Thursday, December 10, 2015

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.

Effects of chemicals in aquaria? Very predictable -- Effects in lakes? Much more complicated

Advancements in chemical engineering and results from controlled experiments have resulted in a large number of selective aquatic pesticides with predictable effects in controlled environments.  However, conditions in the field are rarely controlled. So in the past, success hinged on the intuition and experience of a grizzled aquatic weed applicator or fisheries manager using low-tech strategies not dissimilar to "winging-it." 

A common technique for successful rotenone applications is to first draw down a lake's water level in order to concentrate both the pesticide and the fish species you're targeting.
Still, past chemical-application failures -- whether real or perceived -- have put chemical control of aquatic species under an intense microscope by both the public and regulators, so the stakes were high for Schuckman, both environmentally and economically.

"Rotenone runs $50-86 a gallon and we estimated that we needed several hundreds of gallons for Yankton," he explains. "We had to be precise." 

Precise treatment prescriptions require a detailed lake map
One key to successful pesticide application is achieving the correct concentration of chemical in the water.  Because most riverine backwater lakes are not simple bowls that never change, Schuckman was not confident in the accuracy of his early-1980's era, hand-drawn Lake Yankton contour map (Figure 1, below). Successful pesticide application, he knew, would require both speed and accuracy. Unfortunately, he didn't have the time or budget to wait for a dedicated hydrographic survey crew. Thankfully, a colleague soon explained to him how he could use a Lowrance fish finder/GPS to create lake maps automatically.

Figure 1.  Original 1980 hand-drawn contour map of Lake Yankton on the border of Nebraska and South Dakota. Depths are in meters.  Basing fisheries-management decisions on maps like this is still common throughout the U.S. (but changing, thanks to easy and affordable sonar/GPS units like Lowrance and automated mapping with BioBase EcoSound).
The Technique
Schuckman signed up for BioBase, updated his Lowrance HDS-5, popped in a SD card, hit "Record Sonar" and began motoring back and forth, keeping his passes spaced approximately 130 ft (40 m). It took him about 11 hours to map the lake, and another hour or two processing his recorded sonar data in BioBase to create perhaps the most detailed bathymetric map of Lake Yankton on the face of the Earth (Figure 2).

Figure 2. Most accurate and precise bathymetry map of Lake Yankton on Earth created in 11 hours with Lowrance HDS and BioBase.  Data were collected by Nebraska Game and Parks fisheries biologists with no mapping experience.
Using the EcoSound offset and polygon tools, Schuckman then estimated precise water volumes in targeted areas after the lake was drawn down 3.5 feet (e.g., -3.5 ft offset). Using the polygon tool, Schuckman digitized the simulated draw-down area to estimate water volumes (Figure 3, Table 1).  
Figure 3. Polygon created in BioBase to estimate the size and volume of specific areas targeted for Rotenone application. Polygons can be exported as .shp files and converted to .gpx to view on Lowrance GPS chartplotters on treatment boats, making applications more precise.
Table.1 Cost and volume estimates based on simulated draw-down scenarios from BioBase of Lake Yankton for Rotenone applications (data courtesy Nebraska Game and Parks).

Further, Schuckman printed maps and zones for each staffer involved in the project (Figure 4).

"Detailed [depth] maps generated by the BioBase technology allowed us to simulate lake draw-down scenarios and maps for our partners, such as the U.S. Army Corps of Engineers, U.S. Fish and Wildlife Service, and South Dakota Game Fish and Parks," he says. "This allowed our partners to visualize different draw-down scenarios and [us to] convince them to cooperate with the project. We were also able to segment the lake and generate volume estimates for precise chemical application to kill the [invasive] fish."

Figure 4. BioBase map of a drawn-down Lake Yankton, complete with staff assignments for Rotenone application. (Map courtesy Nebraska Game and Parks)
The Result
In early September 2014, Schuckman (seen perhaps by his invasive fish victims as an evil Dr. Nefario) had the lake drawn down while his Minions conducted precision strikes with the toxic piscicide (Figure 5).  Shortly after the treatments, all the rough fish were dead and quickly became food for scavengers or decomposed and returned to the Earth (Figures 6 and 7).

Yankton Daily Press & Dakotan
Figure 5. Fisheries staff donned in Personal Protective suits while applying precise quantities of rotenone to treatment areas on Lake Yankton (Disclosure: in the above photo staff are rinsing the barrels after the treatments were done.  Actual treatments took place from sprayers on airboats or drip stations). Photo credit: Yankton Daily Press & Dakotan

Figure 6.  Common carp and other rough fish killed by rotenone treatments on Lake Yankton in September 2014
Figure 6.  Fisheries staff proudly displaying trophy kills of invasive Big Head Carp.  These invasive fish were eradicated shortly after the Rotenone application to Lake Yankton
The success of the project is chronicled in the Yankton Daily Press and Dakotan (Search "Lake Yankton Renovation"), with the capstone story one year later celebrating the amazing recovery of the lake. Stocked largemouth bass, bluegill, walleye, black crappie and catfish have now replaced the carp, which Schuckman believes were completely wiped out by the treatments. Further, clarity in Lake Yankton increased 24-fold, going from three to six inches before renovation to over eight feet a year after renovation. Abundant aquatic plants are now  providing sustainable habitat and food sources for fish and waterfowl.

“It’s like a brand new lake," Schuckman says of the Lake Yankton renovation. "[In 2016], anglers will be harvesting two-year-old bluegill that have already spawned and will be over eight inches”

The Upshot: Employee of the Year!
The success of the Lake Yankton project proved to be one of Schuckman's biggest career achievements -- the director of The Nebraska Game and Parks Dept. awarded him a prestigious Employee of the Year award in November 2015. Schuckman, in turn, extended ample praise for the cooperation of partners, stakeholders, competent staff, and technology that allowed him to focus on more important details.

"BioBase mapping took all the guesswork out of this project and allowed us to make good, precise plans to undertake a very successful project," Schuckman says.
When he's not standing sentinel over Nebraska's Sandhill Lakes, you may find Jeff Schuckman chasing both small and large game throughout the Rockies and plains of the Midwest (Antelope from Wyoming shown here) 

Monday, November 30, 2015

Using Insight Map Creator to view Photos and BioBase maps on your Lowrance Chart

Few may know about a powerful GIS conversion tool that will convert virtually any spatial file into a format (.AT5) viewable on your Lowrance Chartplotter.  And best of all, it's free!  Insight Map Creator is one of several of Navico's GoFree products available at Here you can register for a free GoFree account and download the IMC software.  There are lots of examples and tutorials about how to convert vector and raster GIS data to .AT5 digital charts that are covered in the documentation folder that won't be repeated here.  Rather, we'll walk you through two applications that many BioBase users will find extremely valuable.

Display HD ArcMap Aerial Imagery GeoTiffs on your Lowrance HDS chart

Add Basemap Imagery and zoom into a high resolution (in this case 1:15,000) area of interest so that shoreline detail can be seen (e.g., think about the zoom level you want when using the chart on the water).  Project Dataframe into WGS84 World Coordinates.
In the Data View, export (File - Export) a high res (≥ 300 dpi) image as .TIF and write a .TFW world file.  Pan the map and export slightly overlapping snapshots (same zoomlevel and resolution) so that IMC can stitch together a mosaic.  Small ponds and lakes will probably require only one aerial shot, large systems like the Guntersville example shown will require many.

Simple User Interface of GoFree's Insight Map Creator (IMC).  Run the x64 .exe program after downloading and unzipping. Select Raster Mode from the View menu.  Use a fine resolution (at least 1 meter per pixel) to get shoreline detail. If your source data only covers one resolution and you want your final map to represent this specific resolution, you have to set Min and Max resolution to the same value. If your source data covers more than one resolution, you set the Min Resolution to the resolutions of your most detailed images and the Max Resolution to your least detailed image. Make sure that your source images match the resolution steps as close as possible to minimize the loss of quality due to the re-sampling process.  Add the folder where the source files can be found, specify where the created AT5 files should go, then click "Build."  A successful build should show a folder containing "Bound AT5s." Consult the documentation with your download for more specific details about the process and other advanced settings.
Get your HDS Chartplotter ready to import AT5 imagery

  1. Make sure your Chart has "Shaded Relief" selected (Chart Options on Lowrance HDS)

     2.   Insert a MicroSD card with all .AT5 files saved to the card.  Select Photo Overlay (Full) in the Chart Options

Screen capture of a successfully loaded HD aerial image overlain with other navigational aids included in HDS basemaps.  Use aerial images as navigational aids, and to target fishing or sampling areas (e.g., partially submerged timber, or in the top example "Guntersville Grass")
Create a HD image of vegetation biovolume coupled with an aerial photo.

The process we describe can be used to create any spatial image for your HDS.  So, if you wish to reproduce the HD map you see on your PC in BioBase as a chart in your Lowrance, just follow the steps outlined in your Support & Resources in your BioBase account (Creating Publication Quality Imagery) and the steps outlined above.
EcoSound Aquatic Vegetation heat map (% aquatic plant biovolume) as seen in BioBase.
Aquatic vegetation heatmap data exported from BioBase, imported into ArcMap and converted to a raster .TIF following "Creating Publishable Quality Imagery" BioBase tutorial and then converting the exported .TIF to .AT5 using GoFree's free Insight Map Creator (see directions above).  Researchers or anglers can use these vegetation maps to strategically target sampling or fishing areas.

Tuesday, November 24, 2015

BioBase Helps Manage Honeoye Lake Macrophyte Harvesting Program

Guest Blog By Terry R. Gronwall, Chairman of the Honeoye Lake Watershed Task Force (Honeoye, NY)
Honeoye Lake is one of the smaller (~1,800 acres) Finger Lakes in Upstate New York.  We have been managing our macrophyte population by using a harvester for about 25 years.  The objective of our harvesting program is to both provide relief for the recreational lake users and to remove biomass containing phosphorus from the lake every summer.  We average around 800 wet tons of biomass removed per season.

When we learned about ciBiobase we saw this service as a way to make our macrophyte harvesting operation more efficient by concentrating our efforts on areas in the lake that have macrophytes growing through most of the water column.  This is shown as the red zone on our macrophyte maps.  We plan to monitor our actual harvesting rates relative to our macrophyte maps over the summer harvesting season to see if we achieve our goal of increased productivity.

Aquatic plant harvester in operation on Honeoye Lake in the Finger Lake District of New York.

Aquatic plant biovolume heat maps created via automated cloud-based processing with BioBase.  Citizens passively recorded sonar and gps data to a Lowrance Elite 7 HDI on Honeoye Lake.  Multiple files were uploaded from a SD card in the unit to BioBase and merged to create the uniform maps displayed above.
Tri-panel image showing transect coverage (left) and resultant bathymetric map (middle) and bottom hardness maps (right) produced simultaneously along with vegetation maps in BioBase 

Our 2014 pilot ciBioBase program is being funded by an Ontario County Water Resources Council Grant.

Thursday, September 10, 2015

BioBase 3 Step Process: Important Details!

A primary strength of BioBase EcoSound is its simplicity and that is reflected in the easy 3 step process of "Collect," "Upload," and "Analyze" (Figure 1).
Figure 1. The core process of EcoSound depicting the 3 Steps of "Collect," "Upload," and "Analyze."
But there are many strategies that users can employ that will ensure that they will get the best EcoSound outputs possible.  We'll focus on several questions under each of the three categories


What is collected?
BioBase EcoSound analyzes the downlooking 200 kHz broadband frequency from any Lowrance, Simrad, or B&G sonar/gps chartplotter capable of recording files as .slg, .sl2, or .sl3 to high capacity storage media (e.g., SD, MicroSD).  Each of the 10-20 acoustic signals per second has detailed information about the depth (depth to the top of the substrate), bottom hardness, and the height of aquatic vegetation canopies if present.

How do you collect data?
After you open your BioBase account, go to the Support and Resources page and print off the quick start guide for your unit (Note: Elite Ti users should reference the HDS quick start guide).  These guides gives you important instructions about setting configurations and how to record your data.

Choose the hardware, watercraft, and mount that will best suit your needs.  You will get the most consistent and clearest signal from a fixed transducer mount either on the transom or through the transducer hull.  Take careful measure to ensure the proper transducer angle and to minimize the creation of cavitation (air bubbles) near the transducer face.  Your unit will come with a detailed transducer installation guide - read it and follow it carefully!  Cavitation can create false vegetation detects or missed bottom detects and greatly affect the speed at which you are able to map.  Click here to learn more about transducer selection and installation.

Once you have a good understanding of how to mount your transducer, you have a range of portable options available if you need to either get into small water bodies or transfer the equipment to multiple vessels.  This post has a great gallery of photos from the BioBase mapping community demonstrating a range of portable options.   With any mount, ensure that the GPS position is very near the transducer such that X,Y, and Z positions are all aligned.  For console-steer boats, consider a Point-1 GPS external antenna.  Learn more about GPS here.

How far apart do I space my transects?
Using geostatistics, EcoSound creates bathymetric, aquatic vegetation, and bottom hardness digital models with point data much like how land topography is mapped (e.g., "Digital Elevation Models" or DEM's; Figure 2)
Figure 2.  Schematic simulating the actual bottom area quantified by a 20-deg Lowrance Transducer (model HST-WSBL - white box) and 6-deg Airmar Transducer (model TM-260 yellow box).  At 5 ft, the 20-deg transducer insonifies a 1.76 ft area, whereas the 6-deg insonifies only a 0.5 ft area,  Given the rapid ping rates, most applications will have very high overlap of adjacent pings and thus be quantifying the entire bottom directly under the mapping vessel.
Once you understand where actual measurements are being recorded, you can make an informed judgement on the appropriate level of bottom "sampling" with transects.  As with any kind of sampling, the appropriate level of sampling depends greatly on the study or management objectives. Users might be able to use painting as a useful analogy for a starting place to guide transect spacing decisions.  For instance, if you are painting a large flat wall, you use a large roller and your objective is to get the best coverage as fast as possible.  Similarly, if you are mapping a large lake or bay with gently changing bottom features, you can space transects relatively wide (e.g., 100-300 m) and drive a modest speed (e.g., 8 mph or 12 km/h) if you have a good install with your transducer.  In contrast, if you are painting an ornate cabinet with detailed carvings, then you have to use a small brush and spend a lot of time getting that small brush into all cracks and crevices.  Same goes with a highly complex lake or reef bottom.  In these cases, close transects (e.g., 5-m) with a narrow beam transducer, and slow speed (2 mph or 3 km/h) might be called for.  Our Transect Design Blog goes into these issues in more detail.

Log Sonar while doing other activities
Running BioBase EcoSound surveys does not need to be a dedicated activity that you now have to layer onto your other obligations.  Rather, EcoSound is a tool for passive data capture during activities you are already on the lake conducting.  For instance, biologists are on lakes and bays everyday throughout the globe bouncing spot to spot taking samples of aquatic plants.  Most have a gps and sonar on their boat to find where they are going.  EcoSound allows them to be recording and capturing detailed spatial information about exactly how much plants are growing not only at their sampling spot, but between sampling location.  Many Aquatic Plant Biologists using EcoSound for the first time are shocked by what they missed with their original surveys.  This analysis provides possibly the most eye opening example of how spatially dynamic aquatic plant growth is in glacial lakes.

The second example is sampling fish with electrofishing.  Habitat degradation is often cited as one of the primary causes of global fisheries declines, yet rarely are habitat data collected in conjunction with fisheries data.  Recently, Lowrance and BioBase teamed up with the global leader in Electrofishing Smith-Root to demonstrate how Fisheries biologist can integrate Lowrance HDS into their electrofishing boat and collect important fish habitat data while electrofishing (Figure 3).  BioBase EcoSound allows you to simultaneously collect both fish and habitat data, thus leading to better informed Fisheries Management decisions.  Read more about this partnership here.
Figure 3. Integrate Lowrance HDS into your Electrofishing Boat to monitor boat function, view structure real-time, and record important fish habitat data.  Inquire with Smith-Root about how to retrofit old boats or outfit new ones.

Cloud-computing has quickly become the new standard for managing large datasets.  Remote servers and databases are better able to manage the large data-rich .sl2 files than most desktop programs and external storage media.  Use our desktop upload tool to select your .sl2 file from your card and upload.  After your upload is complete, the file hits one of our dozens of servers that goes to work analyzing every signal.  Our algorithms perform many automated tasks including:

Data Cleansing
Signal quality is reviewed for every signal.  Those not passing certain tests, are discarded (at 10-20 data points per second, you can afford to discard some bad ones).  These tests include whether the operator was going too fast (e.g., 20 mph for depth, 12 mph for vegetation, 10 mph for composition), whether the signal was too noisy, or whether depth was lost for some reason.  Bad soundings are removed automatically.

Feature Extraction
With 10-20 data points per second, aggregation is necessary to create manageable outputs that aren't "too busy."  Therefore, EcoSound algorithms create georeferenced data "points" that represent averaged areas (see Figure 2).  These X,Y,Z points can be exported from BioBase and imported into GIS for important exploratory analyses (e.g., to understand data coverage and spacing of attribute points) or statistical analysis (e.g., statistics from transect studies).  Most other hydroacoustic processing software stops here.  BioBase takes it one step further and creates robust geostatistical maps.

Geostatistical Interpolation
Finally, once the coordinate points are created for all layers, the points are sent to a generic kriging algorithm that uses geostatistical models to make predictions of depth, vegetation, and bottom hardness in areas not sampled.  Kriging creates a uniform grid (grid cell size is user configured and 5 times less than the track buffer) for each EcoSound layer.  Redundant point data while idling gets averaged into one grid cell value.  By knowing the value of neighbor points, kriging can predict the value in an unsampled location.  Read more here...

Quality Control with Real People!
Although automation has led to huge productivity gains in the last century, quality control by humans is a critical component to a full solution.  Accordingly, BioBase Quality Control Engineer staff review every uploaded sonar log and review the quality.  Staff ensure the signal looks clear, that the output is free of evidence of improper installation (e.g., slanted transducer, Figure 4), and that the digital shoreline (lake polygon shapefile) aligns with the Bing aerial imagery and has sufficient zero values along shore such that contours do not intersect shore.  In general, QC staff will review your trip and make adjustments to sensitivity or shorelines within 24 business hours of your upload.  Maps should be considered "provisional" prior to QC review.  After QC staff check off, users can do their own QC checks prior to analyzing the map data in depth.

Figure 4.  Sample output with a improperly installed transducer that would be flagged by BioBase's Quality Control Team.  QC Staff check every file and will alert you to verify the output and possibly make corrections.

Trip Replay
After you receive an email informing you that your trip is ready for viewing and QC have completed their review, you can replay your sonar log synced with your track and interpolated map and accompanying data.  You can add or delete data by clicking on areas on the map, on the sonar log, or in the data table below the map and choosing delete.

Polygon Tool
Digitize an area of interest such as a bed of an invasive aquatic plant species.  The EcoSound polygon tool will use the polygon like a cookie-cutter and clip the statistics for just your specific area.  Further, BioBase has a partnership with United Phosphorus Inc. to help aquatic plant managers create precise herbicide treatments with their polygons using the UPI Treatment Tool. Finally, these polygons can be exported as shapefiles and converted to .gpx for viewing on your Lowrance Chartplotter.  This feature enhances precision of aquatic plant management and dredging activities.

Data Offset
Gain accuracy in water elevations by using the offset tool to correct for your transducer depth or create a map with a benchmark elevation as discussed in this blog.  If you are working in a coastal area with tide stations, your trip will be automatically offset to Mean Lower Low Water (MLLW) every 5 minutes as described here.

Trip Reprocessing
If you make edits to your map or want to fill in gaps in your map with a buffer, you'll need to send the trip back to the BioBase servers to update the map and datasets.  You can increase map detail by decreasing the buffer, with a minimum buffer of 5-m and 1-m grid cell resolution.  You can fill in gaps and create a generalized map by increasing the buffer.

Merge Trips
With multiple-use subscriptions or special single-lake subscriptions, you can combine files from anyone using a Lowrance HDS or Elite HDI/Chirp to slowly build the best map ever created.  One amazing example is the effort put forth by citizens on Ten Mile Lake in Northern Minnesota simply by passively recording their sonar while they were out boating or fishing during a 2 year span.  Most commonly, BioBase users use the merge function to combine multiple smaller sized files into a larger aggregate for an entire waterbody.

Export Data
The primary strength of BioBase is its ability to rapidly process very large raw datasets and produce valuable spatial data.  As we've discussed, BioBase has many "turn-key" features that are valuable to the everyday practitioner who may not be trained in Geographic Information Systems (GIS).  However, the value of BioBase outputs increase dramatically for those who export BioBase data and run spatial analyses or create custom map layouts with BioBase and other data layers.  As ESRI Silver Partners, we support use of BioBase data layers in ESRI products like ArcMap and actually have step-by-step tutorials that will walk you through how to create GIS data layers from your BioBase outputs

Automated Reports

Another popular feature of BioBase EcoSound is that automated summary reports are produced with every upload or merge and stored on a dedicated file server for sharing with partners.  Partners just see the report and do not have access to your account.  Further, if you add waypoints to your map, they can also be shared.  For example, if I want to include a BioBase aquatic vegetation summary report in a larger .pdf report that I am sending to a client or study sponsor, I just include the link in the report and now the person with whom I am sharing has dynamic html with which they can interact and find the statistic(s) that most interest them.

These reports have many numbers and might be confusing at first, but simply hover over the question mark with your mouse, and it will tell you what the numbers mean.  Data summaries are created from the "point" data along your track and also the kriging interpolated "grid" data that is created from the point data.  If you are primarily interest in monitoring repeated transects or the max depth of vegetation growth, use the point data statistics.  If you are doing back and forth mapping (most EcoSound applications), use the grid statistics.


Thursday, July 9, 2015

CHIRP from a bottom mapping perspective

Maybe you've been hearing about this term in sonar circles called "Chirp" and noticing that most consumer sonar units now come with Chirp capability. Indeed, Chirp is a game changer for more precise definition of acoustic targets suspended from bottom (e.g., fish) and the technology is helping more anglers find fish in a wide range of aquatic environments (Figure 1).  But what does Chirp mean for mapping the bottom of waterbodies?  Does it provide any advantages or disadvantages over traditional 200 kHz frequency broadband sonar that is the foundation of Insight Genesis and BioBase
EcoSound mapping services?  Here we take a brief look at Chirp, explain what it is, and present some findings from preliminary tests in a couple of different lake environments.
Figure 1. Sample sonar screen grab from a Lowrance HDS Gen3 running high Chirp frequencies over numerous fish targets.

Compressed High Intensity Radar Pulse
Acoustic target separation is often tied to the pulse length or duration.  Longer pulses give better depth penetration, but less target separation.  For suspended targets, Chirp represents the best of both worlds by sweeping many short pulses of a range of frequencies within a relative long pulse burst.  Three Chirp ranges (Low 40-60 kHz; Medium 85-145 kHz; and High 130-210 kHz) typically accommodate most situations for locating fish targets throughout a range of depths.

Chirp Performance For Tracking Bottom in a Range of Conditions
It has been well established in recreational marine circles that Chirp is a benefit to mapping suspended targets, however differences in how bottom is declared with Chirp vs the traditional single 200 khz frequency (for which BioBase EcoSound and Insight Genesis was developed) is a question for which we recently sought an answer.

Tracking Bottom in Dense Submersed Aquatic Vegetation
Tests were conducted in Gray's Bay of Lake Minnetonka in August 2014.  Repeated transects were run over a dense bed of submersed vegetation with a Lowrance Elite 7 Chirp, and HDS Gen2 with a Chirp compatible SonarHub running both traditional 200 kHz and High Chirp frequencies.  Below is a plot showing the EcoSound depths from both the 200 kHz and High Chirp Frequencies (Figure 2).
Depth was significantly greater and was closer to truth based on sonar log verification with the traditional 200 kHz frequency than High Chirp.  However, the actual difference in depth declarations between the frequencies was only 6 inches on average.  Plant canopies apparently more quickly extinguish the Chirp signal than the 200 kHz.  Based on these findings and other tests, the 200 kHz frequency remains the recommended frequency for mapping aquatic plant dominated bottoms.
Figure 2.  Average depth declaration by BioBase over repeated transects in dense submersed vegetation (avg plant height of 3 ft) running both Chirp and 200 kHz frequencies.

Bottom Declarations Over Soft Bottoms
Frequently, we get questions regarding whether EcoSound can determine the depth of sediment.  The answer is yes, but only if the "true" bottom is known (e.g., "as built" bathymetry in a human-engineered system) or a desired bottom can be modeled (e.g. how deep does it need to be for waterway management objectives).  If a true bottom can be described, then Lowrance and EcoSound should tell you the precise depth where the water meets sediment.  Simple subtraction of map layers in ArcGIS with Spatial or 3D Analyst (Raster Calculator) will produce detailed sediment maps like produced by the Central Arizona Project.  A question that piqued our interests however, was the difference between 200 kHz and Chirp bottom declarations in relatively soft bottoms.  Because the Chirp signal appears to attenuate more quickly than 200 kHz, could Chirp be a solution for more precisely mapping the depth of the sediment water interface in softer, plant free bottoms?

The St. Johns River Water Management District at Lake Apopka FL helped address this question by sharing Chirp and 200 kHz frequency sonar logs over bare soft bottoms on Lakes Apopka and Griffen in Florida, USA.  Analysis of approximately 100 data points across both frequencies found almost no differences overall and deviated only one to three inches from true bottom determined from the sonar log (Figure 3).

Although the vast majority of user sonar logs have bottoms that are clearly defined visually and acoustically, there are some bottoms that are so soft and unconsolidated that they are source of philosophical discussions of where the "bottom" actually is.  Further research and testing is needed to determine whether Chirp can be a unique solution for better depth tracking in these and other special use cases where bottoms are highly flocculent.  The more rapid attenuation of the Chirp signal than the 200 kHz frequency in plant bottoms (which may present a similar acoustic signature to a soft bottom) suggests it could be a solution in a narrow range of use cases where the 200 kHz channel penetrates too far into the bottom.

Figure 3. Bottom depth declarations (solid line) with Chirp (Top) and 200 kHz (Bottom) over a soft bottom on Lake Apopka, Florida USA.  Although in this case, Chirp produced a slightly shallower depth (8.0 ft) than 200 kHz (8.7 ft), overall we found very small differences between frequencies in depths over moderately soft, plant-free bottoms.

Conclusion: Use 200 kHz for Mapping
EcoSound and Insight Genesis mapping algorithms were developed and optimized for the 200 kHz frequency.  Over plant-free bottoms, both 200 kHz and High Chirp should perform similarly and precisely map the sediment-open water interface.  However, in bottoms dominated by submerged vegetation, the 200 kHz frequency will produce the best depth declarations and clearest delineation of the vegetation-sediment interface.

Monday, June 15, 2015

Offset Tool and Public Water Databases to Create Accurate Depth Maps

One of the best features of BioBase EcoSound and its sister technology for anglers, Insight Genesis, is the ability to aggregate partial maps created over time into a complete map later.  The recent blog post on Ten Mile Lake in Minnesota, USA, details a notable example of the power of aggregation.  However, changing water levels over the course of time can impact the accuracy of aggregated maps if recorded water depths are not offset against a standard benchmark water elevation.

45 uploaded sonar logs; 18 feet of water level variation
Forty-five sonar logs recorded on Lake St. Croix (a wide spot on the St. Croix River in Minnesota, near Stillwater) were uploaded over the course of a year. Over that time, river levels ranged 18 feet (Figure 1). So a sonar log recorded in trip from June 2014 combined with a log from a trip in April 2015 will not produce a good map without a water-level correction. The more difficult decision facing water-resource professionals and anglers is what benchmark to use for their aggregated map.
Figure 1.Water levels from the Army Corps of Engineers Water Control District in St. Paul MN. The USACE is one of several free online sources of real-time water-level data for dammed rivers and reservoirs.
Using public databases to retrieve water level information

In the U.S., three Federal Government Agencies collect, maintain and distribute real-time water-level data for thousands of lakes, rivers and reservoirs: The U.S. Army Corps of Engineers (USACE) through its RiverGages website, the National Oceanic and Atmospheric Agency (NOAA) via the National Weather Service's National Advanced Hydrologic Prediction Service, and the U.S. Geological Survey via the National Water Information System. These databases should cover most large U.S. rivers and reservoirs.

For inland lakes, you might need to hunt a bit more for information on water levels, but Google is an amazing product and will help you determine if a state, local unit of government or water authority/district houses this information for your lake of interest.  If they do, they likely publish the data on its website. In Minnesota, for example, the State Department of Natural Resources administers a popular citizen science lake-level monitoring program and I found a 10-year hydrograph for a lake I've mapped in the past (Figure 2).  Note that despite some anomalies, water levels rarely vary more than 1 foot in this isolated headwater lake, which has a water-control structure at the outlet. So in this case, offsetting trips to lake elevation isn't hugely important.
Figure 2. Water levels from Square Lake, Washington Co. Minnesota USA from citizen collected water level gauges.
But let us return to Lake St. Croix, where offsets are important. Now we have to make a decision about what our benchmark water elevation should be against which all other trips should be adjusted. In the case with the St. Croix River, we needed a map that would be accurate at "normal" pool elevations during fishing outings in spring 2015.  As such, my partner with whom I am cooperatively mapping the river, looked at the Army Corps hydrograph and we chose a benchmark of 676 feet above sea level as our mapping benchmark.  My partner offset his May 2014 trips by -9 feet during the high-water periods on the St. Croix and documented the date, water-level during the trip, benchmark elevation, and the source of the data in the trip offset tab in EcoSound (also found in Insight Genesis; Figure 3).
Figure 3. Example offset and documentation for a high-water period on the St. Croix River near Stillwater, MN. Offsets to benchmark elevations and proper documentation are critical for accurate merges when trips are combined over periods of time when water elevations are changing. Transducer offsets can also be added if users desire to bring the water level up to the surface of the water
Figure 4, This merge consisting of 45 sonar logs (and growing) spread over a period of a year of wildly varying water levels is emerging as the most accurate and precise map of the St. Croix on the planet because careful attention was paid to offsetting every trip to a standard water-level benchmark.
Using observation and relative benchmarks for offsets

Often in rural areas, lake levels are not formally monitored and anglers and aquatic managers need different tactics to properly offset EcoSound or Insight Genesis trips.  First, users could use a physical, temporary mark (crayon?) on the dock at the launch for instance to indicate the water level during each trip and offset each trip the distance between the current trip and the chosen benchmark trip.  Alternatively, but perhaps less precisely, users could use shoreline indicators to understand the location of the lake's high water level and where the current elevation is relative to that high water mark.

How Offsets Affect Vegetation Maps in BioBase

EcoSound renders aquatic plant height as percent of the water column that is filled with vegetation (% biovolume). Plants that grow very close to the face of the transducer or to the surface of the water will show as red and register a 100% biovolume value (Figure 5a and b).
Figure 5a. Percent of water depth fill with vegetation in Gibbs Lake, Rock Co., WI, USA with no depth offset. Don't use an offset to create vegetation maps in scenarios when vegetation is actually growing to the surface.

Figure 5b.  Summary statistics from automated vegetation report
If you add a positive offset, plant height will not change, but the proportion of water volume fill of vegetation will decrease and the map will get "cooler" (Figure 6a and b). If you add a negative offset, as is typical with automated tidal offsets to Mean Lower Low Water (see 11/27/2013 blog), plant height will decrease (biovolume increase) if the offset water depth is less than the plant height. Lake Managers conducting vegetation surveys may use the offset tool strategically if plants were growing just to the transducer face but not above it. Adding the transducer-depth offset will change 100% values to more accurate sub-surface values.
Figure 6a. Same map as Figure 5a but with a 1-ft depth of transducer offset.  Use the transducer offset to characterize sub-surface vegetation growth just below the transducer
Figure 6b. Vegetation summary statistics in Figure 6a adjusted with the offset.  Notice the maxium biovolume values increase with depth but always remain lower than 100% (surface of the water).
The concept and practice of offsetting your maps with EcoSound and Insight Genesis is simple, but will make a world of difference in the quality of your maps for fishing or conservation. We hope you've found these tips useful.

Wednesday, April 15, 2015

Transect Design: Consideration of Scale

One of the most frequently asked questions by BioBase EcoSound users is, "how far apart should I space my transects for creating maps?"  Although as always, the most appropriate response is: "it depends," we still offer solutions below that cover the most common use case scenarios.  We thank our partners at NC State University Department of Crop Science for contributing useful data from Waccamaw Lake in North Carolina USA.

Full Bay/Lake Map on a Large Lake
Transects can be designed in ArcMap using the Fishnet Tool in the ArcToolbox (see BioBase Support & Resources).  In this case, 200 m transects perpendicular to the longest shore with one nearshore loop was created.  The total length of transects in this instance equaled 189 km (117 mi) and would take 23 field hrs to map driving 8 km/h (5 mph).  ESRI Shapefiles or Google Earth .kml path files can be converted to .gpx for your Lowrance Chartplotter.  Convert the Trail to a Route and let out Outboard Autopilot do the mapping for you!
Aquatic Vegetation biovolume from raw sonar data from a Lowrance HDS, processed by BioBase, and imported and converted to raster with ArcMap.  In BioBase, the map buffer around each side of 200 m transects were increased to 100 m which produced a complete map and increased the resolution of each local prediction (i.e., a grid cell) from 5-m x 5-m (default) to 25-m x 25-m.  In this case, a coarse-resolution full lake map was the objective for more precise targeting of follow up surveys.
Follow up, intensive surveys in areas of interest
Zoomed in area near boat launch where an invasive aquatic plant species was located during initial BioBase mapping surveys.  Follow-up intensive surveys were carried out to more precisely map infestations.
Coarse-resolution aquatic vegetation BioBase biovolume map created from 200-m transects (left) and detailed biovolume map created from follow up intensive BioBase surveys (right).  Overall vegetation statistics are generated for this NW area of Waccamaw.  Note only subtle differences in the overall numbers, but great difference in the precision and detail between maps collected at different survey intensities.  Scale of inference and tradeoffs of alternative approaches should be considered when designing surveys and implementing management actions
Mapping small bays and fingers? Try concentric circles

For mapping small bays, inlets, fingers, canals, try a concentric circle approach to mapping.  Create a new trail on your Lowrance chartplotter and start logging data while traveling as close to shore as navigable.  Methodically work your way inward as you encounter your previous trail while avoiding overlap.  When you get to the middle, stop recording, you have a complete map! 
Situational awareness - mapping vegetation edges
Use a perpendicular to shore approach if you are interested in mapping the edge of aquatic plant growth in a deep lake.  Or if using a concentric circle design, ensure that you travel in a weave-like fashion over the bed edge.

Situational awareness - creating the smoothest bathymetry map
Get the smoothest bathymetry with a concentric circle transect design
Situational awareness - dealing with extremely steep slopes

Traveling along very extreme slopes can present mapping challenges because how rapidly depths change and because the acoustic beam intercepts the bottom at an angle. Indirect sonar returns increase the likelihood of erroneous bottom typing.  In these cases, the best bathymetry is achieved by avoiding the slope and mapping along the top and bottom of the shelf.
Situational awareness - mapping small patches

Patch of hard bottom (brick red on map) in an otherwise soft-bottom lake (light tan).  Surveyor noticed double echo on sonar chart while mapping and diverted course to methodically cover hard patch and thus more precisely map its extent.  
We hope this gallery of images and explanations can help BioBase users make the most efficient use of their time on the water mapping and produce the best possible aquatic habitat map!  For more information search this blog, aquatic resource mapping user forum, or contact us at

Monday, February 16, 2015

New Polygon and UPI Treatment Tools

One of the most popular features of BioBase is the polygon tool that allows users the ability to trace out areas of their maps for detailed calculations of mapped attributes (e.g., area, depth, water volume, aquatic vegetation statistics).  Until now, users could not use the same polygon on multiple trips.  That has changed and now any polygon a user creates in any trip will be available in all trips to that waterbody!  Now, users can monitor change to aquatic habitat within specific areas of interest (Figure 1).  Further, users can upload and overlay waypoints within polygons, and thus inform the composition of the polygon area (e.g., aquatic plants, substrate composition, muck depths, reefs, etc.)
Figure 1. Comparison of changes to aquatic vegetation in 2013 and 2014 within the same delineated polygon area of a lake in Minnesota.  Waypoints showing the presence of the native aquatic plant, coontail was also uploaded and overlain simultaneously to demonstrate how species information can be combined with the vegetation biovolume map to better understand aquatic plant bed composition
BioBase teams up with UPI to deliver precision herbicide treatments
Since its launch in 2011, BioBase has taken the guesswork out of aquatic plant bed mapping and delineation.  Now with a partnership with United Phosphorus Inc, we've developed a treatment recommendation tool that automates the estimation of UPI herbicide based on the user-delineated polygon area, target species, desired product and application rate (Figure 2).  Whole Lake treatment recommendations can be created if >20% of the lake area is mapped.  Users control the accuracy and precision of treatment recommendations by their mapping coverage.  A whole-lake prescription will be more accurate and precise if 100% of a lake is mapped with 40-m transects than 20% of a lake with 100-m transects.  Optimal mapping coverage in different aquatic plant environment is an area of research that we are hopeful will grow!

Figure 2. After a polygon is created, authorized users can click on the UPI Treatment Tool button and generate an herbicide recommendation based on one or more polygon areas or the entire lake.
Figure 3. After a treatment is saved, a treatment history is created.  Click on the "view report" for report for the last sample treatment (see example).
Embed Treatment Reports in Final Reports or Forward to Permitting Officials
Applicators and lake managers can also quickly produce automated vegetation summary and treatment reports (Figure 4).  These static html reports are stored a remote file server and can easily be shared with lakeshore owner customers, partners, or government regulators.  No account information outside of the trip owner is disclosed or accessible by recipients.  These reports demonstrate the objective and transparent nature of BioBase and UPI tools, thus minimizing uncertainties (and controversy??) by all interests involved in projects.
Figure 4. Example automated UPI treatment report generated with any UPI treatment recommendation.  Hyperlink of html report can be embedded in any electronic report or email 
By using objective, quantitative tools delivered by BioBase and the UPI Treatment Tool, the precise amount of herbicide can be delivered to infestations and thus control costs, maximize effectiveness, limit non-target impacts, and ensure regulatory compliance.  If you are interested in using the UPI Treatment Tool (both current and interested future BioBase subscribers), please contact your regional UPI Sales Rep.

For detailed instructions on how to use the Polygon Tool consult the Operators Guide in Support & Resources in your BioBase Account or see our YouTube Demonstration Video