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
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.
Example from a big lake:
Example from a small pond:
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.
2020 has been a busy year for BioBase improvements and new feature releases. Previously exclusive to BioBase’s sister consumer mapping platform, C-MAP Genesis, BioBase users can now export their bathymetric, aquatic vegetation heatmap, or bottom hardness map in a file format (AT5) that is compatible with most newer generation Lowrance and Simrad chartplotters. This feature enables researchers and aquatic resource managers to return to surveyed areas of interest and precisely target follow-up surveys or management actions (e.g., strategic taking of water or aquatic plant samples, placement of fish habitat structures or aeration equipment, precision applications of aquatic herbicides, etc.)
In the images and captions below, we’ll walk you through how to do this in your biobasemaps.com account.
- Register your Lowrance or Simrad Chartplotter in your BioBase Account
2. Export the GPS Chart file from the desired EcoSound Trip or Merge from BioBase.
3. Unzip the downloaded file and save to a MicroSD card (<32 GB).
4. View and Use in your Lowrance or Simrad!
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.
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).
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
- Input KML File
*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.
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!
By Ray Valley
Aquatic Biologist and BioBase Product Expert
One of BioBase’s strengths is its simplicity. You don’t need an advanced engineering degree in hydrography to make a high quality bathymetric map with an off-the-shelf sonar device. If you have your transducer installed correctly, settings correct on your Lowrance, and achieve good coverage on your waterbody of interest, then BioBase’s EcoSound algorithm will produce a very precise, high quality bathymetric map output within minutes of upload to biobasemaps.com. The speed and ease of bathymetric mapping wins the day for many of our users, but perhaps even more valuable, is the benchmark you are setting for an unknown day in the future when something has changed on the lake and you need to have some “historical” information to understand how much change has taken place
Use Case: Monitoring Sedimentation
One of our most frequently asked questions by new users is “will BioBase measure sediment thickness or the depth of the sludge?” This was a source of a recent blog. Interestingly, the answer is different depending on how long our customers have been using BioBase. For the user who has no prior information about how deep the lake or pond is supposed to be, BioBase may not provide detailed enough information about the actual thickness of the sediment (sediment depth is correlated with EcoSound hardness but it is highly variable; see this blog for further details). However, for the pond management consultant who happened to “BioBase” a client’s pond in 2013 while she happened to be on site for another matter and is now hearing from the client in 2019 that his pond is “filling in,” the answer about whether BioBase can tell him how much sediment has filled in is a most definite yes! For this pond consultant, it was a most fortuitous (or perhaps prudent?) thing that she decided to voluntarily map her clients pond in 2013. Now with a 2019 survey, she can precisely quantify exactly how much sediment has accumulated and where over the 7 years by doing a simple subtraction of the depth and water volume between surveys and comparing maps. The comparison of maps can be done a fancy GIS way like described in this blog. Or a quick and easy way through BioBase (see examples below).
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.
A. Adams, M. De Jesus, G. Cummings, and M. Farooqi
Texas Parks and Wildlife Department, Inland Fisheries
Texas Parks and Wildlife Department Inland Fisheries (TPWD IF) biologists traditionally use “stand-alone” mapping interfaces to generate 2-dimensional (2-D) aerial outputs of fish habitat and benthic surveys of aquatic systems. Preliminary work has shown promise in the use of a different method, which generates interactive 3-dimensional (3-D) high-definition (HD) outputs. During field surveys, a Lowrance© Elite 9Ti GPS unit with TotalScan™ transducer was used to generate data points along boat transects on waterbodies of interest. A waterbody “Vegetation Analysis Report” and HD maps were then generated from these data using web-based mapping algorithms through BioBase©, and ArcMap 10.3© GIS software. Aquatic vegetation biovolume, bathymetric mapping, and benthic substrate composition outputs, produced by BioBase© aided biologists in selecting best management strategies, regarding aquatic vegetation management and angler access development at three central Texas impoundments. This tool can prove valuable to fisheries managers needing a higher resolution of survey results to fine-tune management strategies. At a cost of $2,5001 US for a yearlong subscription, cost-benefit would have to be assessed by individual users, based on their needs.
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.