What sonar do I need for BioBase mapping?

What kind of sonar hardware should I buy for BioBase Mapping is the most common question we are asked. Admittedly, continual change in technology, products, and features can be intimidating and sometimes confusing. With this blog, we focus on what you need to know to get started with BioBase

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BioBase Tip: Enable mobile location and see your location on BioBase maps.

Users of BioBase may be interested to know you can view your location on a BioBase map on your mobile device if you allow your browser to access your location

Navigate to your browser settings and allow location. Screenshot is from Chrome on Samsung Galaxy

Then log into your account at https://www.biobasemaps.com and navigate to your waterbody of interest and view the trip/merge. The gray dot should show up automatically on your location. Users may find this useful to field verify mapped areas or navigate to areas of interest. However, downloadable full Lowrance/Simrad charts are also available for both EcoSound and EcoSat giving the user a bigger map screen and more navigation/waypoint features.

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Mapping Hidden Channels with Genesis Live

River channel thalwegs (the line of lowest elevation within a valley or watercourse) are often dynamic, and sometimes hidden features of large river systems.  Especially low slope or impounded systems.  The thalweg is a critical geomorphological feature of river and reservoir systems and affects everything from sediment transport, to fisheries habitat, to algae or invasive plant control.

Thus a good bathymetric contour map is a necessary pre-requisite for effective river and reservoir management.  Here, we walk you through how to use new real time technologies (C-MAP’s Genesis Live) to produce smooth, precise, and accurate maps of hidden river thalwegs all within one trip to the site and with automated post-processing with BioBase’s EcoSound.  We’ll use an annotated image gallery to take you through this process.

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Interpreting bottom hardness in shallow lakes and ponds: digging deeper into the data

BioBase’s EcoSound bottom composition (hardness) algorithm has become quite popular for researchers and lake/pond managers to determine where sedimentation from the watershed may be occurring.  However, interpreting sonar returns in shallow environments (e.g., less than 7 ft or 2 m) with off-the-shelf sonar is challenging, especially if aquatic vegetation is present.  Each situation is different and the objective of this blog is to inform you of how to interpret your EcoSound map in situations when you encounter counter intuitive bottom hardness results.

Here are some high level points to remember.

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Helpful Resources for Getting Started with BioBase’s EcoSound

BioBase is a powerful data collection and mapping tool for aquatic environments. To get the best results with BioBase – EcoSound, it is important to use proper hardware installation and data collection procedures. This post contains links to the resources that will help you get started with BioBase and get great data.

First, BioBase is only compatible with Lowrance and Simrad Sounders/Chartplotters. This blog offers helpful advice for which sonar to choose

Our quality control team reviews every uploaded trip and looks for glaring issues with the trip like evidence of a slanted transducer, signal loss, or poor signal quality. Its critically important that you have your transducer installed correctly. We recommend you take it to marina to have it professionally installed.

Our Quality Control Team may email you if they notice any significant issues with your trip, and suggest ways to fix the issue or ways to improve data quality before logging again. Waterbody boundary adjustment is part of the BioBase service but there will be a delay between when your trip is automatically processed and when Quality Control staff are able to adjust the boundary of your waterbody. Please allow one business day for quality control before finalizing or sharing your maps, or check the quality control review status by viewing a trip’s report.

OrchardVegReportQC

If there is a quality control reviewer’s name on the report with comments, the trip has been reviewed. You can also see any comments that were not emailed to you on the report.

It is also important to keep your Lowrance software updated. Software updates can be found here. Outdated software can result in inaccurate or lost data!

Our YouTube channel has many helpful videos, including data editing tutorials.

This post gives an overview on how EcoSound works along with some answers to frequently asked questions that many new users have.

The EcoSound Quick Start Guide shows recommended settings to use while logging sonar. Print this guide and keep it on your survey boat.

The EcoSound Support and Resources page has links to the EcoSound Full Operator’s Guide as well as several tutorials, including guides for using EcoSound data in QGIS.

If you ever need any assistance, contact the BioBase support team at info.biobase@navico.com

Consumer Sonar for Bottom Mapping: Updated Reference List

Another FAQ we get is wondering if there are published studies using BioBase technology? There are many legacy applications on which the BioBase technology is based. Further, now that a sufficient passage of years has accumulated to support the “research to publication” cycle, we’re happy to share several BioBase-specific studies published in the peer-reviewed literature.  This is far from an exhaustive list and we’ve intentionally left out the niche growth in consumer side-scan technology for creating habitat maps.  If there are good published papers you know of that are not on this list, please share in the comments.

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FAQ of the year: Does BioBase EcoSound Map Sediment Depth?

Thanks to advances in physical, chemical and biological technologies and funding that are focused on reducing sedimentation or muck depth in waterways, many water resource practitioners are eager to determine how much sediment is in a waterway of interest and how much could be removed. As such, we frequently are asked: “Will BioBase tell you how deep the sediment is?”

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Citizen Lake Mapping: Power of Aggregation!

Ten Mile Lake in Hackensack, Minnesota is one of many crown jewel lakes of Minnesota.  It’s no wonder the Ten Mile Lake Association is serious about lake monitoring and conservation.  When BioBase approached TMLA member and hobby Fisheries Biologist Dr. Bruce Carlson in late 2012 demonstrating how members could passively log their sonar data and map habitat while enjoying a pleasure cruise or fishing, Dr. Carlson jumped at the opportunity.

Two hundred and twenty four trips spanning two seasons (2013-2014) and 5,065 acres (2,049 ha) later, Dr. Carlson and colleagues have produced the most accurate and detailed map of Ten Mile Lake on the planet (Figure 1)!

Figure 1. Track lines from 224 Lowrance sonar logs uploaded to BioBase and merged (left) and resultant contour map (right) produced automatically for Ten Mile Lake, Hackensack, MN USA.  Ten Mile Lake is a 208-ft (63-m) deep lake with 16-ft (5-m) clarity.

When comparing the hand-made maps of 1947 from the long-dissolved MN Dept of Conservation one has to wonder if creating this map took a dedicated and highly trained survey crew all summer to create this map (Figures 2-4)?  Now a critical mass of anglers or pleasure boaters with no mapping experience can create a community-sourced contour map that rivals anything produced by the most trained hydrologists using the most expensive “survey-grade” echosounders.

Figure 2. Original map of Ten Mile Lake created in 1947 by the MN Department of Conservation (left) next to the aggregated map produced by TMLA volunteers in 2014 after uploading to BioBase.  Maps created in the mid 20th Century remain the only maps offered to anglers and recreationists by a large number State Natural Resource agencies. Often these old maps are digitized and artfully recontoured and shaded for resale.
Figure 3. Close up of the 10-ft contours displayed in the 1947 Department of Conservation map compared with the 2014 aggregated map created by TMLA volunteer uploads to BioBase.
Figure 4. Tight zoom of 10-ft contours from 1947 MN Department of Conservation map (ink blob on top) compared with 3-ft contours from aggregated map created by TMLA volunteer uploads to BioBase.

Not just an improvement in aesthetics!
The efforts of TMLA and volunteers from other Lake Associations across the US (e.g., Lake Paradise, Honeoye, Prior Lake) are producing not only pretty maps but also updated digital maps for the public and highly detailed fish habitat and aquatic plant data for aquatic researchers and managers.

First, public trips uploaded and aggregated both from BioBase and C-MAP Genesis mapping services from anywhere across the globe go to Social Map where they are available for viewing and downloading for free to Lowrance, Simrad, and B&G chartplotters (Figures 5 and 6).

Figure 5.  Insight Genesis Social Map coverage of Sweden.

 

Figure 6. Example map of Anten (Sweden) as viewed from Insight Genesis social map.  Professionals (BioBase) and Anglers (Insight Genesis) can community-source their mapping efforts to “fill-in” unmapped areas and create up to date digital maps for the public.

Second, Fisheries across the globe are threatened by a range of impacts too long to go into detail here and Aquatic Invasive Species are a global pandemic.  Researchers and managers mourn the decline of native aquatic species and often target habitat degradation or loss as a primary driver.  But rarely does information on habitat match the detail of the information on species declines. Citizen Scientists are now helping Natural Resource Agencies fill in the habitat knowledge gaps.  Returning to our example on Ten Mile Lake, now with updated bathymetry provided by TMLA volunteers and data sharing with MN Department of Natural Resources (DNR), Fisheries researchers have precise knowledge about how much cold, well oxygenated water is available for cisco (an important cold-water forage fish for popular gamefish).  Similarly, thanks to the efforts of the Prior Lake Spring Lake Watershed District and citizen volunteers on Prior and Spring Lakes, the response of invasive aquatic plants to watershed and in-lake management actions can be monitored.

Harnessing the power of technology and citizen science to conserve aquatic resources
“Doing more with less” or “working smarter not harder” are common cliché truths that will continue to limit the reach of publicly funded natural resource management programs into the foreseeable future. Through advances in affordable off-the-shelf consumer technology, automation, and the collective enthusiasm of citizen volunteers, good information on aquatic habitat need’nt suffer from declining public natural resource budgets.  Rather, by enrolling the help of citizens and technology such as described here, aquatic biologists and managers can focus their energies on using the information to make wise aquatic resource management decisions.

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.

An Unfair War with Aquatic Invasive Species

The Importance of Aquatic Vegetation Abundance Mapping and Long Term Monitoring from a Layman’s Perspective

 

From a layman’s point of view it can be very difficult to understand the importance of lake weeds as they relate to aquatic invasive species (AIS).  I should know . . . I’m a layman.  I started asking questions, and it turns out it’s a bit more complex than I thought.  Sure, I want the Minnesota Lakes I love to be clear with tons of fish, but do we really need these weeds?  Of course we need some “weeds” (“aquatic plants”), and, if you get rid of too many you can throw the entire lake ecology out of balance for years.  When I asked how much is a good amount and how it is being tracked in Minnesota I was disappointed with the answer.  During my time working for the software company Contour Innovations, focusing on automated lake mapping, I’ve had the pleasure of working with some of the most talented aquatic biologists in the Country, both in-house and through our customer base.  I’ve spent the last few years learning the language and attempting to catch on from a neutral, outsider’s perspective.  Slowly, I realized that the complicated topic could be effectively communicated to anyone that cares about and has an interest in water quality . . . which should technically be everyone.

Let’s face it, the DNR has done a great job demonizing invasive species for good reason and with some positive results.  There’s more awareness now and budgets in place to attempt to manage the spread and introduction.  But, eradicating AIS once introduced into a lake is only half the story.  . .
I’ve learned a lot over the last few years but I still had some questions:  Why should our customers really care about the total habitat when Eurasian Water Milfoil has already invaded their lake?  Don’t they just want to know where the Milfoil is so they can get rid of it?  If a monitoring program can’t distinguish between species does it still have a use in aquatic research or management?  I originally thought that identifying where the Milfoil is located is key, but I actually found the opposite to be true.  If we live by the idea that “AIS are bad and should be eliminated at all costs,” wouldn’t the results be easier to obtain? 
The concepts of ecosystem balance are extremely complex but vital.  After early discussions with our biologists it become clear to me that abundance is one of the most important metrics to consider when monitoring water quality and lake health.  This remains true if an invasive species has already been introduced or it’s just knocking on the doorstep.  We need to focus our analysis on total abundance and the overall aquatic habitat instead of speciation as a sole predictor of lake health.  What really matters is knowing if your lake is at risk of the negative impacts from invasive species and if your lake ecology is within certain “healthy” parameters.  A lake’s resilience to invasive species and current water quality regime is going to be a major indicator of lake health and prospects for the future.  It’s also important to quantify your management interventions and determine if they are having their desired effect.  These were difficult questions to answer in the past. 

Invasive species are coming.   We can try to stop it but more likely we’re just delaying it.  The reason these species are thriving is because they’re designed to thrive.  With the right conditions they can easily steal the resources required to grow from other plants, effectively eliminating competition from the lake.  They’re opportunistic and the microscopic amount required for infestation is astonishing.  We should accept this fact and be realistic about what we’re dealing with.  It doesn’t mean we roll over and stop the cleaning stations or citations for failing to drain your bilge, but a proactive management and monitoring plan is a good idea.   

Let’s understand our lake’s resilience and identify if it’s at risk.  Let’s get our resource managers identifying which lakes need close attention and devote our stretched budgets to the ones that need it.  The chips are already stacked against us and without good quantitative data, they’re stacked even further.   With mismanaged resources it becomes a war we can’t win.

At a certain level of productivity, an invasive species will win the war against a diverse ecological aquatic habitat and turn into a lake of a single species.  This isn’t a good thing for any lake ecosystem or water quality.  It’s all about balance and a healthy lake habitat can help keep an infestation in check.  It’s also possible that certain management techniques could push a lake towards a higher risk scenario if decisions were made without quality abundance data.  Understanding the risks of this happening are key in designing a management plan to be proactive instead of reactive.  Identifying hot spots in abundance and potential causes could be more important than identifying where the invasive species exist.  The best thing is that it’s never too early or late to start. 

The entire ecosystem is tied together.   The cumulative effect of lake stressors can lead to the low resilience required for an invasive species to thrive.  Identifying the stressors and dealing with them could prove more valuable than eliminating an invasive species.  Much like a healthy body can deal with the flu virus better than an unhealthy one, a lake with good shorelines, healthy fish communities, and healthy diversity of plant abundance can keep an infestation in check.  In certain conditions, taking plants out of the lake might be a bad decision that could have a negative effect on lake ecology depending on the lake regime and characteristics of the lake.  
In fact, there are ideal targets and optimal or idea habitat levels and conditions.  Our own Ray Valley, a 10 year veteran of the Minnesota DNR, has devoted a majority of his career to habitat monitoring and interactions between plant abundance, fish, lake resilience and relationships to water quality.  His research on ecosystem balance, namely lake resilience, is instrumental in understanding what’s really happening in a lake and when lakes are at risk.  Much of this is actually tied to plant abundance and changes over time.
Through a long term monitoring program it’s possible to identify the red flags.  Plant abundance growing at deeper depths from year to year could show an increase in water clarity allowing more light penetration.  This might be caused by a recent zebra mussel infestation or a shift in the lakes ecology.  Regardless, something as simple as the depth aquatic plants grow tells us a ton about the direction the lake is going.  In another example, unusual increases in plant abundance in specific areas could indicate, among other things, a home with a leaking septic tank on the lake, a change in the landscape, changes in sedimentation, a run-off issue or a bigger problem upstream.  All of these, left unchecked, could cause more problems for the lakes balance and resilience leading to higher risk of negative impacts of an invasive species introduction.   These changes don’t show up in a visual reconnaissance, presence/absence surveys with a rake, or a single map.   But getting these items resolved could be the management technique that keeps an invasive species from dominating a lake habitat in the future and early detection of these problems could prevent an unfair fight against AIS in the future.
Complete dominance of an invasive species is another story but it’s also the exception.  I’ve seen a number of groups continue to dump massive amounts of money into management without quantitative goals or the ability to effectively quantify the whether they are meeting their management expectations.  Maybe we’re not asking the right types of questions or maybe the technology didn’t exist to get the information we need.  No one is at fault yet.  Once the dialog shifts away from hysterical talking points and towards pragmatic management approaches, we’ll start making real strides in getting ahead of AIS and start achieving improvements in our precious lakes.

So where do we start?  With crowd-sourced solutions like ciBioBase.com we can all start getting the volume of data we really need to have this realistic and proactive discussion.  With cloud computing we’ve broadened the base of individuals that can participate allowing passionate home owner groups to take matters into their own hands instead of waiting for an understaffed DNR.   Aquatic plant abundance maps that took a highly trained hydrographer a week or more and to complete can be done by anyone with a boat, a depth finder and GPS, and 20 minutes for computers do the work of processing the collected data.  This is the future of monitoring and lake management.  There are no longer barriers to getting the kind of data we need for identifying the red flags, eliminating stressors and improving lakes across Minnesota and the globe.
So, let’s understand the lakes heartbeat first.  Let’s get a clear picture of the lakes resilience and its current status for optimal health.  Then we move forward to a future with cleaner lakes.

This article represents and aggregation of my thoughts as I’ve journeyed through this industry and tried to learn the ropes.   This is merely an appeal to think differently about our lakes, expectations, and what the future holds.  The future of our most important resource is brightest if we take a step back, think about what we’re doing and where we need to go.
 
Let’s have those realistic and proactive discussions with real data . . .
                                                         -Matt Johnson, CEO, Contour Innovations, LLC

 

CONTOUR INNOVATIONS AND CIBIOBASE

ciBioBase (ciBioBase.com) removes the time and labor required to create aquatic maps! ciBioBase leverages log file formats recorded to SD cards using today’s Lowrance™ brand depth finders and chart plotters. Data you collect while on the water is uploaded to an online account where it is processed by our servers automatically! We rely on automation to make vegetation mapping cost effective by reducing the technical skills, staff, and hours to produce vegetation abundance maps from raw sonar collection. With the human element gone, you get accurate and objective mapping at lightening speeds! The result is a uniform and objective output all over the world!
I’m proud to be a part of this step in the right direction of a positive future for lake management and overall quality of our most precious resource.  We’re shaking things up and this is a time when everyone benefits.  We work as a huge team to define the best uses and features of one of our products, BioBase, to change the lake management industry.  We’re using expert opinions and powerful cloud computing to create amazing contour and vegetation maps and gain important quantitative metrics of lake health.

Our Company has a culture that considers its social responsibility and contribution.  Our sales team is motivated by how they are changing the future of lakes and resources management.  I was most intrigued by what we might be contributing to the future of a resource that means so much to me.  I’m still intrigued!