Thursday, December 12, 2013

Virtual Eyes to See Aquatic Resources in 3D

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

Needless to say, aquatic resource managers and researchers have lagged behind our landlubber counterparts in understanding how aquatic organisms relate to "aquascapes."  Fisheries biologists have long dropped their nets into an abyss and magically, fish appeared when they pulled them up the next day.  Or, a rake/grapple thrown from a boat at a handful of transects or sampling points was the extent of the sophistication that biologists used to characterize plant growth in the littoral zone of lakes.  Biologists and researchers through the years have grown quite skilled at developing fancy statistical models to make sense of these messy, imprecise data.

Technology is now cleaning up the messiness of aquatic resource data and bringing in a new level of intuitive sophistication and precision.  Advancements in consumer sonar like Lowrance HDS with StructureScan give the researcher an ultra-sound-like picture of the environment they are studying in a small, rugged, and affordable package.

DownScan, StructureScan, Down Scan, Structure Scan Lowrance, ciBioBase
DownScan Imagery of small sunfish hovering over Eurasian watermilfoil plants in Prior Lake, MN as viewed in the ciBioBase Trip Viewer
Lowrance, StructureScan, Side-scan
Side-scan image of boulders, gravel, and sand from a river in Pointe Au Baril, Ontario Canada from a Lowrance HDS8 Gen 2 LSS-1 Transducer.  For a large image library of other impressive StructureScan Images, just go to Google Image and type in "Lowrance StructureScan"
Advancements in cloud computing via ciBioBase has enabled your 8-yr old laptop to do super computer processing tasks and you don't need a hard drive the size of a closet to store your data. Centralization and automation of industry-standard acoustic data processing tasks creates visually intuitive maps and spatial datasets that are uniform across data collectors and geographical areas.  And, to top it off, your maps are often finished processing quicker than it takes you to make a pot of coffee after returning from the field.

Finally, third party spatial analysis and visualization platforms like those powered by ESRI (e.g., ArcGIS and associated plug-ins, ArcScene, etc) can take your BioBase datasets to the next level by opening up a wide range of advanced analysis and visualization tools.  For instance in the two embedded videos, we demonstrate two outputs derived from the Lowrance HDS -> ciBioBase -> GIS chain of analysis that give the aquatic researcher/manager a birds-eye view of the environment they are managing.  GIS for the aquatic researcher is now more than putting dots on a map.  Time to play some catch up...

YouTube demo of ESRI ArcScene Fly Through of the North Umpqua River upstream to Lake Lemolo in West Central Oregon.  Digital Elevation Data were obtained from the USGS National Map Viewer and Lemolo Bathymetric data were collected with Lowrance HDS by Joe Eilers, MaxDepth Aquatics Inc. Bend, OR and processed through ciBioBase.

ESRI's ArcScene is used to create a 3D view of a kelp forest mapped with  Lowrance HDS by Rick Ware Coastal Resources Management Inc., Corona Del Mar, CA.  Date were processed with ciBioBase, exported, and then brought into ArcScene.

Wednesday, November 20, 2013

New BioBase Merge and Buffer Features

Are you making a list of things to be thankful for?  What about adding NEW FEATURES IN BIOBASE just in time for Thanksgiving?!?  We're releasing new features today that include the ability to delete outdated merges from your account and the ability to change the buffer on single and merged trips!

(1) New "DELETE MERGE" Controls


After some testing and use case analysis we've just launched a new feature that will allow you to keep your merge list nice and clean or redo a merge.  This is great in scenarios where users would like to continuously add new data to a merge or would like to reprocess a merge without adding to the list of available merges in their account. 

New Delete Function for ciBioBase Merges
A merge is created based on the combined data sets of individual trips and if the data sets change, a new merge has to be deleted then reprocessed.   At times, our QC team helps make adjustments to your output for the best map or to shapefiles boundaries for the best interpolation and then communicates these changes to you.  They also show up in your reports for individual trips.  Now, an old merge can be deleted and you can kick off a new merge with the updates.  We think this will be a useful tool for better account management!

(2) New Interpolation Buffer Controls from 5-300 Meters


Many of you request different buffers for your trips to fill in gaps when our standard 25m buffer isn't enough.  We're happy to oblige but we wanted to help you do it faster!   Now you can change buffers in your account without us.

New User Controls to Change the Buffer Size of Your Maps
We still always use a 1/5 rule meaning that the grid cell size will be adjusted to 1/5 of the buffer size (ex1: 100m buffer, 20m grids; ex2 50m buffer, 10m grid cell size).  If you need a different combination than the 1/5 rule (like a 1m grid and 10m buffer) let us know and we can do it for you and let you know the ramifications.   In the reprocessing tab you can send individual trips back for reprocessing with an increased buffer of up to 300 meters.  In the merge tab you can kick off a new merge with a pre-set buffer as part of this new merge feature (see the image above).  If you need to change the buffer in the merge you can make changes in the trip reprocessing tab when it's complete.   It's sounds complicated in writing but we're confident that you'll see the changes as soon as you play around with it!  Once you've uploaded and paid for processing on a per lake or unlimited subscription model, all edits and reprocesses are free!  As always, contact us with questions.

*Please keep in mind that an error coefficient of the interpolation is positively correlated with the increase in a buffer and you'll want to communicate this with a customer or constituent.  As you increase your buffer, you'll be estimating more between transects which could be affected by highly variable point data or aquatic systems.  Also, the buffer is always on both sides of the transect meaning that if you have 50 meters between your transects you only need a 25 meter buffer because 25 meters on both sides of the transect will complete the map.

New Pricing for 2014


We're not ready to fully announce our new pricing for 2014 but we wanted to let you know that we've made some big changes and the results will be much cleaner.   The new subscription model will help smaller municipalities get started with BioBase.  We'll also be announcing new stormwater monitoring options and pricing packages for municipalities that need to start keep an inventory of these assets or would like a more efficient way of process and warehousing the data.   Just a little teaser . . .but let us know if you have specific questions.

Monday, November 18, 2013

Platypus Offers New Opportunites in Pond Mapping

Researchers Paul and John Scerri and their team at Carnegie Mellon University have developed an autonomous vehicle called Platypus that can be used for a wide variety of aquatic applications.  One application we see customers struggle with is mapping small ponds.

Platypus getting fitted with a Lowrance HDS and transducer
Recently, the Platypus development group teamed up with Tim Wood at Aquatic Edge Consulting and Contour Innovations to test the use of a Platypus for sonar data collection and bathymetric and vegetation mapping of a pond.  They rigged up the autonomous vehicle with a small Lowrance HDS 5 and sent it into the waterbody.

Getting the data collection process going and testing while on the water

A close-up view of Platypus
They quickly acquired the data set recorded to their SD card, uploaded the .SL2 files to their account at and within minutes all of their files were done processing and could be merged into a full map.  The pond map output looks great!

You can check out a video of the operation here: Platypus in action

Platypus gathering sonar data for BioBase
Customers were happy, no one got wet, and the results speak for themselves.  Great job guys!

If you have an innovative way of collecting data for processing with ciBioBase, let us know and we'd  be happy to help!

Tuesday, October 29, 2013

New Survey Findings: Use of Geographic Information Systems by Fisheries Management Agencies

Recently Brandon Eder from the Nebraska Game and Parks Commission and Ben Neely from the Kansas Department of Wildlife, Parks, and Tourism published some interesting findings in Fisheries pages 491-495 regarding the use of GIS in fisheries management agencies in the US and Canada (see abstract below).  Technology is opening horizons and aquatic resource practitioners now have a variety of intuitive tools at their disposal to characterize and describe the complex spatial environments they are charged with managing.

Better characterization and description of aquatic environments leads to better management decisions and public welfare.  How can we promote more academic training and utilization of GIS tools for aquatic resource practitioners?  Eder and Neely have some advice that is worth a read.

ABSTRACT: Use of geographic information systems (GIS) in fisheries science has increased in prevalence since its introduction in the late 1980s, but use among and within fisheries management agencies has not been quantified. We surveyed 89 administrators of fisheries management agencies in the United States and Canada to determine the current status of GIS in fisheries management and received 54 responses (61% return rate). Survey respondents indicated that GIS was used to help manage fish populations, and 63% of respondents believed that GIS was either “very useful” or “extremely useful” for meeting agency objectives. However, most GIS work conducted by fisheries management agencies was executed by few individuals within the agency or by contracted service. Barriers preventing more widespread use by managers within agencies included lack of knowledge or training and limited time to use GIS in job duties. Our results suggest that GIS is an important tool for fisheries management. Further, GIS use within an agency might be increased by focusing on increased biologist participation in training exercises, integration with existing job duties, and recognizing diversity among GIS software.

Wednesday, October 16, 2013

Guest Blog: Precision aquatic plant assessment and management in Michigan Lakes

By Jennifer L. Jermalowicz-Jones

Restorative LakeSciences is actively involved in the management and restoration of nearly 60 lakes in the state of Michigan and on water bodies in other states such as California and Wisconsin.  As an innovative specialty firm of advanced-degreed limnology experts, our goal is to provide thorough educational training to lake communities while using the most innovative technologies for lake improvements.  ciBioBase software (Contour Innovations, LLC) in combination with the Lowrance® HDS8 side- and down-scanning capabilities allows us to precisely determine the biovolume of the submersed aquatic vegetation in inland lakes.  Additionally, it also assists in the determination of individual aquatic vegetation bed areas that are mapped by aquatic botanists to be treated precisely with systemic or contact aquatic herbicides or with other removal technologies (Figure 1).  This technology has resulted in highly effective reductions of nuisance aquatic vegetation biovolume and bed densities due to the precision of treatments.  As a result, all of our lake management communities have been satisfied with the strategy and can easily see significant progress within a single season.
Restorative Lake Sciences, Evans Lake, Michigan, ciBioBase, BioBase, Eurasian watermilfoil, mapping, aquatic plants
Figure 1. ciBioBase aquatic vegetation heatmap collected by Grant Jones, Field Operations Manager, Restorative Lake Sciences (left) and Eurasian watermilfoil beds delineated with companion species surveys and the ciBioBase polygon tool.  Polygons were exported from ciBioBase and uploaded to Google Earth.
Jennifer L. Jermalowicz-Jones, MS, Ph.D Candidate, is the Water Resources Director at Restorative Lake Sciences and oversees over nearly 60 inland lake projects which include aquatic vegetation mapping and management, lake sediment reduction studies and management, algal quantification and identification and algal management programs, and watershed management programs.  She has over 24 years of experience in lake research and management and is pursuing her doctoral degree from Michigan State University in Water Resource Management.  She is also the President of the Michigan Chapter of the North American Lake Management Society, serves as the Science Advisory Chair on the Michigan Lake and Stream Associations Executive Board of Directors, has won numerous awards and grants for her aquatic ecosystem research, and has presented numerous papers at state and national conferences on water resource and lake management.

Monday, October 7, 2013

Amendment to ciBioBase Guest Blog: GIS Tools helping CAP manage sedimentation

Earlier this year, Senior Biologist Scott Bryan from the Central Arizona Project (CAP) blogged about how the CAP is using ciBioBase to manage sedimentation in Arizona's lifeblood 336-mile aqueduct.  Since then, CAP GIS Wizard Glenn Emanuel has worked some amazing magic on the ciBioBase grid exports using Spatial and 3D Analyst Extensions for ArcGIS (Figure 1).
Central Arizona Project, sedimentation, Lowrance, ciBioBase, BioBase, sonar, mapping, acoustics
Figure 1. Images showing the change in sediment volume prior to and after experimental dredging activities in a Forebay of the CAP canal.  The Raster Calculator in ArcGIS's Spatial Analyst was used to subtract a "current" bathymetry from a baseline bathymetry (e.g., "as built") to estimate sediment height and volume.  Images are 3-dimensionally enhanced using 3D Analyst for ArcGIS. Image courtesy of Scott Bryan and Glenn Emanuel, Central Arizona Project
The data and images allow CAP to make informed decisions regarding the efficiency of sediment removal operations.  In addition, ArcScene was used to produce a 3D scene of the forebay (Figure 2), which can then be animated with a video fly-through.

Central Arizona Project, sedimentation, ciBioBase, ArcScene, Lowrance, BioBase, sonar, mapping, acoustics
Figure 2. "Fly-through" images of sediment height  in Little Harquahala Forebay in the CAP Canal collected by Lowrance HDS sonar and GPS, ciBioBase cloud processing software, and finally exported/imported into ArcScene.  Image courtesy of Scott Bryan and Glenn Emanuel, Central Arizona Project.
Any user of ciBioBase properly equipped with the proper third party GIS software can create these amazing map products that are more than just pretty pictures.  They create a real-life, tangible perspective of aquatic resource conditions that ciBioBase users are interested in managing, protecting, and restoring.

Friday, October 4, 2013

Getting good BioBase EcoSound outputs depends on a good transducer mount!

EcoSound is a powerful and intuitive aquatic resource data processing engine that professionals across the globe are coming to recognize.  However, the quality of automated outputs greatly hinge on a proper Lowrance transducer mount.  If the transducer is off at an angle, the acoustic cone will intercept bottom at an angle and will falsely read depth, bottom composition/hardness, and vegetation height (Figure 1).
Figure 1. Example sonar log from a transducer face that is not 180 degrees with bottom as seen in Lowrance's SonarViewer

Strategies for installing your transducer.
There are a wealth of online resources via YouTube, Google, and our own blog series (for example see our portability blog) about proper transducer mounts.  Just search "Lowrance Transducer Installation" and you'll have a wealth of self-help resources at your disposal.  An output from a properly mounted transducer should look like Figures 2 and 3 where the bottom signal is clearly distinguishable from aquatic vegetation.
Figure 2.  Screen shot from a Lowrance HDS7 Gen2 Touch of a clear bottom signal and submerged aquatic vegetation from a properly mounted 200 kHz skimmer transducer.
Figure 3.  Example of what a clear 200 kHz signal over a vegetated bottom looks like in the EcoSound Trip Replay screen.
Often, aquatic vegetation grows to the surface of lakes and one of the unique strengths of EcoSound is that the vegetation detection algorithm recognizes conditions that appear to be surface growing vegetation and classifies the growth as such (i.e., biovolume = 100%).  Still, in order for the algorithm to function in these environments, some signal must periodically pass through the vegetation canopy and get "peaks" at bottom deeper than 2.4 ft (EcoSound minimum depth for vegetation mapping; Figure 4).  If you are mapping areas shallower than this depth, you can add manual vegetation coordinates to unmapped areas (see a CI YouTube video on how to do this)
Figure 4.  Example of a good signal in surface growing vegetation.  The bottom still tracks occasional depths of greater than 2.4 feet.  Long periods of no depth signal or depths less than 2.4 feet will result in unmapped areas and will require manually adding vegetation coordinates to your EcoSound output.
Monitor SONAR screen while you map
Because having a clear transducer signal is so critical for quality EcoSound data and map products we recommend that users verify a clear Sonar signal in an open water area prior to logging.  Drive your boat at different speeds and evaluate at what speed "slivers" start to appear in the bottom signal (Figure 5).  These slivers represent acoustic "misses" and typically result from cavitation of water around the transducer face.  Periodic slivers or misses while recording are ok, but we recommend that users monitor their SONAR page and take measures to minimize these disturbances (e.g., slow down or adjust the depth of the transducer a few inches - sometimes that's all it takes).

Figure 5. An example of where the acoustic signal "missed" the bottom target (white slivered areas).  These misses typically result from either an improper transducer mount or excessive speed of travel that causes cavitation near the transducer face.
A Transducer Field Checklist
It might be helpful to ask these questions prior or during recording while looking at your SONAR screen and if the answer is yes to any of them, stop recording and make adjustments.
  1. Does the bottom, fish, or plant targets appear slanted?
  2. Does yellow surface clutter extend a long way into the water column and might possibly obscure vegetation target separation?
  3. Is my depth signal flashing or am I getting no digital reading?
  4. Is my range window jumping around indicating it can't find depth?
  5. Am I getting a lot of white slivers in my bottom reading?
Editing your EcoSound output
If bad signal does sneak past your scrutinizing eyes, fear not, you can always edit your output with EcoSound's Trip Replay feature as seen in our YouTube video series.

By installing your transducer correctly and monitoring your output you're almost guaranteed a quality map of lake, river, or coastal habitats with EcoSound.  Contact us at to learn more. 

Tuesday, September 17, 2013

Color Enhancing your Sonar Log

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

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

Figure 1. Trip Reprocessing Tab that allows ciBioBase users to reprocess their trips with new edits.  Try reprocessing your sonar log at a higher color (e.g., 240) for "cooling" the colors in your sonar log in ciBioBase and to bring out subtle bottom features.
Sometimes, your Sonar Log may look a little too "hot" making it difficult to distinguish between plants and bottom (Figure 2).

Lowrance, ciBioBase, Sonar Log
Figure 2.  Sonar Log showing colors that may be "too hot" to distinguish between plants and bottom.
Try reprocessing the sonar log at a colorline of 240 (default is 220).  This will bring in "cooler" colors to the sonar log and may help you better distinguish subtle bottom features and gaps in plant beds (Figure 3).

Figure 3.  Sonar Log reprocessed with a colorline of 240.
Alternatively, Lowrance has a powerful free desktop software program called SonarViewer which allows you to replay your Sonar Log with options to dynamically control sensitivity, colorline, zoom, and range (Figure 4).
Figure 4.  SonarViewer is a free download from Lowrance and has a range of tools for enhancing the contrast of bottom features detected by your Lowrance HDS or Elite.
Use SonarViewer to review your files prior to upload to ciBioBase if you suspect possible signal quality issues or are testing different transducer setups for optimal signal quality.  Signal Quality should also be continually monitored by watching your SONAR page on your HDS or Elite while collecting data on the water.  A helpful rule of thumb is that a signal that is clear and crisp to your eyes is most likely clear and crisp to ciBioBase algorithms.

Friday, August 30, 2013

BioBase Youtube Video Demo Series

We've recently launched a YouTube channel (Username: Contour Innovations) where we will be posting videos answering common questions we receive with technical feature demos and personal appearances by some of our famous employees. Please search for our channel "Contour Innovations" on Youtube or click here and follow us to keep up to date with new features, innovative uses of BioBase and in-depth explanations of key technical procedures.

Biobase demo videos.  Lowrance waypoints

If you have a specific question about one of our features, let us know and we can get a video on the topic up ASAP.  Also, we'd be happy to review and post your video if you would like to record a topic or trick where you've found great success for streamlining a process.  We'll upload it for the BioBase community.  We're always interested in innovative techniques from our members!

You can view our first video on using the BioBase waypoint upload tool here: CI on Youtube

Wednesday, August 14, 2013

Quantitative Aquatic Vegetation Management

Aquatic plants are often integral components of lake ecosystems and invasive species often disrupt the ecological balance of lakes.  Past aquatic plant assessments were qualitative and imprecise leading to poorly informed management decisions and prescriptions which have carried significant environmental and economic costs.  New acoustic and cloud computing technologies have revolutionized the aquatic industry and now highly precise estimates of aquatic plant abundance, growth patterns, and response to management can be quantitatively assessed.  New BioBase reports take this into consideration in multiple areas:

Aquatic plant management and monitoring
Aquatic plant management and habitat assessments with quantitative metrics
BioBase creates a standard report for each file that is uploaded to the system.  One section of the standard report (Biovolume by Quantity) identifies the relationship between data collected and % of data points that fall within a certain biovolume (% of the water column occupied by plants) range.  For example, in the image above 6.8% of data points collected and processed had plant biovolume above 80%, 5.19% of points had biovolume between 60-80% and 11.99% of data points showed biovoume above 60% (5.19+6.80).  If a management technique was used it would be very easy to identify, with quantitative plant management metrics, that objectives were met.  This may mean that nuisance plants above 60% biovolume were reduced by 90%.  Now we know if this is the case.

Using qualitative or subjective determinations of plant growth with only periodic surveys has led to problems of repeatability by other surveyors, lack of precise understanding of how much growth has changed over time, and an inability to rapidly detect change in lake conditions.  Now we can objectively determine if management techniques are having their desired effect.

Lake managers and plant monitoring groups can now take data to the next level with the three dimensional aspect of plant delineation using water column percent biovolume and BioBase standard reports.

Wednesday, July 24, 2013

Contour Innovations Launches NGIN Websites for Lake Associations

Contour Innovations is excited to announce the release of a new web service called NGIN (pronounced "Engine') developed to provide powerful website tools for lake home owner associations.  The NGIN platform provides powerful tools and features to help increase membership and revenue for your association, keep the community informed about upcoming events and management efforts, and display your BioBase maps through a public or private interface.

Paradise Lake Improvement Board's NGIN Site
These are more than just great websites!  NGIN websites are a robust platform featuring a suite of timesaving tools that empower lake associations to connect with lake enthusiats and stakeholders like never before.  We can help you increase membership and get the word out about your association!

Lake NGIN is easy to manage and cheaper than one member's cell phone plan!

The Lake CI NGIN website is a sample site set up by Contour Innovations (CI) to demonstrate the power of our Lake NGIN wesite product.
By keeping everyone in the community and around the lake informed about meetings, management efforts, and upcoming events NGIN can help you increase membership and revenue from dues and contributions.  Once everyone sees how much you care you'll quickly see an increase in participation.  One of the most exciting features of the NGIN site is the seamless integration of BioBase lake maps.

Seamless BioBase Map Integration:  It's quick and easy to show off the work your board and volunteers have done to monitor change in aquatic vegetation in your lake.  If you decide to make your maps public, anglers can have access to full lake maps to help them improve their odds of catching fish and falling in love with your lake.  Another option is to keep maps private for members who register on your NGIN website or pay premium dues for association membership.  This is a great way to drive revenues to help fund your management and monitoring efforts.

Add board minutes in seconds and integrate with social media like Facebook and Twitter with ease.  Ask us how we can help with your associations website needs.  We've got lots of cool ideas! Contact us at

Monday, July 22, 2013

CI In the News (St. Cloud Times): Harmful species to hot spots: Technology helps all

Recent feature by Kevin Allenspach from the St. Cloud Times describing how Clarke and lakeshore owner citizen scientists are integrating ciBioBase to better inform aquatic plant monitoring and management in Central Minnesota.

You can read the story here.  Let us help you make your own news (we have lots of ideas)!

Saturday, July 20, 2013

ciBioBase Vegetation Mapping

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

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

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

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

Wednesday, June 26, 2013

Optimal Percent SAV Biovolume? 50% is a Good Start

At Contour Innovations we've long argued the importance of objectively assessing submersed aquatic vegetation (SAV) abundance to better inform management decisions.  Our last blog post discussing a recent controversy over the role of herbicides in indirectly affecting fisheries declines in Wisconsin reinforces why this is so important.  When we talk abundance per se, we need a metric that is quantitative, yet is intuitive.   The percent of the water column taken up by vegetation growth (i.e., percent "biovolume") represents such a metric and is the primary variable that is mapped in ciBioBase.  Zero means no growth (blue).  100% represents growth all the way to the surface (red; Figure 1).
SAV, Aquatic Vegetation map, Lowrance HDS, Surface growing vegetation
Figure 1. SAV Biovolume map (left), boat tracks (red lines), boat location (red dot), and sonar chart of vegetation growing to the lake surface on Orchard Lake, MN.

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

If no plant growth is bad (0%), but plant growth all the way to the surface (100%) is bad, then good MUST be somewhere in between.  Indeed!  From a Fisheries standpoint, 40-60% average biovolume is good because there is habitat for vegetation-dependent species like largemouth bass, bluegill, northern pike, and indicator species like blackchin shiners that are sensitive to vegetation loss (Figure 3).
Figure 3.  Probability of sampling blackchin shiners as a function of increasing SAV % biovolume  in Square Lake, MN (Adapted from Valley et al. 2010 Hydrobiologia 644:385-399)

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

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

CI is currently involved in a collaborative research project where acoustic data with Lowrance HDS was passively collected while conducting point-intercept surveys.  Acoustic data (.sl2 files) were uploaded to ciBioBase and the Biovolume value for each species survey point was extracted from the exported raster grid ("Extract Value From Point" in the Spatial Analyst Toolbox in ArcGIS or see our Point-Intercept on Steroids blog).  Figure 4 displays a wealth of information about the status of plant growth and management in the surveyed lakes.  With on-the-fly data entry for the plant species surveys and uploading of the .sl2 file to ciBioBase, a similar graph could be produced within hours of finishing a survey, and thus facilitating informed and rapid decision making.
Figure 4.  Biovolume at invasive species sample points and native sample points free of invasive species.  Non-vegetated sites are not included in the analysis.  Lakes range from intermediate nutrient levels, Mesotrophic (M), to high nutient levels, eutrophic (E).  Berry, Gibbs, Swan, Wingra, and Round are in WI; Gray's, Gideon's, and St. Alban's Bays are bays of Lake Minnetonka, MN; Waccamaw is NC; Tracy, Kissimmee, Istokpoga are FL lakes.  All MN and WI lakes are infested with Eurasian watermilfoil.  All NC and FL lakes are infested with Hydrilla.  Waccamaw is bog stained and the hydrilla is a recent infestation

Specifically this graph tells us the following:

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

Tuesday, June 18, 2013

The Wake Up Call to Action for Objective Lake Monitoring and Management

The unexpected consequences of fighting Eurasian Watermilfoil, preventing fish from successfully reproducing?  Response by Contour Innovations’ President Matt Johnson

Recently, freelance journalist and underwater photographer Eric Engbretson published an article entitled 'The unexpected consequences of fighting Eurasian Watermilfoil, preventing fish from successfully reproducing?' on a news service blog sponsored by Fishiding.  The article's focus was Lake Ellwood Wisconsin where Wisconsin DNR Fisheries Biologist Greg Matzke presented evidence of declining Largemouth bass, Northern pike, and bluegill populations and evidence of recurrent reproduction/recruitment failures of these species.  Much of what is presented can be found in a draft WI DNR Fisheries Report.  Matzke speculates that declines in populations of these vegetation-dependent species may be due to a loss of aquatic vegetation over the last 10 years by repeated whole lake treatments.  In the DNR Report Matzke presents spotty, often subjective estimates of aquatic plant abundance which makes it difficult to confidently associate aquatic plant declines due to treatments with declines in fish populations.

It’s often difficult to respond to topics like this because, as a non-biologist and an employee of private company that provides a product for this field, I’m always concerned that my comments would be misconstrued as commercial, driven by my interest to sell products or my failure to understand the biology behind the “whole picture.”  I approach this topic as an outsider that gets to observe the industry and sometimes provide a unique perspective without a specific interest or deep understanding of a particular biological issue.   It is this observation stance that allows me to recognize that this article is a wakeup call regardless of position.

Every opinion, no matter what side of a topic you land on, will go nowhere if we don’t have objective information to make an argument or defend a position.  This is something both government biologists/regulators and aquatic service providers should agree on here.  This report is an opportunity to finally connect all groups within the aquatics field to perform holistic investigations, recognize when there’s a lack of good data, and take steps to acquire critical data.  It’s an opportunity to have the discussion the aquatics field deserves.  Failing to at least put resources towards making the connection between data inadequacy and historical needs from this article is a failure in the structure of the aquatic industry and maybe even society.  Compliance is one thing while a constant quest towards better data-intensive monitoring and management is quite another.

Sometimes this lack of “good data” is a result of a failure of technology to provide the tools required to gather and analyze the information we need, and sometimes it’s for other reasons like budget, human resources, access, and priorities.  I struggle with the paradox that the some people who argue that we need to look at the data before we make decisions on Ellwood are some of the same people I’ve seen resist an objective method that can provide these results.  It doesn’t add up.  Without objective, repeatable aquatic plant assessment methods, the field never moves forward and everyone gets to pick a side and stay there. Consequently, circumstantial evidence and speculations are used to assign a cause and place blame.  This puts the accused on the defensive using lawyer tactics to avoid any accountability.  This gets us nowhere

A way forward . . .

Contour Innovations is already helping to facilitate collaboration between fish monitoring and invasive plant management with fantastic, even unexpected results.  All involved hope the data sharing model grows into the future of monitoring and management.  By using an objective, passively logged and repeatable system of plant abundance and characteristic monitoring, multiple interests are benefiting simultaneously.   Fisheries managers are using quantitative measures of aquatic plant habitats to formulate fisheries management goals, Invasive aquatic plant managers are using these same data sets to evaluate invasive nuisances and are taking measures to address the nuisance while not compromising fish habitat.  This is a different way of thinking proactively instead of reactively and we can’t miss opportunities to highlight the need.  We can claim that the technology is the future, but technology is merely a catalyst for the necessary paradigm shift.

Our position has remained consistent since the Company’s founding, but is more relevant now than ever: That is, prudent management and regulation of lake ecosystems requires that decisions be based on objective, quantitative information about the status and trajectory of the system(s) of interest.  Continued decisions in an information-poor or anecdotal-evidence environment risk situations and blame like those observed on Lake Ellwood.

We haven’t picked a side but the industry and field needs to embrace or seek a more standardized or objective way of measuring aquatic plant abundance data.  I’ve heard a lot of requests for automated speciation data but here we are wishing we had objective abundance data.  There are some “cool” parts of our systems but we started BioBase because it fills a need.  Subjective methods of plant monitoring are already outdated. This has never been more apparent.

Friday, June 7, 2013

Guest Blog: Using ciBioBase to determine sedimentation in the Central Arizona Project canal

by Scott Bryan

The Central Arizona Project (CAP) is a multipurpose water resource development and management project that provides irrigation, municipal and industrial water to much of Arizona.  The primary means of water conveyance is a 336-mile concrete-lined aqueduct that transports water from the Colorado River, on Arizona's western border, across the State to Phoenix, and then southward to the aqueduct terminus near Tucson.  Each year, over 1.5 million acre-feet of water is delivered to our customers.

Since its completion in 1993, the aqueduct system has experienced increasingly severe sedimentation that creates problems within the pumping plants and in the aqueduct itself.  Because the sediments can decrease the flow capacity of the aqueduct, cause damage to pumps and internal systems, and restrict flow through critical filtration units, it is imperative that dredging operations occur periodically.

sedimentation, ciBioBase, water volume, depth, mapping, bathymetry
CAP forebay dredging in 2009
In the past, CAP performed intensive sonar based sediment studies to determine bathymetry and the amount of deposition in the forebay of each of the 13 pumping plants.  The surveys show when and where dredging operations should occur.  These surveys were contracted to outside companies with costs ranging from $40,000 to $120,000 annually.

In 2012, CAP began to use the sonar technology provided by ciBioBase to conduct its own bathymetry surveys in the pumping plant forebays.  Water depths are compared to historical baseline surveys and the volume of sediment in each forebay can easily be calculated.  Annual surveys allow us to compare sedimentation from year-to-year to determine loading rates and critical areas to target sediment removal.  Surveys of all 13 forebays can now be accomplished in three days rather than six months, and when compared to the expensive surveys from the past, are equally as accurate.

ciBioBase, bathymetry, water volume, depth, Lowrance, acoustics, mapping, sonar, sedimentation, dredging
Blue-scale bathymetric map of a CAP forebay.  The light blue contours show an area that is extremely shallow and is in need of sediment removal.

ciBioBase, sedimentation, Lowrance, downscan, sonar, mapping, bathymetry, depth, water volume
Example transect design and resultant bathymetric map coupled with the sonar log viewer.  Notice the detailed image of the forebay's trash racks produced by Lowrance HDS DownScan
This new approach to bathymetric and sedimentation mapping saves time and money, allows us to evaluate results immediately, and makes dredging operations more efficient and timely. 

Scott Bryan is the Senior Biologist for Central Arizona Project (CAP).  After receiving an M.S. in Fisheries Management at South Dakota State University, Scott worked as a research biologist for Arizona Game and Fish for 10 years, then specialized in lake and stream management for seven years at a private consulting firm in Albuquerque.  Scott's current position at CAP includes a broad scope of work, including aquatic and terrestrial vegetation control, fisheries and wildlife management, invasive species research, and water quality monitoring.

Monday, April 29, 2013

Mapping Ponds with BioBase

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

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

Friday, April 19, 2013

New ciBioBase Website and Mapping Dashboard

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

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

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

Thursday, April 11, 2013

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

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

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

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

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

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

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

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

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

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

Literature Cited

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

Monday, April 8, 2013

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

By Dr. Ian J. Winfield and Joey van Rijn

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

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

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

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