Training EcoSat Vegetation Classifications: User tips

What is EcoSat?
EcoSat delivers a one-of-it’s-kind semi-automated cloud processing of very high resolution satellite imagery to map nearshore vegetation and coastal benthic habitats.  EcoSat uses the latest multi-spectral imagery from reputable providers such as Digital Globe (World View 2,3 and 4), Airbus Defence and Space (Pleiades), and ESA’s Sentinel program and industry standard image processing techniques.  Sophisticated Amazon Web Service cloud infrastructure rapidly processes imagery, creates reports and imagery tiles, and delivers detailed habitat maps to user’s BioBase dashboard where it can be analyzed and shared.  Average turnaround time from imagery tasking order to delivery of results is 90 days.  The rapid and standard processing methods are allowing entities like the Florida Fish and Wildlife Conservation Commission to establish regular monitoring programs for emergent vegetation.  The extremely long and expensive one-off nature of conventional remote sensing mapping projects using non-repeatable tailored techniques has prevented natural resource entities from assessing the degree that habitats are changing as a result of environmental stressors such as invasive species invasions and climate change.

Continue reading “Training EcoSat Vegetation Classifications: User tips”

Guest Blog: Correlations between EcoSound Biovolume and Aquatic Plant Biomass

Andrew W. Howell and Dr. Robert J. Richardson
 
North Carolina State University; Dept. Crop and Soil Sciences
 
Why do we want to sample submersed vegetation biomass using sonar?

Invasive aquatic plants, such as non-native hydrilla (Hydrilla verticillata), negatively impact waterway systems in the southeastern United States and on a global scale. Often, these aquatic weed species impede recreational activities, power generation, and disrupt native ecological systems. Costs associated with aquatic weed management include expenses accompanied with monitoring, mapping, and implementing control measures. Prompt detection and accurate mapping of submersed aquatic vegetation (SAV) are critical components when formulating management decisions and practices. Therefore, SAV management protocols are often reliant upon the perceived extent of invasion. Traditional biomass sampling techniques have been widely utilized, but often require significant labor inputs, which limits repeatability, the scale of sampling, and the rapidness of processing. Advances in consumer available hydroacoustic technology (sonar) and data post-processing offer the opportunity to estimate SAV biomass at scale with reduced labor and economic requirements.

The objectives of this research were to document the use of an off-the-shelf consumer sonar/gps chartplotter to: 1) describe and characterize a relationship between hydroacoustic biovolume signature to measured hydrilla biomass; 2) develop algorithm for on-the-fly assessment of hydrilla biomass from interpolated biovolume records; 3) define seasonal hydrilla growth patterns at two NC piedmont reservoirs; and 4) create a visual representation of SAV development over time. From these objectives, the expected outcome was to describe a protocol for passive data collection while reducing the economic inputs associated with labor efforts involved in biomass sampling and post-processing evaluations. In our research, a Lowrance HDS-7 Gen2 was utilized to correlate biomass from monospecific stands of hydrilla within two different North Carolina piedmont reservoirs using BioBase 5.2 (now marketed as EcoSound – www.biobasemaps.com), cloud-based algorithm to aid in post-processing.

Continue reading “Guest Blog: Correlations between EcoSound Biovolume and Aquatic Plant Biomass”

C-MAP PARTNERS WITH EOMAP TO RELEASE ECOSAT

FOR IMMEDIATE RELEASE
June 22nd 2017

Emanuela Ferina
Global Marketing Manager, C-MAP
emanuela.ferina@c-map.com

Ray Valley
Aquatic Biologist & Biobase Product Expert 
ray.valley@c-map.com 

Building on the Power of the BioBase Cloud Mapping Platform, New Product Generates Full Inventories of Shallow Water Habitats

C-MAP®, a leading supplier of digital navigation products to the maritime market, in partnership with a global leader in remote sensing services, EOMAP GmbH & Co KG, announced today the launch of EcoSat.
A new semi-automated wetland and coastal habitat mapping product that is part of the BioBase Cloud Mapping Platform, EcoSat uses the unique reflectance properties of vegetation and sea bottoms from high resolution satellite imagery and creates distinct polygon objects with spatial properties like area and perimeter. EcoSat’s power is doubled when combined with its sister product EcoSound which uses sonar and GPS data files to map depth and submerged vegetation. EcoSat complements BioBase’s core functionality of submerged habitat mapping with sonar with new capabilities to inventory habitats in vast nearshore areas of aquatic environments. Aquatic habitat managers across the globe can use EcoSat to quickly assess and monitor changes in wetland complexes, shallow lakes, tidal estuaries and marshes, and benthic habitats. EcoSat will also be an invaluable tool for the assessment and monitoring of invasive aquatic plants. The Florida Fish and Wildlife Research Institute (FWRI) is currently using EcoSat and EcoSound to generate full aquatic vegetation inventories in high profile Florida lakes.
“The combination of the latest habitat image classification procedures and the high-performance of the BioBase Cloud environment brings significant benefits to all users that don’t have access to large data processing capacities,” said Marcus Bindel, EOMAP data analyst.
Leveraging the expertise of a team of remote sensing experts at EOMAP, EcoSat rapidly processes raw satellite imagery and creates unique habitat classifications (e.g., polygons in a shapefile). Shapefiles and raw imagery – that are often hundreds of megabytes – are uploaded and processed by BioBase’s powerful cloud-based servers. Shapefiles and imagery are stored in a user’s or organization’s private online account for easy access and sharing. BioBase customers can interact with these detailed EcoSat files simply with any internet-enabled device. Users can also export custom charts of the EcoSat classifications to their Lowrance or Simrad chartplotter and navigate directly to a habitat of interest.
“BioBase is a first-of-its-kind, off-the-shelf cloud solution for organizations and businesses that need full aquatic habitat inventories quickly,” said Greg Konig, head of product development, C-MAP. “Prior to BioBase automated mapping technologies, aquatic managers and researchers would spend countless hours at high costs just to produce a map. But not anymore.”
For more information on C-MAP Light Marine and Commercial products, visit www.c-map.com. For more information about EcoSat and the BioBase Cloud Mapping Platform, visit www.cibiobase.com.
About C-MAP:
C-MAP is a world-leading provider of marine information with products ranging from electronic navigational charts to fleet management, vessel and voyage optimization. C-MAP offers the world’s largest marine navigation digital chart database, helping customers to address the complexity of maritime operations through integrated, intelligent information systems. For more information, visit www.c-map.com.
Processed polygons of emergent vegetation beds in Lake Tohopekaliga, FLfrom high resolution satellite imagery combined with submerged vegetation mapped with BioBase – EcoSound

Download automatically created Lowrance or Simrad Chart files from EcoSat and verify classifications directly from your watercraft  

BioBase EcoSound does Seagrass, Kelp, and Tides Too!

Although BioBase EcoSound 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 EcoSound.  BioBase EcoSound 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.

Continue reading “BioBase EcoSound does Seagrass, Kelp, and Tides Too!”

Composition Algorithm Improved!

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

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

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

Figure 1. Continuous, unitless data are created with each GPS coordinate to reflect relative hardness from soft 0-0.25 (light tan), to medium 0.25 – 0.4 to hard 0.4 – 0.5 (dark red).

How does it compare with actual data?  Verification results from independent researchers
Unlike conventional models or software programs that use limited datasets in a narrow range of conditions to calibrate and verify model outputs, BioBase is able to draw from our central database and network of professionals using the system to develop new or improved algorithms.

For revisions to the composition algorithm, Navico technical staff worked with scientists from the University of Florida (Mark Hoyer), USGS in Little Rock AR and Reston VA and  (Drs. Reed Green, Nancy Rybicki and Elizabeth Striano), and across the pond with the Center for Ecology and Hydrology (Drs. Ian Winfield, Helen Miller, and Joey van Rijn) evaluating the agreement of their independently collected bottom composition data with companion BioBase hardness datasets.  Despite field error in the precise estimation of actual hardness and overlap with simultaneously collected BioBase data, we were encouraged by the high agreement of compared data sets.  See for yourself below!

Figure 2.  Sediment depth measured by a coring device as it relates to simultaneously collected Lowrance acoustic data which was processed for bottom hardness with BioBase.  Data were collected in Lochloosa Lake, Alchua Co. Florida USA by Mark Hoyer; Director of Florida Lakewatch at University of Florida – Gainsville.  Seventeen sites were also sampled in Lake Sampson (Bradford Co., FL).  Sediment thickness at those sites only averaged one inch.  All companion BioBase composition data indicated hard substrates, and thus complete agreement.  Lastly, in Newnan’s Lake (Alachua Co. FL) fewer agreements between sediment thickness and BioBase composition were found due to the acoustically reflective organic peat substrates in the lake.
Figure 3. Sediment depth measured by a 3/4 inch all thread pipe pushed to the “point of refusal” as it relates to simultaneously collected Lowrance acoustic data which was processed for bottom hardness with BioBase.  Data were collected in Millwood Lake, Ashdown Co., Arkansas USA by Dr. Reed Green USGS Arkansas Water Science Center.  Publication of sediment depth patterns on Millwood can be found at: Richards, J.M., and Green, W.R., 2013, Bathymetric map, area/capacity table, and sediment volume estimate for Millwood Lake near Ashdown, Arkansas, 2013: U.S. Geological Survey Scientific Investigations Map 3282, 1 sheet,http://dx.doi.org/10.3133/sim3282.
Table 1. Agreement between visually estimated substrate hardness while collecting Lowrance/BioBase composition data from 9 of 23 samples in coastal Back Bay, Virginia Beach VA, USA in 2012.  BioBase composition data at the remaining 13 sites were not generated due to depth or vegetation thresholds.  Bottoms cannot be typed where vegetation fills > 60% of the water column or in depths less than 2.4 feet from the transducer face.  Data were collected by Dr Nancy Rybicki and Elizabeth Striano, USGS – Reston VA as a component of a vegetation assessment study.

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

Figure 4B.  Bottom substrate (and Northern Pike) as viewed from a camera mounted on a Remote Operated Vehicle (ROV) in Windermere.  See Figure 5A for the Hardness Score and Corresponding BioBase Hardness data

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

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

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.


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!

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.

What is BioBase All About?

We’ve made historical bathymetry and aquatic habitat mapping quick and cost effective!

 BioBase has three main concepts: (1) Data Collection (2) Automated Data Processing and (3) Interactive Display. Acoustic data our subscribers collect using Lowrance HDS depth finders is automatically processed and warehoused online in a private account.

Our algorithms process for depths (bathymetry) and plant canopy height (sav abundance). By collecting data each time you or one of your colleagues are on the water, you are able to develop a historical database of aquatic habitats.

This powerful System uses the raw acoustic data you collect and sophisticated cloud based algorithm processing and GIS tools. Data collected on SD cards while on the water is uploaded to an online account where it is processed by our servers automatically. This innovative mapping solution has instantly made historical SAV and lake ecological habitat studies cost effective by reducing the technical skills, staff, and hours to produce vegetation abundance maps from raw sonar collection. The result a comprehensive and historical look at lake status and SAV changes over time in relation to important characteristics such as invasive species, herbicide performance, abundance, and resilience.

These historical maps can be used to monitor management successes, allocate efficient management, and provide detailed displays when reporting results.

One of the major benefits of cloud based software is that as we make changes to our algorithm or push out new features, everything is automatically associated to every trip you’ve uploaded to the System. For example: We recently pushed out a total water volume analysis tool in our standard reporting. Every trip uploaded to the System before this feature was available now has total water volume details.

CI BioBase also provides an objective output that is consistent from trip to trip. This provides objective uniform reporting for every trip uploaded to the System. We’ve removed the human element from the processing! Our servers don’t take breaks or vacations!

You can check out BioBase for yourself by logging in using our demo account:

You can log in here: www.biobasemaps.com
Username: demo@cibiobase.com
Password: demo

Since you no longer have to do the processing, the door is open to gathering data each time you’re on the water regardless of whether you’re actively managing a particular water body. The best time to plant a tree was 20 years ago; the second best time is now. Start building a historical database of the lakes you manage today with BioBase! Don’t wait until you have a project on a particular lake to gather historical data. Now anyone can map depths and vegetation every time they’re on the water!

Subscription required for each person collecting data. Unlimited subscriptions available!

www.biobasemaps.com