The Professional Spotlight series is a deep dive into the global BioBase community where we highlight the unique ways sonar driven mapping is assisting research, conservation and sustainability.
The BioBase team sat down with Dr. Chris Harrod for a look into how he uses BioBase. Chris (from the UK) is a full professor of Fish and Aquatic Ecology at the University of Antofagasta in Antofagasta, Chile. He does a mixture of research, teaching, and administration tasks but our interest with him was the applied research techniques for which he was using BioBase. His research is focused on a macroalgae called kelp (aka seaweed) and its importance as a source of food/energy to fish and invertebrates in the coastal zone. He is also interested in how kelp can function as habitat, food, an anchor of sediment and even slow the turbulent waters of the Pacific Ocean.
Lake Minnetonka is one of the largest and most heavily used recreational lakes in Minnesota and is composed of an interconnected system of bays (Figure 1). Every summer, a rooted invasive aquatic plant, Eurasian watermilfoil creates thick bottom to surface mats in many areas of the lake. While these mats may occur anywhere on the lake, they generally are thickest in certain shallow areas such as the Diamond Reef area in the main lake of Lake Minnetonka (officially described as Lower Lake North). This reef is popular with anglers, power boaters, and sailors. On any given night or weekend, well over a hundred keelboats may take part in regular club racing events or regattas here. World class level sailors, including Olympic champions, America’s Cup, and other accomplished sailors regularly race on the lake and the competition can be intense. When competition is tight, every advantage is important.
Figure 1. Lake Minnetonka; a popular recreational and fishing lake just west of the Twin City metropolitan area of Minnesota. The red box highlights an area popular with boaters, anglers, and sailors. The blue contoured areas represent areas uploaded and processed by anglers using the Genesis mapping service and aggregated into the C-MAP social map. Social maps can also be viewed in the C-MAP App.
Fascinating study recently published in the esteemed scientific journal Ecology and Evolution demonstrating how Lowrance HDS and BioBase were used to create the first bathymetric and vegetation map of Lake Ossa in Cameroon, Africa. These maps along with other environmental data collected by researchers were used to create a habitat suitability model for the charismatic African Manatee, whose populations are now threatened in Africa due to habitat degradation.
This is an open access journal from Wiley and available here for download.
Below is the abstract
African manatee (Trichechus senegalensis) habitat suitability at Lake Ossa, Cameroon, using trophic state models and predictions of submerged aquatic vegetation
Aristide K. Takoukam, Dylan G. E. Gomes, Mark V. Hoyer, Lucy W. Keith-Diagne, Robert K. Bonde, Ruth Francis-Floyd,
First published: 07 October 2021
Abstract
The present study aims at investigating the past and current trophic status of Lake Ossa and evaluating its potential impact on African manatee health. Lake Ossa is known as a refuge for the threatened African manatees in Cameroon. Little information exists on the water quality and health of the ecosystem as reflected by its chemical and biological characteristics. Aquatic biotic and abiotic parameters including water clarity, nitrogen, phosphorous, and chlorophyll concentrations were measured monthly during four months at each of 18 water sampling stations evenly distributed across the lake. These parameters were then compared with historical values obtained from the literature to examine the dynamic trophic state of Lake Ossa. Results indicate that Lake Ossa’s trophic state parameters doubled in only three decades (from 1985 to 2016), moving from a mesotrophic to a eutrophic state. The decreasing nutrient gradient moving from the mouth of the lake (in the south) to the north indicates that the flow of the adjacent Sanaga River is the primary source of nutrient input. Further analysis suggests that the poor transparency of the lake is not associated with chlorophyll concentrations but rather with the suspended sediments brought-in by the Sanaga River. Consequently, our model demonstrated that despite nutrient enrichment, less than 5% of the lake bottom surface sustained submerged aquatic vegetation. Thus, shoreline emergent vegetation is the primary food available for the local manatee population. During the dry season, water recedes drastically and disconnects from the dominant shoreline emergent vegetation, decreasing accessibility for manatees. The current study revealed major environmental concerns (eutrophication and sedimentation) that may negatively impact habitat quality for manatees. The information from the results will be key for the development of the management plan of the lake and its manatee population. Efficient land use and water management across the entire watershed may be necessary to mitigate such issues.
First ever bathymetric map of Lake Ossa in Cameroon created with Lowrance HDS and BioBase. Lake map can be viewed in genesismaps.com/socialmap.
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
The rollout of the new BioBase EcoSound vegetation and bottom hardness algorithm required substantial refactoring of our core processing code. Read about the changes here. While we were under the hood, we took the opportunity to implement some enhancements that our frequent BioBase users should appreciate. NOTE: Users still select the unit (Imperial or Metric) in the primary user profile area of their BioBase account (My Account).
Sonar technology continues to improve bringing anglers and aquatic managers better, more clear pictures of the underwater environment on which they are so intently focused. Launched in 2011, BioBase’s EcoSound technology was the first cloud aquatic mapping system designed to process sonar logs from off-the-shelf Lowrance® sonar and create maps of bathymetry, aquatic vegetation biovolume, and bottom hardness for aquatic resource professionals. Today, BioBase is the leading cloud software solution for automated lake and coastal seagrass mapping.
Between 2011 and 2014, the algorithm underwent five major revisions. The bottom hardness algorithm has undergone two major revisions, with the last one in 2014. Thus, our code base was due for an overhaul in order to maintain performance and compatibility with newer generation Lowrance and Simrad sonar. This refactoring effort was also an opportunity for us to improve the vegetation and bottom hardness algorithms. Many of these improvements also carry over sister consumer technology C-MAP Genesis, which uses many of the same algorithms and backend processing architecture
BioBase’s primary strength is its power as an automated processing engine delivering high quality geospatial data layers on aquatic habitats with very little user input outside of the physical effort to drive a boat and passively log sonar over an area of interest. In addition to the online analysis tools within BioBase like the polygon tool and automated statistical reports, users can export raw depth, vegetation, and bottom hardness data along their track, in X,Y,Z grid format, Google Earth imagery, Lowrance or Simrad Charts, AND NOW ESRI SHAPEFILES OF DEPTH CONTOURS! This feature has been in high demand for survey companies and governments who require detailed water volume analysis for aquatic habitat and fisheries management. Below we walk you through some helpful tips about the feature and how to use it.
When viewing an EcoSound trip or merge of interest, select Export Data – Depth Shapefiles
Example from a big lake:
If the trip or merge you are exporting covers more than approximately 500 m in any one direction, you will see multiple folders in the exported .zip file. For speed and performance, BioBase processes outputs in “blocks.”Example of exported shapefile blocks in Lake Tohopekaliga; a 74 sq. km lake in Florida. Outputs were viewed in the open source GIS program QGIS. NOTE: shapefile exports do not come with a projection and are in the WGS 84 global coordinate system (CRS 4326)
Example from a small pond:
5.8 acre (24,281 sq. m) pond as viewed in BioBaseExported 1ft contours. In this example, exports are completely contained within one block. The user can control whether contours are in imperial or metric, but the values are always stored in metric (e.g., 1ft contour is a value of 0.3048 in the GIS attribute table)Depth Areas as polygons are also bundled into the zipped export. This will allow the user to carry out detailed water volume analysis as a function of depth with fewer post-processing steps than were originally required when data was only exportable as points.
BioBase continues its mission to deliver water and fisheries resource professionals high value data products in the hopes that you can focus less of your efforts on making maps and more on the important tasks of research and conservation.
At C-MAP, we are excited to announce the release of a new feature that allows users to export exact replicates of their BioBase EcoSound maps as Google Earth images (.kmz and .kml; Figure 1). This YouTube video will walk you through how it’s done.
Figure 1. Image of seagrass cover in Newport Bay, CA USA mapped with Lowrance, processed with BioBase EcoSound and exported as a Google Earth .kmz file. Example can be found in the free demo account on http://www.biobasemaps.com.
BioBase processed raw sonar logs and creates habitat maps with sophisticated algorithms. The outputs you see in BioBase are tiled georectified images (.png) of the outputs. The Google Earth feature converts the .png images to Google Earth’s .kml and .kmz file format. .kml downloads are smaller and reference the images on BioBase servers. .kmz downloads are larger and are exact copies of the images stored on our servers. The .kmz option is best for users who wish to archive local copies of their BioBase maps.
These images allow BioBase users to share spatial files with their stakeholders in a free Google format with which many are familiar and use regularly. Recipients can interact with the output zooming in and out to their desire and also adding custom logos and waypoints as they wish (Figure 2).
Figure 2. Add your own logos and other information to the Google Earth exported BioBase EcoSound image
Further, there are a range of open source tools that will convert .kml and .kmz to GIS files for use in ESRI and QGIS products. Given the popularity and widespread use of .kml and .kmz files, there are a range of other applications that we are eager to hear about. Please feel free to share in the comments below.
Converting EcoSound .kml/.kmz files to ESRI Layers (.lyr)
Special thank you to Kevin Johnson and Jennifer Moran at FL Fish and Wildlife Conservation Commission for sharing a tutorial about how to convert .kml/.kmz files to ESRI Layer (.lyr) files for analysis and overlays in ESRI GIS products:
Open ArcMap
Open ArcToolbox > Conversion Tools > From KML > KML to Layer
Input KML File
Toggle to saved .KML file Lake_Kerr_Biobase.kml (example) > Open
Output Location
Default output location is Documents\ArcGIS > Click the folder icon on right and toggle to appropriate folder
Output Data Name (Optional)
Will typically show the name of the kml, change if preferred
Select Checkbox for Include Ground Overlay (optional)
Only necessary for Raster data. Not necessary for lines/points/polygons
*This will take some time to process/load and will show up in ArcCatalog as “FileName.lyr”. Processing will depend on the file and image size. After it displays in the catalog, drag and drop or select Add Data to display the layer on the map.
**Arc GIS may shut down/disappear. You may not receive a green checkmark for execution completion. Reopen the program and go into your Catalog. Should not need to reconvert from .kml.
Lake Kerr (FL USA) aquatic vegetation heat map as seen in BioBaseLake Kerr (FL USA) aquatic vegetation heat map as seen in Google EarthLake Kerr (FL USA) aquatic vegetation heat map converted to a .lyr file in ArcGIS
Ok, it’s a bit overdue. But better late than never! BioBase customers will now see an updated and enhanced viewer for their EcoSound and EcoSat. No longer will users have to struggle to get their map to fit within the little square box of the old viewer with a Bing zoom level that either zoomed too close and cut off parts of the waterbody, or too far to see detail. Below we show you a few screenshots of the major improvements. You can see for yourself by logging into your own account or clicking the Log into DEMO button on the home page of biobasemaps.com, finding a waterbody of interest, and click on the Analyze/Edit button.
In the 8+ years BioBase has been in service, we’ve seen our share of sonar logs and maps (both good and bad). We’ve learned some things and improved back-end processes that have resulted in you getting better maps processed faster. But we’ve also learned from you, our users, about strategies and techniques that result in better outcomes, and what to avoid. Here are eight of those lessons learned:
1. Good transducer installation is critical
You could be the most experienced hydrographer in the world and execute the perfect survey design, but your map will be mostly worthless if your transducer is not securely attached to your boat or is slanted at an angle. We’ve devoted a fair amount to this topic in previous blogs, so we won’t dwell on it here. The two key take aways are: 1) ensure the transducer is installed straight in all directions keeping in mind the slant of the hull in the water fully loaded. Replicate that tilt with your tongue jack when installing your transducer. 2) Install the transducer where the flow of water is smooth and laminar over the transducer face at all speeds. If you lose your transducer signal as the boat speeds up, you probably have an issue with cavitation (water turbulence) around the transducer face. Adjust the transducer height (sometimes only a very small amount) or move it away from rivets or anything else near the hull that could cause cavitation. One of the benefits of working with consumer devices like Lowrance and Simrad is that there is a wealth of online self-help resources and service centers that can help you install your transducer correctly. A simple Google Search “Lowrance Transducer Installation” will turn up all the resources you need. This one from Lowrance is one of our favorites. If you have multiple survey boats and want to make your unit portable, I strongly recommend purchasing and installing multiple transducers on all of your boats rather than a portable transducer bracket. In the grand scheme of things, consumer-sonar transducers are cheap and the consistent results you will get from a firmly mounted transducer is worth it!
Figure 1. Example of a slanted transducer and what affect it has on BioBase maps. A simple Google Search of “transducer installation” will turn up many very good self help resources about how to properly install your transducer.
