Friday, April 21, 2017

The BioBase you've come to love is now EcoSound!

What used to be known as BioBase will now be called EcoSound; a product name that better describes its function - using sound to characterize ecological environments.  We're not getting rid of the BioBase name; it's just going to mean a lot more!  Without changing function of the system, EcoSound uploads and merges will still be housed and displayed in a BioBase dashboard and on BioBase servers.  Soon BioBase will be getting an online face lift and users will have an easier time navigating to the information they need when they need it.  You've requested some changes and development is underway!

BioBase: The cloud platform re-positioned to support more than just sonar processing
With the move to C-MAP, BioBase is receiving a renewed focus to deliver the aquatic industry new and improved automated tools for the assessment of aquatic habitats.  In addition to renaming our sonar processing service EcoSound, the BioBase brand is being elevated to represent its primary role as a powerful cloud processing platform and a dashboard for visualization and analysis of a wide variety of spatial aquatic data.  BioBase will soon represent more than just an automated sonar mapping system.  More about this in a separate announcement coming soon!


Tuesday, January 31, 2017

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.

Classic Literature
Duarte, C.M. 1987. Use of echosounder tracings to estimate the aboveground biomass of submerged plants in lakes. Canadian Journal of Fisheries and Aquatic Sciences 44: 732-735

Maceina, M and Shireman, J. 1980. The use of a recording fathometer for determination of distribution and biomass of Hydrilla. Journal of Aquatic Plant Management 18:34-39.

Maceina, M.J., Shireman, J.V., K.A. Langland, and D.E. Canfield Jr. 1984. Prediction of submerged plant biomass by use of a recording fathometer.  Journal of Aquatic PlantManagement 22: 35-38.

Stent, C.J. and Hanley, S. 1985. A recording echosounder for assessing submerged aquatic plant populations in shallow lakes. Aquatic Botany 21: 377-394

Thomas, G.L., Thiesfeld, S.L., Bonar, S.A., Crittenden, R.N., and Pauley, G.B. 1990. Estimation of submergent plant bed biovolume using acoustic range information. Canadian Journal of Fisheries and Aquatic Sciences 47: 805-812.

Recent Literature
Sánchez-Carnero, N., Rodríguez-Pérez, D., Couñago, E., Aceña, S., & Freire, J. 2012. Using vertical Sidescan Sonar as a tool for seagrass cartography. Estuarine, Coastal and Shelf Science 115: 334–344. http://doi.org/10.1016/j.ecss.2012.09.015

Meadows, GA 2013. A review of low cost underwater acoustic remote sensing for large freshwater systems. Journal of Great Lakes Research 39: 173-182. http://doi.org/10.1016/j.jglr.2013.02.003

Netherland, M. D., & Jones, K. D. 2015. A three-year evaluation of triclopyr for selective whole-bay management of Eurasian watermilfoil on Lake Minnetonka, Minnesota. Lake and Reservoir Management 31: 306–323. http://doi.org/10.1080/10402381.2015.1085114 BioBase Paper

Radomski, P., & Holbrook, B.V. 2015. A comparison of two hydroacoustic methods for estimating submerged macrophyte distribution and abundance : A cautionary note. Journal of Aquatic Plant Management 53: 151–159. BioBase Paper

Valley, R. D., Johnson, M. B., Dustin, D. L., Jones, K. D., Lauenstein, M. R., & Nawrocki, J. (2015). Combining hydroacoustic and point-intercept survey methods to assess aquatic plant species abundance patterns and community dominance. Journal of Aquatic Plant Management 53: 121–129. BioBase Paper

Winfield, I. J., van Rijn, J., & Valley, R. D. 2015. Hydroacoustic quantification and assessment of spawning grounds of a lake salmonid in a eutrophicated water body. Ecological Informatics, 30, 235–240. http://doi.org/10.1016/j.ecoinf.2015.05.009. BioBase Paper

Valley, R.D. 2016. Case Study Spatial and temporal variation of aquatic plant abundance : Quantifying change. Journal of Aquatic Plant Management 54: 95–101. BioBase Paper










Friday, January 20, 2017

FAQ of the year: Does BioBase 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?"

As much as we would like to say unequivocally "Yes!," and have an easy button solution, the reality is it's not that straightforward.  Off-the-shelf Lowrance transducers are designed to track the water sediment interface, especially at the standard 200 khz broadband frequency.  This blog discusses bottom tracking in a little more detail.  BioBase algorithms do evaluate the acoustic reflectivity of bottom signal and will create a relative bottom hardness output.  Bottom hardness generally correlates with sediment depth but the relationship is variable depending on the system and we recommend users calibrate their bottom hardness outputs in their local system of interest.  The better approach in our opinion is knowing how deep the pond of interest should be and then comparing that to what the current conditions are to arrive at sediment depth.

Model Sediment Depth Based on Knowledge of the Desired Condition
Because BioBase can produce a near real-time high-precision picture of current bathymetry, basic knowledge of the baseline/"as built" or desirable bathymetric design can be used to infer sediment depth and create highly precise, professional quality maps.  The Central Arizona Project's management of Arizona's primary aqueduct is probably the most widely cited example of this process.  Our optional GIS Services can take your BioBase map and pre-treatment or baseline map and create a custom sediment depth map. See below for some great examples used by other lake management service providers.

Simulating sediment depth subtracting BioBase-assessed bathymetry from "As Built" bathymetric design in a home owner association pond in CA. Work completed by Waterwork Industries, Windsor CA (http://www.waterworksindustries.com/).  BioBase GIS Services conducted the analysis and created the custom map

Post Dredging Bathymetric Assessment conducted by Ecoresource Solutions, Inc., Arvada CO (http://www.ecology.services/).  Mapped created by BioBase GIS Services.
Post Dredging Bathymetric Assessment conducted by Ecoresource Solutions, Inc., Arvada CO (http://www.ecology.services/).  Mapped created by BioBase GIS Services.
Contact us if you are interested in learning more about how we can help you map sediment depth.

Wednesday, January 4, 2017

Announcement: BioBase Under New Ownership


In late 2016 Navico - the parent company of BioBase - was acquired by Goldman Sachs Merchant Banking Division and Altor Fund IV.  Also in 2016, Goldman Sachs and Altor acquired an industry leading marine cartography and services company called Digital Marine Solutions (DMS), which promotes their products and services under the C-MAP brand (www.c-map.com).  As of January 2017, BioBase and related digital services will be transferring from Navico to DMS (operating under the C-MAP brand).  We are working now on a new organizational structure and product roadmap that will establish DMS as the preeminent marine charting and cloud data services provider across both recreation and commercial sectors.   "...alongside the C-MAP brand we will now have a cloud-based infrastructure and range of web and mobile applications for recreational markets, such as Insight Genesis and BioBase which provide differentiated and high-quality crowd-sourced mapping services that lead the competition," stated Paul Ostergaard, Digital Marine Solutions Chairman. BioBase customers can expect the same high-level of service and minimum disruption with this change. Over the long run, the move to DMS and strategic company investments will bring new high-value features to BioBase and establish it as the aquatic and marine industry standard for processing, visualizing, and analyzing spatial data.  BioBase feature development and technical sales and support will still operate out of the same Minneapolis office where it was born and we anticipate an even faster development cycle in the coming years.  We hope to announce some great features that are already in the pipeline under this new structure and resulting roadmap.  Please direct any questions about this transition to Ray Valley (ray.valley@c-map.com) or Matt Johnson (matt.johnson@c-map.com).

Monday, December 12, 2016

Uploading Waypoints from your Lowrance Unit to BioBase

As we wrote about in our now dated waypoint post, BioBase's waypoint feature is a simple but useful tool for adding data points to your maps. Since we added the waypoint feature in 2013, we have gotten many questions about how to export waypoints collected with a Lowrance plotter and upload the points to BioBase. This post will guide you through exporting waypoints from your newer generation Lowrance HDS or Elite Ti unit and uploading them to BioBase.

1. The first step is to navigate to the home screen of your unit by pressing on the pages button.

2. Scroll down on the left menu to find the "Files" option and select it.

3. Under "My Files", select "Waypoints, Routes, Trails and Trips database

4. Select "Export..."

5. Select .gpx as the file format
 

6. Select your SD card as the destination folder

7. Save the file as a new file
 

8. Remove your SD card from your Lowrance unit, insert it into your computer, and save the .gpx file to your computer

9. Use a third-party software program to convert the .gpx file into a .csv file. We recommend the Minnesota DNR's DNRGPS program

10. View our YouTube video, below, for a walk-through on uploading the .csv file to BioBase. Ensure that the .csv file is properly formatted before uploading.



A BioBase map displaying uploaded vegetation species waypoints

Tuesday, December 6, 2016

Announcing BioBase Stormwater!




Announcing New Product: BioBase Stormwater

Displaying

Get a Lowrance, BioBase Subscription, and GIS Layer Package for only $900!

 Restoring and protecting water quality in urban landscapes starts by having a comprehensive understanding of the storage capacity of ponds designed to treat and filter stormwater runoff. Stormwater ponds that have filled in over time don't serve their purpose, and pollution of higher profile downstream waters often results. Does your municipality have up-to-date bathymetric profiles of all of municipal stormwater ponds? For the price of a song, BioBase can help municipalities acquire and manage this information.

Displaying

Assemble a fully outfitted mapping kayak for less than $600

The full kit shown above was just over $500 USD (including the kayak) and pieces were purchased from a range of retailers (BioBase sells Lowrance, Lowrance Accessories, and some RAM mounts direct). Eligible* subscribers taking advantage of BioBase Stormwater (Essentials Package) get an Elite 5 TI Sonar/GPS Chartplotter for an equivalent of $100.


Collect data easily and quickly

Swiftly glide in concentric circles while you passively log your sonar and GPS. Follow your trail as you work your way into the middle of the pond.  Less than an hour later, you should be done with all the hard work. Upload your Sonar Log from your MicroSD card to BioBase and let our cloud-servers create high resolution bathymetry maps for you automatically in less than an hour!

 Displaying

Go fully autonomous with Platypus robotic boats

BioBase has partnered with Platypus LLC to offer ultra rapid, fully autonomous solutions data acquisition and processing. At a cost that rapidly decreases with the larger number of ponds (as low as $18/acre) you elect to map, Platypus staff or partners will travel to your municipality and deploy one to several autonomous boats enabling them to map large numbers of ponds over a short period of time.  This video shows the process in action with their Lutra prop boat. These ultra light boats draft inches of water and reduce labor and occupational safety hazards associated with manned boats. Build an online quote here or contact www.senseplatypus.com to learn more about their autonomous boats and pond mapping services.

Displaying

With the Stormwater Professional Subscription, our GIS staff will summarize pond statistics and package into a GIS Layer

For $900 (Stormwater Professional Package), you'll get all the benefits of the basic Stormwater Essentials subscription, plus our GIS staff will take it a step further and summarize pond statistics (size, max depth, water volume) and assemble both point and polygon boundary data into a GIS layer. Additional GIS Services are available to suit the unique needs of your municipality to efficiently manage water resource assets and comply with state and federal regulations.

Contact info.biobase@navico.com if you are interested in getting more details about BioBase Stormwater or scheduling a demo.

*Eligible customers - Local units of government or private service providers who remain within defined municipal boundaries.  Private service providers can purchase multiple subscriptions for multiple municipalities if desired. Qualifying customers are eligible for one Elite-Ti. Contact info.biobase@navico.com for more information

Thursday, November 10, 2016

Minnesota LGU Taking Citizen Aquatic Plant Monitoring to New Level!

At conferences, we often encounter curious coordinators of citizen monitoring programs about how they could use automated consumer technologies to monitor aquatic habitats.  When they learn what BioBase does, a frequent question is: "That sounds pretty cool and something we could certainly apply, who else is using BioBase for citizen science applications?"

In response, we always highlight the Prior Lake Spring Lake Watershed District (PLSLWD) in Minnesota USA.  PLSLWD is a leader when it comes to leveraging the talents of volunteers, partners, and Lowrance and BioBase technology to implement a comprehensive, standardized aquatic plant monitoring program.  To learn more about the PLSLWD's program and implementation strategies, check out this report.
Schematic showing the collection of merged files collected by citizen volunteers.  A PLSLWD intern coordinated efforts across multiple volunteers, informed citizens about desired travel routes, and even preloaded transect guides in their Lowrance Chartplotter for citizens to follow.


Maps of Bottom Hardness (top), Bathymetry (middle), and Aquatic Vegetation Abundance (% of water column filled with vegetation or biovolume, Bottom) collected by citizens on Prior Lake with Lowrance Sounders/Chartplotters and processed automatically by BioBase Automated Lake Mapping System.

Friday, September 23, 2016

BioBase does Seagrass, Kelp, and Tides Too!

Although BioBase was originally developed for aquatic vegetation mapping in inland lakes, users along both US Coasts have helped us diversify its toolbox to now be a powerful coastal habitat mapping tool as well!

One of the biggest challenges of mapping coastal habitats is their tidal influence with depths changing harmonically based on the moon phase and other factors.  Fortunately however, widespread tide stations and large public databases of tide predictions allow for accurate and precise offsets to georeferenced and time-stamped sonar logs from Lowrance HDS or Elite units uploaded to BioBase.  BioBase immediately queries the nearest tide station to your upload (up to 75 km) and adjusts your depth and seagrass or kelp biovolume to the Mean Lower Low Water (MLLW) datum every 5 minutes.  Tidal statistics (Avg., start, stop, high, low,) are archived in your account for each trip.

Simulate Tidal Conditions with the Data Offset Tool
Figure 1. demonstrates what seagrass density conditions looked like in a harbor in Newport Bay CA USA on 12/5/2012 at MLLW (Data collected by Rick Ware; Coastal Resources Management Inc., Corona Del Mar, CA).  Areas of red indicate where seagrass or eelgrass (Zostera marina) grows to the surface at MLLW and may interfere with the passage of vessels in and out of the Marina.  Thus, these habitats may be high risk of damage.  Full access to the trip displayed in Figure 1 among other trips, is available for free to anyone in our public demo account

We can also simulate what this same area looks like under high water conditions (Mean Higher High Water - MHHW) using the data offset tool in BioBase (Figure 2).  MHHW data were retrieved from the interactive NOAA tide web tool and the average tide (1.5 ft) for the hour that data were collected in this area in Newport Bay was added to the MLLW average offset (3.84 ft; Figure 3).
Figure 1. Mapping tracks (red lines) overlain on a seagrass density heat map with depth contours.  Areas of red are where seagrass grows close to the surface at low tide (MLLW).  Areas of green are low-lying seagrass areas.  The cross section of the sonar log displaying the high resolution imagery of StructureScan is displayed on the right and synchronized with the map upon each upload (Trip Replay). Data were collected with Lowrance HDS and uploaded to BioBase
Figure 2.  Data Offset tool in BioBase can be used to offset depths to a benchmark elevation (e.g., full pool for reservoirs), or custom tides as is the case here.  MHHW data were retrieved from the Newport Bay Entrance Tide Station and added to the MLLW offset to simulate high tide conditions

Figure 3.  Trip-specific tide data retrieved  from the NOAA Tidal Prediction web page.  60-min values during the precise hour of data collection were added to the MLLW offset in the Data Offset tool in BioBase.
Compare effects of tides in the automated reports
Comparing results from the automated reports (Figures 4 and 5) one can see the effect that tides can have on biovolume and potentially seagrass habitat conservation.  Notice that percent vegetation cover (PAC) does not change much with tides, but biovolume (BVp), which brings in the 3rd dimension of plant height, does.

Figure 4.  Excerpt of automated report for MLLW conditions in Newport Bay.  Statistics on survey area, water volume, vegetation summary statistics, waypoint summaries, and important metadata are available with each upload.
Figure 5. Excerpt from BioBase trip report with a MHHW offset added to the output.  PAC (grid).  Compared with  MLLW data in Figure 4, PAC only increased from 64.5% to 71.3% but average biovolume in vegetated areas decreased from 38.8% at MLLW to 16.7% at MHHW. 
Interpreting outputs in extreme tides
In some areas of the Pacific Northwest it is not uncommon to see 10 ft tides.  Mapping seagrass at high tide in areas high and dry at low tide, represents a great opportunity to passively map the cover and density of seagrass beds. In areas exposed at low tide, BioBase will reclassify any seagrass detected to 100% biovolume, displaying a red area of seagrass coverage (Figure 6).

Figure 6A.  Map displaying density of seagrass beds at MLLW in Puget Sound, WA USA with a 9.3 foot average tide.  200 khz Sonar chart on right shows the actual depth during the time of assessment and seagrass growth on bottom.
Figure 6B. Zoom of Figure 6A and display of tide-corrected point data along boat track (red line).  Highlighted cell corresponds to the orange dot on the map on the left and the area just to the right of the faint white line on the sonar graph on the right.  If the seagrass plant height is greater than the tide-corrected depth, the bv registers a n/a and it is considered 100% (red) in the biovolume map.  If plant height is less than the corrected-depth, biovolume is recalculated as the proportion of plant height to corrected water depth. Zero plant height and biovolume areas remain

Use the Polygon Tool to delineate and monitor sensitive seagrass areas.
Figure 7 demonstrates how a polygon could be drawn and used to calculate seagrass cover statistics in a specific area and time.  You can use the same polygon on subsequent trips to monitor change over time and evaluate protection or restoration.

Figure 7.  The Polygon Tool was used to draw a boundary around a bed of seagrass in a shallow area of Puget Sound, WA USA where boat traffic is high.  The same polygon can be used to monitor change across multiple trips in the same area (users should take reasonable measures to travel the same path repeatably to generate the most comparable results)

Automated Tools for Kelp Detection and Mapping
Kelp, a widespread marine macroalgae is also the focus of global conservation efforts.  Kelp can grow to be very tall and provide habitat for a variety of nearshore marine life.  We have seen great success by researchers like Rick Ware from Coastal Resources Management Inc using Lowrance HDS and BioBase to map kelp forests of the US Pacific Coast (Figure 8).  As seen in the Broadband 200 khz sonar log on the right, BioBase detected Kelp up to 9.8 m (32 ft) long!  Ground truth data collected by Mr. Ware confirmed this acoustic signal was indeed kelp.  This trip is also publically available in our demo account.
Kelp, BioBase, mapping, Lowrance
Figure 6.  Kelp beds off the Southern California Coast detected by Lowrance HDS and BioBase and confirmed by researchers.
Let us know how you are using BioBase to address questions in tidal influenced habitats.

Monday, September 19, 2016

Portability Options for Your Lowrance

We recently sent out a mailer to our subscribers letting them know about the portability solutions that we have come up with.  Within minutes we received photos and details from many of our customers about how some they have used a little ingenuity to mount their Lowrance HDS units on unique water craft.  Below we have a photo gallery of images that could help you design your own portable setup.  Of primary importance however is a mount that minimizes cavitation (air bubbles) directly under the transducer (e.g., surface noise) and maintaining a correct angle on the transducer.  See recent blogs on this topic. The preferable solution is to permanently mount separate transducers following DIY guidance like shown here on each survey craft and just move the Lowrance Elite or HDS display from boat to boat.  But if the job calls for a fully portable mount, we can help!

Coastal SeaGrass  Mapping


Rick Ware, Senior Marine Biologist with Coastal Resources Management, Inc. sent us these images of his set up for portability on their Achilles inflatable.  He commented that the same system can be used on his single and double kayaks as well.

Creative Low-cost Kayak Set-ups


When the water body you plan to map calls for a small craft a kayak works great.  The external mount for the transducers works and is preferable to shooting through the hull, however, drag and surface growing vegetation can cause issues.  The ideal mount is described here by Lowrance's Lucas Steward on a stand-up kayak with a scupper hole and Lowrance's scupper-hole transducer mount (part no. 000-10606-001).  Here's a couple of shots (top/bottom) of the scupper-hole set up and pond data collections with a Lowrance Elite 5 or 7 Ti


Or, you can buy a battery and mounting kit like shown here


Florida Air Boat



Dean Jones, with the Center for Invasive and Aquatic Plants sent us these images of his portable set up on the back of an air boat.  Since the early goings of vegetation mapping with BioBase we've worked hard to find and test a good mount for an airboat.  Dean has found a great solution that works every time!  He's getting great maps

Although the Lowrance units are always easy to install sometimes our users need a little creativity to meet their unique requirements.  Necessity is the mother of invention . . .

Thru-Hull and Narrow Beam Third Party Options

Ryan Moore also with the Center for Invasive and Aquatic Plants was looking for narrow beam options for more precise mapping of aquatic plants and installed an Airmar B164 bolt-thru-hull transducer.


Navico's full line of compatible transducers can be browsed and purchased at the Navico Store.

Below is a gallery of photos you may find helpful for setting up your Lowrance unit and accessories

Creative set up from guts of an old trolling motor (try Craigslist.com), a $20 machined aluminum cap, and $3 in hardware. Photos courtesy of Michael Dorland.
From our German distributor Echolotzentrum Schlageter.  They also make a professional heavy-duty dual mount for your skimmer + LSS2 transducer.

Spring-back bracket from Transducer Shield and Bracket http://www.transducershieldandsaver.com/product/sbb-4-spring-back-bracket/.  Photos courtesy of Josh Bowen at Duke Energy Carolinas.

Lowrance HDS, portable, transducer, skimmer, LSS-2

Lowrance HDS, portable, transducer, mount

Portable Lowrance HDS7 Touch Set up on a 14-ft Carolina Skiff (Photo Courtesy of Aquatic Systems Inc)

Photo courtesy of Bruce Sabol, Army Corps of Engineers Research and Development Center.  In this example, high speed may cause excessive surface noise on your Sonar screen.  Slow speed or adjust transducer placement if this is an issue.



Lowrance HDS, portable, bracket, GPS, external, mount


Photo courtesy of Bruce Sabol, Army Corps of Engineers Research and Development Center


Lowrance HDS, NMEA, GPS, installation
Photo courtesy of Bruce Sabol, Army Corps of Engineers Research and Development Center

Lowrance HDS, NMEA, GPS, installation

The NMEA2000 protocol is a great innovation to network a range of accessory devices, but adhering to installation instructions is important or your HDS or Elite Ti unit will not find the device.  In addition to the diagrams and shots above, Lowrance's Jacob Scott provides a very instructional video. Always verify that the GPS signal is being received by the antenna before proceeding to map lakes (check System-Satellites-Configure - look for the name of the internal antenna - e.g., Point-1 - to be displayed and active).  External GPS directly over the transducer is important for creating the most precise map output.


Although it eliminates portable options. the mount that ensures consistent, strong, and correct signal is a permanent mount and ideally, installed professionally by your local marine dealer or service center.
Hydraulic tilt professionally installed.  Good for stowing.  Photo courtesy of Amy Peters; South Florida Water Management District

Another creative kayak installation; photo courtesy of Dr. Reed Green; Adjunct Professor University of Arkansas Little Rock.
Lowrance StructureScan Kayak ciBioBase
StructureScan mount on a kayak.  Photo courtesy of Dr. Reed Green Adjunct Professor University of Arkansas Little Rock.
Lowrance skimmer transducer mount through a scupper hole in a kayak.  Photo courtesy of Dr. Reed Green Adjunct Professor University of Arkansas Little Rock.




UPI Michigan's unique portable solution!


Rig up a fixed but swinging arm that carries the benefits of locking the transducer into the correct position when in use, but allowing the user to stow when needed.


From our Finnish Service Manager, Petteri Partenen: "This mount was made for a portable structure scan solution. [Simrad] NSS12 was in a pelicase with batteries, LSS HD and WIFI-1. On the pics it was on test on a Navy tender. GS15 GPS antenna was mounted on top of the mount to have an accurate position at the transducer location."