infestations is much more efficient than using visual cues to know where the edges of aquatic plant beds occur.  We discuss this in more detail here.
Space transects according to the desired level of detail
In most cases, it's unfeasible to completely cover the waterbody you are trying to map. But what area must we cover to produce an accurate and sufficiently precise map?  Users should be prepared to answer the following questions:
  1. What is the size of the waterbody I am trying to map?
  2. Do I want a whole lake map or just a sample area?
  3. How complex are the habitats/bottoms I am trying to map
  4. What level of detail do I need?
  5. What are the consequences of missing some detail if my transects are too wide?
  6. How much time and money do I have available to devote to the mapping project
By default, BioBase produces a 5-m by 5-m square level of detail (grid cell size) for all mapped layers and creates 5-m grid cell predictions to 25 m away from the trip path (i.e., 5 grid cells).  If the adjacent transect is less than 50-m away, the map will be complete.  If the adjacent transect is greater than this distance away, then the area > 25-m is "blanked" and no output is produced.  Users can increase both the grid cell size and buffer "fill" by increasing the buffer in the Trip Reprocessing tab in their BioBase account.  By increasing the buffer, users can "generalize" or "smooth" BioBase outputs.  In some cases smoothing will reduce local precision without sacrificing overall accuracy.  But in cases where significant bottom features are not sampled (e.g., holes, humps, points, patches), then increasing the buffer will reduce accuracy and precision.  This returns us to critically evaluating questions 4 and 5.  Below are some visual examples of how transect spacing and design can affect mapped outputs:

Try a Hybrid Approach
You can cover big water while not sacrificing detail if you employ a hybrid approach that combines wide spaced transects with closer follow up transects in areas of interest.  North Carolina State University showed us how this can be done in North Carolina's largest natural freshwater Lake Waccamaw (8,938 ac, 3,617 ha).  The invasive aquatic plant, Hydrilla, recently invaded Waccamaw and researchers in NC State's Aquatic Weed Science Program (led by Dr. Rob Richardson) needed to know how widespread the plant was to develop a good management plan.  They started with running 300 m transects on a couple of boats, while also collecting vegetation point samples.  This took about a week to finish the field work and a map with 60-m grid cells was processed and merged in BioBase in a matter of hours (Figure 9).
Figure 9.  300-m transects (red lines) on Lake Waccamaw overlain onto a submerged vegetation map processed by BioBase.  Red represents vegetation growth close to the surface, green is low-growing vegetation.  Blue areas have no vegetation growth.  Grid cells were 60 m.
Physical plant species samples suggested that most hydrilla growth occurred near the boat launch in the NW part of the lake which was not surprising since most new species introductions originate at boat launches.  Accordingly, NC State researchers required some more detailed information about the plant beds in this area and implemented a more intensive survey in the launch area.
Figure 10. 50-m transects (red lines) on Lake Waccamaw recorded over an area near the boat launch with relatively high hydrilla cover. Grid cells are 10-m
When we zoom in and look at the map outputs of the alternative mapping strategies we can make some informed,visual conclusions about alternative mapping strategies (Figure 11).

Figure 11. Vegetation biovolume maps of the NW corner of Lake Waccamaw processed by BioBase and converted to a raster in GIS.  The map on the left was created with 50-m transects; the map on the right was created by 300-m transects.
The first striking comparison between the 50-m transect map and 300-m transect map is the difference in the detail, patchiness, and highs and lows of vegetation Biovolume.  However, when you look at the statistics, on the whole, the percent area that has vegetation present and the overall vegetation height (expressed as avg percent biovolume) doesn't look too much different.  This is a visual, geospatial representation of the difference between accuracy and precision.  Both are accurate results and show the same general trends.  However, the map on the left is more precise due to the higher number and closer spacing of transects than the map on the right where the map was generated from maybe one or two transects.

Now you are empowered!
This blog was meant to cover mapping strategies A to Z quickly and get you on your way to creating high quality BioBase outputs with your Lowrance or Simrad Sonar and Chartplotter.  If this brings to mind questions or creative ways you've navigated these issues, please comment or sign up and post a forum discussion at http://aquaticmapping.prophpbb.com/.  We are always impressed with the innovative mapping solutions of BioBase user community.  This community had presented these great examples that help newcomers to the technology get up and running quickly!


Tuesday, November 4, 2014

Choosing and Installing your Lowrance Transducer

The transducer connected to your Lowrance echosounder plays a critical role in producing quality map outputs.  Fortunately, the mechanics of producing quality hydroacoustic signals has been honed by 57 years of research and development by engineers at Lowrance.  Still, users play an important role in optimizing outputs by selecting the correct transducer and installing it correctly

Selecting a Transducer
There are several resources that can help you choose the correct transducer.  On one of our support pages, you can read about the types of Lowrance transducers, and common installs (e.g., transom, shoot-thru, bolt-thru).  Further, we have another interactive site that demonstrates the size of bottom that is scanned at different depths for different frequencies and transducer models.  The most common transducer for Lowrance HDS for inland applications (both fishing and mapping) is the dual frequency 83/200 kHz skimmer® broadband transducer (model HST-WSBL).  This is a popular transducer due to its small size, low cost, ruggedness, and reliable performance.

Still, Navico and our partners at Airmar Technology Corporation offer a wide range of compatible transducers for Lowrance and Simrad multi-function displays.  See the Navico Store for a full range of options.  Thus, the advanced user has a range of options to customize their setup to their use cases (e.g., inland vs offshore, small shallow ponds vs large deep lakes; Figure 1).
Figure 1. Airmar TM260 narrow-beam dual frequency transducer (left) and the much smaller Lowrance HST-WSBL dual frequency wide-beam skimmer® transducer (right) with a ping-pong ball as a reference to scale.
BioBase mapping outputs are currently optimized for the 200 kHz broadband frequency.  But users have the option of choosing narrow (6-deg), medium (12-deg), or wide (20-deg) beam angle transducers.  The beam angle determines the size of the acoustic footprint of each pulse and thus the local sample area (Figures 2 and 3).  Most Lowrance HDS Sounders for use in inland waters come equipped with the wide-beam HST-WSBL transducer.
Figure 2. Qualitative differences in signal return and simulated beam angle of the Airmar TM260 6-deg 200 kHz transducer and the Lowrance HST-WSBL 200 kHz 20-deg transducer.  Data were collected on Orchard Lake, Dakota Co., MN USA over a bed of dense aquatic vegetation (coontail and northern watermilfoil).
Figure 3.  Schematic demonstrating the overlap of acoustic beams across alternative 200 khz transducers given normal (10 pps) to fastest (20 pps) ping rates.  Beam angle is to scale, but actual cone overlap depends on boat speed.  For most inland mapping, overlap in the Y direction (i.e., in the direction of the boat path) across different beam angles is high and the actual difference in acoustic footprint can only be seen in the X direction (i.e., to port or starboard sides)

Although the TM260 and HST-WSBL represent both ends of the spectrum in terms of beam angle, both tracked bottom depth similarly (within 6") in aquatic plant environments in recent tests on a Minnesota lake (Figure 3).  Thus, in most common shallow-water circumstances we may expect similar map outputs with both narrow- and wide-beam transducers.
Figure 3.  Differences in depth declaration in an aquatic plant bed from a narrow beam transducer (Airmar TM260) and wide-beam transducer (Lowrance HST-WSBL) from repeated transects.  Data were collected by a Lowrance HDS-9 Gen2 Touch and analyzed by BioBase Automated Mapping System.  Dots are means from pooled samples along 3 repeated transects for each transducer.  Error bars represent 95% Confidence Intervals.  Overlapping confidence intervals mean that differences were not statistically significant.
Types of Mounts
There are a range of options for mounting your Lowrance or Simrad transducer that we discuss and demonstrate in a popular blog published in 2013.  In Table 1, we list the major types of mounts BioBase users deploy to survey aquatic habitats.

Table 1. Examples of 4 different transducer mounts: TransomPoleShoot-thru, or Bolt-thru mounts.

*Shoot-thru mounts with pliable, puddy-like duct-seal are portable, Shoot-thru mounts with epoxy are permanent.

**For this analysis, scupper-hole transducer mounts are considered "bolt-thru" but are not permanent


For the highest quality outputs and most reliable performance, we recommend the bolt-thru transducer mount, especially for high-use, dedicated survey vessels.  The transom mount is recommended as a high quality, flexible option where a permanent mount is not feasible.  However, misalignment of a transom-mounted transducer is a common issue that is often overlooked.

Importance of Proper Transducer Alignment
A transducer that is not parallel with the ground can result in inaccurate depths, vegetation detection, and bottom hardness estimates (Figure 4).

Figure 4.  Example BioBase output where a transom mounted transducer was slanted downward.  In this case, with the boat moving from SW to NE along shore, signal strength is much more diminished on the downslope than on the upslope where the signal is more direct.

Although properly aligning your skimmer® transducer seems simple to accomplish (Figure 5), boat transoms are often a vulnerable place for a transducer to be and can be knocked off alignment by a variety of unintentional actions (e.g., trailer loading, obstructions in water, etc.).  Often a misaligned transducer can escape the notice of even the most skilled operator.

Figure 5. Schematic of a properly installed skimmer transducer on a boat transom.


Monitoring your SONAR page while recording and correcting issues quickly when they arise is the best way to ensure high quality BioBase maps.  If you do suspect that your transducer is misaligned while recording, first stop recording, adjust your set up, test, and then begin recording again.  Make note of the filename where you observed the problem and you can later edit your output in BioBase if the file was only partially affected.  If the entire file was erroneous, avoid uploading to BioBase and merging it with other files

Get Expert-level Map Outputs By Only Following a Few Easy Steps
Advances in consumer sonar and gps technology coupled with automated cloud computing has removed a great number of prerequisites for creating high quality aquatic habitat maps.  Yesterday, practitioners were required to possess a great understanding of the fundamentals of hydroacoustics, GIS, and cartography and had to calibrate their hardware by precise "knob-turning."  Today, with Lowrance and BioBase, you can grab a Lowrance HDS off the shelf, take some care installing your transducer, record your sonar while on the water, upload to BioBase, and high quality maps will be produced automatically.  Contact us at info.biobase@navico.com for a free demo!

Friday, October 3, 2014

NCSU Launches Aquatic Resources Mapping Forum!

"I want to map stormwater retention ponds for my municipality, how should I mount my Lowrance unit?" "Can you estimate aquatic plant biomass from BioBase outputs? If so, how?"  Questions like these from a growing global BioBase user base can now be answered by other experienced colleagues.  North Carolina State University's Aquatic Weed Science Program has recently launched an Aquatic Resource Mapping Forum designed to support a user community of broad interests related to mapping Aquatic Habitats.  "...this forum is designed to foster a community of individuals who share a common interest (Aquatic Mapping and Monitoring) and to provide a forum for that community to discuss various aspects of the science and ask for help when needed," noted Dr. Brett Hartis, NCSU Aquatic Extension and Research Associate and moderator of the forum.  We strongly encourage anyone with an interest in aquatic mapping to sign up for the forum and subscribe to email alerts for Topics that interest you.* BioBase experts from Navico will weigh in occasionally with posts that will support and benefit the broad community of users.


Go to http://aquaticmapping.prophpbb.com/  and sign up for a free account.  To subscribe to Topics, click on a Topic and scroll down to the footer.  Click "Subscribe Forum".  The text will then switch to "Unsubscribe forum" which will indicate you are subscribed to get email alerts each time someone posts.

Wednesday, September 3, 2014

Know more about how BioBase works: Operator Guide Updated

How far apart should I space my mapping transects?  How do I delete data? What does "point" and "grid" mean in reports and data exports?  Answers to all these questions and many more can be found in the full BioBase Operator's Guide in the Support & Resources section in your BioBase account.


The Operator's Guide was recently updated with descriptions of new features and includes more detail about how to optimize BioBase outputs, system specifications, and various how-to descriptions.  To ensure you get the best possible outputs in BioBase, we recommend giving this guide a full read prior to implementing surveys.

Tuesday, August 12, 2014

"Back from the Brink" - Around we go

The Aquatic Ecosystem Restoration Foundation provides a critique of the investigation into the fall and rise of fish populations in a Northern Wisconsin lake (Ellwood), and the potential links with an invasive aquatic plant (Eurasian watermilfoil) and a common aquatic herbicide (2,4-D).  See the original news story here.  It's an ongoing saga that we originally commented on in an earlier post

We believe with more rigorous habitat mapping and monitoring, this story (and future ones) will become less interesting because entertaining anecdotes will be replaced with good objective and quantitative data.

Thursday, July 3, 2014

BioBase HMTL5 Adds Tablet Compatibility!


Use BioBase on your iPad in the field!

We’re excited to announce the release of a non-Silverlight, HTML5 viewer to BioBase users.  You can now use the new HTML5 view by clicking the recently added BETA View trip viewer.  BioBase output and maps can now be analyzed and reviewed on computers, mobile phones, and tablets.**


The upgrade will allow users to access BioBase map layers and data on tablets from their research boats.*  By enabling location services, BioBase users can lay their current location over the BioBase map. 

Silverlight view will still be available.  Significantly expanding access to BioBase, the service’s new HTML5 architecture creates new and convenient ways for fisheries biologists, aquatic researchers, pond managers, aquatic invasive species managers and others to access detailed reports and maps to track water depths, vegetation-abundance changes, bottom hardness and many other critical factors that help them manage water quality and habitats from the field.

*Mobile tablet use depends on availability of a wi-fi signal

**The GIS polygon management feature will still require a Silverlight viewer on a Mac or PC. More information here:
[GIS Polygon Management Blog]

Wednesday, July 2, 2014

New Lowrance Elite Software Version

Navico, Inc has recently released a new software version for Lowrance Elite units that fixes many of the issues associated with BioBase mapping.  Lowrance Elite HDI units are compatible with BioBase for, among other things, aquatic vegetation abundance mapping, lake management, fisheries research, and water volume calculations.

The new version for your Elite HDI unit can be downloaded here:


Please contact us through ciBioBase.com with questions.

Tuesday, July 1, 2014

BioBase In The News: Aquatic Habitat Mapping "Off-the-Shelf"


From the Peninsula Clarion in Alaska published on 6/19/2014.  Story by U.S. Fish and Wildlife Ecologist Mark Laker with the Kenai National Wildlife Refuge.

Kenai, USFWS, Aquatic Vegetation, BioBase, Lowrance

"Since I was a little boy, I’ve been interested in exploring the underwater world. My favorite TV show was the Undersea World of Jacques Cousteau. Though our lakes don’t offer quite the array of colors and charismatic species as a coral reef, they can be rich and interesting environments to explore. Just like on land, the richness of aquatic species is associated with habit availability and quality.

For me, the ideal method to explore the underwater world is putting on my mask, fins, and snorkel or SCUBA gear and jumping in the water. On a small scale this works, but for large area, we need other methods. Our current project exploring aquatic habitat involves the elodea infestation in Stormy, Daniels, and Beck Lakes. Elodea is a nasty aquatic invasive plant that has the potential to displace native plant species and choke off waterways.

We have conducted numerous “rake surveys” to determine the presence of elodea on the Kenai Peninsula. This involved tethering a garden rake head to a rope and dragging it across the lake bottom to sample plants. From these surveys, we learned elodea prefers shallow soft bottom areas. Therefore, we wanted to map depth, bottom hardness, and presence of vegetation across entire lakes to understand where the best elodea habitat exists.

The first step in creating our lake habitat map to collect depth data for a bathymetric map. A bathymetric map is the underwater equivalent of a topographic map with contours for depth instead of elevation. All that is needed is location and depth, and lots of it. Not long ago it was an expensive and complicated task to record GPS location and depth, and then process it into depth contours.

Researchers are constantly looking to the consumer market for readily available equipment and solutions. These are called “off-the-shelf” solutions, and can save time and money. For this project, we used the Lowrance HDS Charter/Sonar with StructureScan to measure depths and locations. The recorded data was then processed by Contour Innovations (http://www.contourinnovations.com/). This off-the-shelf solution was recommended to me by ADFG biologist Robert Massengill who was working on another eradication project for invasive northern pike in Stormy Lake.

The Lowrance HDS sonar works by emitting an ultrasonic pulse directly below the boat and receiving the echo as it bounces of the lakes bottom or vegetation. This is also referred to as a down-scanning sonar. The StructureScan operates at a higher frequency which is better for distinguishing vegetation and underwater structures. In addition to down-scanning, the StructureScan utilizes side-scanning technology. As opposed to the down-scan sonar which generates a profile or side view of the bottom, the side-scan sonar looks off to the sides to create an actual image of the bottom.

To collect the data we ran transects (spaced 100 feet apart) back and forth across the lake at a speed of about 6 mph. Typically when boating you try to avoid obstacles, but when mapping you almost intentionally run over them. On Daniels Lake we encountered some glacial erratics that were about 20 feet across – those are some big rocks! Needless to say, Daniels Lake made a few modifications to our prop.

Contour Innovations offers two services: LakeTrax for anglers, and ciBioBase for research. Before acquiring the research version, I experimented with the LakeTrax service by mapping the outlet of Tustumena Lake down to the boat launch. Anyone who has navigated that stretch of water knows there are some nice boulders covered with aluminum strips just upstream of the launch. With just a few hours of mapping, I was able to create a nice bathymetric map and identify hazards. You can save maps back on your Lowrance HDS unit, and in the future avoid leaving any trace of your boat on the rocks.

Beyond lake depth and obstacles, we also needed information about vegetation and the bottom substrate to understand elodea habitat. Therefore, our lake data (called sonar logs) were processed by the research service, ciBioBase, to produce three layers: depth, bottom hardness, and percent vegetation biomass. Bottom hardness is calculated by how well the sound signal is reflected off the lake bottom. Harder surfaces reflect well and soft surfaces tend to absorb sound. Percent vegetation biomass is simply the percent of the water column that is occupied by vegetation (plant height divided by water depth).

From the new data layers we will produce a map identifying areas of the lake with suitable habitat for elodea. These will be important for both treatment and monitoring efforts. Though I’ll still need to put on my mask and fins to see for myself what’s really under the water."

To learn more about how Mark created these map outputs contact Navico at info.biobase@navico.com.  Navico, Inc. now owns Contour Innovations and the BioBase and LakeTrax (branded as Insight Genesis) mapping technology

Thursday, June 5, 2014

Delineating Invasive Plant Beds the Easy Way

Effective management of invasive aquatic plants requires some fundamental but previously difficult prerequisites.  First, you have to find the infestations; not easy when you can't see underwater.  Second, you have to create boundaries of the infestation; also not easy when you can't see underwater or when the plant does not behave and form perfect surface-growing patches that you can trace with your GPS.  So it used to be a game of darts using whatever tools available (e.g. rakes, manual interpretation of GPS and sonar, aquascopes, snorkeling, scribbling on paper maps) to crudely estimate the extent of invasive plant growth.  Needless to say, delineations using this technique have been crude leading to equally crude and often ineffective management.

We demonstrated one example of the differences between manual delineations of the invasive curly-leaf pondweed and more precise delineations using Lowrance HDS and BioBase automated processing.  The results are telling!

Thrid party manual delineation of the early growth stages of the invasive aquatic plant curly-leaf pondweed Potamogeton crispus (with other minor species mixed in) in a Minnesota Lake.  Delineated boundaries were presumably a result of manual interpretation of sonar and GPS.

Actual extent of vegetation growth using Lowrance and processed/mapped with BioBase to verify third party manual delineations.  Heat of colors represents percent of the water column occupied with vegetation (Biovolume).  Red represents vegetation that is close to the surface, green represents vegetation that is low-growing.  Red lines represent the boat path and source of data in the heat map.
Delineation of vegetation beds using the polygon tool in BioBase.  Estimates of the bed were conservative since care was taken to not include delineations outside of the track (extrapolation) because no data were available for growth very close to shore.  If these data were available and added to the map (manual veg coordinate feature). delineations would've been even more precise.
Shocking difference between manually delineated invasive plant beds and through the more repeatable and objective aid of BioBase.  The difference carries potentially large consequences on water volumes, herbicide volume and prescriptions, and efficacy.


Given all the economic, environmental, political, and public-relation risks of imprecise invasive aquatic plant management, can the interests of the public trust afford shotgun approaches?  Many of our BioBase users like Restorative Lake Sciences don't think so and can tell you about their experiences.  Share with us how BioBase is helping you make more informed and precise lake management decisions!

Thursday, April 24, 2014

ECU Research on Lowrance/BioBase Effectiveness for Seagrass Mapping

Read about exciting new research by Dr. Joe Luczkovich's lab at East Carolina University demonstrating rapid, precise and cost-effective acoustic techniques for mapping seagrass habitats in North Carolina USA's Coastal Estuaries.  Dr. Luczkovich and undergraduate research assistant Audrey Pleva talk about the very high accuracy of Lowrance HDS and BioBase for seagrass in shallow areas of Jarrett Bay, Blount's Bay, and Currituck Sound compared with underwater videography

Below is the abstract from: Audrey Pleva and Joseph Luczkovich.  2013. Effects of salinity on submerged aquatic vegetation’s growth and abundance in North Carolina and assessment of a SONAR’s accuracy to measure vegetation. Unpublished report, Department of Biology,  Institute for Coastal Science and Policy, East Carolina University, Greenville, NC 27858.  Contact Dr. Luczkovich if you have questions or would like a copy of the report.  Contact Navico to get updated (cheaper) pricing from what is cited in the report and to get you started assessing seagrass habitats with Lowrance/Simrad and BioBase!

ABSTRACT
 Submerged aquatic vegetation (SAV) is one of the most important estuarine habitats supporting commercially and recreationally important fishes and invertebrates, providing species food and shelter from predation. Salinity levels, an important factor in SAV growth and survival, are rising in North Carolina due to sea level rise bringing salty water from the Atlantic Ocean into NC, posing a threat to freshwater species. SAV species adapted to a certain salinity level are stressed by long and short term changes in salinity, resulting in patchy or smaller beds. In this project, a recently developed survey technique based on a combined video and echosounder system was used to measure the SAV % cover at three sites, each with different long-term and short-term salinity levels. Our hypothesis was that large short-term changes in salinity would be a stressor for SAV, and that as the range in salinity and the average long-term salinity increased, SAV % cover would decrease. We measured changes in water quality including salinity, temperature, and dissolved oxygen, and SAV cover using boat-based SONAR techniques at Jarrett Bay (JBS), Blount’s Bay (BLB), and Currituck Sound (CTS) in North Carolina during the beginning of the growth season where salinity is a very important growth factor. SONAR data were collected along 30 transects at 10-m intervals across the study area at JBS and BLB, but 60 transects at 25-m intervals at CTS. The accuracy of the SONAR technique was assessed using underwater video at 100 randomly selected points along transects at each site. Accuracy was very high (87.8 %) and relatively equal between all three sites. The salinities and % cover were highly variable among sites, in both the short- and long-term measurements, allowing for an analysis of the relationship between SAV and salinity. Overall mean long-term salinity was negatively correlated (r = -0.7) with SAV percent cover. Short-term salinity increases may cause declines in SAV cover, as freshwater species are displaced by salinity-tolerant SAV species.

Example image of seagrass abundance (% of water column with vegetation) in Currituck Sound, North Carolina.  200 khz Sonar image from Lowrance HDS (right) is coupled and synced with kriging interpolated map of vegetation abundance (left).  Areas of red are where vegetation is growing to or near the surface.  Areas of blue are bare.  Green and yellow is lower lying vegetation.  Datasets are summarized in BioBase with several analytic tools, but spatial data can also be exported for analysis in any third party GIS or statistical analysis platform.
See an online pdf of a presentation recently given by Dr. Luczkovich describing some of these results.

Friday, April 18, 2014

Innovations in Storm Pond Assessment and Tracking: Minnesota Demo

Be prepared for new Municipal Separate Storm Sewer System (MS4) rules with cost-effective solutions for inventorying the compliance of all of your stormwater basins.

When: Friday May 2nd, 2014

Where: A stormwater pond site in Roseville, MN (contact Ray Valley for details)

Attendees will learn about innovations to help them rapidly:
  • COLLECTPlatypus LLC will demonstrate bottom depth and composition data collection with Lowrance depth sounders and chartplotters on autonomous boats on a Roseville, MN Stormwater Basin.
  • PROCESS – Navico, Inc., makers of Lowrance and BioBase will demonstrate automated data processing and GIS map creation of collected bathymetric data.
  • TRACK – Flatrock Geographics, Makers of PondTrack (*new*) and MapFeeder will demonstrate cloud-based inventory and data management tools.

Reps from all companies will discuss individual and bundling pricing options. Please contact Ray Valley (651-303-5265 ray.valley@navico.com) to reserve a space. Registration is free but space is limited!



Tuesday, March 25, 2014

Composition Algorithm Improved!

The centralized nature of BioBase cloud technologies coupled with sophisticated, yet low-cost consumer electronics like Lowrance or Simrad depth sounders/chartplotters have created fertile grounds for developing, testing, and verifying algorithms for typing aquatic environments.  The more users upload from a greater range of systems, the more refined algorithms can become addressing a wider range of conditions and use cases!

Early in 2014, we released a revision to our bottom composition (hardness) algorithm that is more sensitive and robust in a greater range of depths and bottom conditions.  Many outside researchers were involved with collecting important "ground truth" information while they logged their BioBase data.  This blog not only serves to describe the new Bottom Composition algorithm, but also publish the results and acknowledge the scientists that helped with this effort.

How it works and the outputs produced 
The Composition algorithm processes the 200 kHz Broadband downlooking signal and produces a data point for GPS signals (Typically 1 pt every 1-2 seconds). Algorithms estimate the acoustic reflectivity of the bottom. Signals bounce more on a hard bottom than a soft bottom where signal is absorbed. Hardness ratings are consistent across all mapped systems and not relative to a trip (e.g., a trip with muck and silt will show all light tan colors). GPS point data along tracks are sent to an interpolation (kriging) algorithm to predict hardness between sampled areas and create a uniform map

Figure 1. Continuous, unitless data are created with each GPS coordinate to reflect relative hardness from soft 0-0.25 (light tan), to medium 0.25 – 0.4 to hard 0.4 – 0.5 (dark red).
How does it compare with actual data?  Verification results from independent researchers
Unlike conventional models or software programs that use limited datasets in a narrow range of conditions to calibrate and verify model outputs, BioBase is able to draw from our central database and network of professionals using the system to develop new or improved algorithms.

For revisions to the composition algorithm, Navico technical staff worked with scientists from the University of Florida (Mark Hoyer), USGS in Little Rock AR and Reston VA and  (Drs. Reed Green, Nancy Rybicki and Elizabeth Striano), and across the pond with the Center for Ecology and Hydrology (Drs. Ian Winfield, Helen Miller, and Joey van Rijn) evaluating the agreement of their independently collected bottom composition data with companion BioBase hardness datasets.  Despite field error in the precise estimation of actual hardness and overlap with simultaneously collected BioBase data, we were encouraged by the high agreement of compared data sets.  See for yourself below!
Figure 2.  Sediment depth measured by a coring device as it relates to simultaneously collected Lowrance acoustic data which was processed for bottom hardness with BioBase.  Data were collected in Lochloosa Lake, Alchua Co. Florida USA by Mark Hoyer; Director of Florida Lakewatch at University of Florida - Gainsville.  Seventeen sites were also sampled in Lake Sampson (Bradford Co., FL).  Sediment thickness at those sites only averaged one inch.  All companion BioBase composition data indicated hard substrates, and thus complete agreement.  Lastly, in Newnan's Lake (Alachua Co. FL) fewer agreements between sediment thickness and BioBase composition were found due to the acoustically reflective organic peat substrates in the lake.
Figure 3. Sediment depth measured by a 3/4 inch all thread pipe pushed to the "point of refusal" as it relates to simultaneously collected Lowrance acoustic data which was processed for bottom hardness with BioBase.  Data were collected in Millwood Lake, Ashdown Co., Arkansas USA by Dr. Reed Green USGS Arkansas Water Science Center.  Publication of sediment depth patterns on Millwood can be found at: Richards, J.M., and Green, W.R., 2013, Bathymetric map, area/capacity table, and sediment volume estimate for Millwood Lake near Ashdown, Arkansas, 2013: U.S. Geological Survey Scientific Investigations Map 3282, 1 sheet,http://dx.doi.org/10.3133/sim3282.
Table 1. Agreement between visually estimated substrate hardness while collecting Lowrance/BioBase composition data from 9 of 23 samples in coastal Back Bay, Virginia Beach VA, USA in 2012.  BioBase composition data at the remaining 13 sites were not generated due to depth or vegetation thresholds.  Bottoms cannot be typed where vegetation fills > 60% of the water column or in depths less than 2.4 feet from the transducer face.  Data were collected by Dr Nancy Rybicki and Elizabeth Striano, USGS - Reston VA as a component of a vegetation assessment study.

Figure 4A.  Hardness data from Windermere (Cumbria, England) as scored by visual estimation from underwater imagery as it relates to hardness from Lowrance and BioBase.  Data were collected in 2012 by Dr. Ian Winfield and Joey van Rijn and described in a previous blog post.  The biological context and other companion composition data are presented in Miller et al. 2014.

Figure 4B.  Bottom substrate (and Northern Pike) as viewed from a camera mounted on a Remote Operated Vehicle (ROV) in Windermere.  See Figure 5A for the Hardness Score and Corresponding BioBase Hardness data
Create your own sediment thickness models
The BioBase composition algorithm will not predict sediment depth, only whether the bottom is hard or soft based on the "echo" of the acoustic signal.  Still, what we show in Figures 2 and 3 are that sediment depth may correspond predictably with bottom hardness as estimated by BioBase.  The primary benefit of BioBase is to provide a full-system understanding of where hard and soft areas exist (Figure 5).  Investigators can follow up with a couple of dozen coring points in areas of interest (e.g., sedimentation deltas) to develop system-specific relationships like those in Figures 2 and 3.  The paradigm shift that BioBase has brought is a new way to focus more detailed sediment depth sampling, rather than using a coring probe as the sole mapping tool.

Figure 5.  Full system map of bottom composition.  Data were exported from a fully interactive free demo account.  Log in and view trips and data and how they correspond to the sonar log.

Monday, February 10, 2014

Navico Acquires Contour Innovations

We commonly post blog content and send email notifications to our BioBase users about exciting new features and BioBase additions.  We’re continuing that trend! 

We are pleased to announce that Contour Innovations, LLC and its product platform has been acquired by Navico Holding AS, parent company to, among others, the Lowrance marine electronics brand.  Contour Innovations has been working very closely with Navico and Lowrance specifically since 2010 when we started developing software that accepted .SLG and .SL2 log files to bring you revolutionary cloud based software products like BioBase and LakeTrax.  This is an extremely exciting announcement for us and as a team we look forward to bringing new features and integrations for BioBase to market faster while focusing on delivering the most innovative and easy to use products for the aquatic plant management community.


Not only will BioBase continue to operate, it will get even better.  Navico plans to expand investment in new features and functions that will allow the platform to continue to provide the tools and support that you’ve come to expect.   Now it will be even easier for us to deliver continued bundle access to Lowrance hardware with the latest software and features.  Navico has plans to add BioBase to its diverse product portfolio and introduce its advanced functionality into new and emerging markets.

We want to confirm that you will still be able to contact Ray, Myself and all of our GIS and quality control support and resource staff.   We’ll still be in the same office in Minneapolis where we have operated since 2011.  All general questions can be directed to email@contourinnovations.com, support@contourinnovations.com, or Ray and myself directly (most of you have our direct cell phone numbers).  Our office line is still a great resource at 651.204.0640. 

We’re excited about this news and look forward to what’s ahead for BioBase, Navico, the Contour Innovations team, the aquatics industry, and most importantly all of you!

Contour Innovations operated with a long term vision for lake management and water quality.  Navico shares this vision!

Please contact us with any questions.

Matt Johnson
715.864.9347
New Director of Business Development for Navico, Inc.