BioBase is a cloud platform for the automated mapping of aquatic habitats (lakes, rivers, ponds, coasts). Standard algorithms process sonar datafiles (EcoSound) and high resolution satellite imagery (EcoSat). Depth and vegetation maps and data reports are rapidly created and stored in a private cloud account for analysis, and sharing. This blog highlights a range of internal and external research, frequently asked questions, feature descriptions and highlights, tips and tricks, and photo galleries.
At BioBase, we are delighted to announce a new subscription model for EcoSound, created to ensure all customers can make the most out of the mapping platform.
Aligned with parent company Navico’s Environmental Sustainability Mission, and to support the widespread adoption of our technology to further the goals of aquatic conservation, BioBase will be providing free subscriptions (with up to 20 GB of storage) to Environmental Agencies, Non-Profits, and Universities engaged in aquatic resource management and research.
In order to make this a smooth transition for our current subscribers, we will move anyone with an unlimited Single-User or Single-Waterbody subscription into the appropriate full-featured Habitat+ subscription with sufficient storage until their subscription is due to expire in 2021.
FREE Subscriptions for Government, Universities and Environment Agencies
Current subscribers eligible for a free subscription should notice little change outside of being eligible for additional “freemium” subscriptions for their institution
Further, Navico will also be offering discounts of up to 35% on Lowrance hardware for US-Based agencies and universities.
Spokane Tribal Fisheries
Airway Heights WA, USA
We recently began collection of baseline data on a small reservoir in northeast Washington State to gain a better understanding of the aquatic community and effects of the hydrological system on the flora and fauna. There is little public access and surveys along this stretch of river are limited. Flowering Rush and Eurasian Watermilfoil, both invasive plant species, have been identified in the reservoir, but distribution fluctuates coincident with changing water elevations and flows. Distribution of the plant community in the reservoir is not well understood. Traditional plant survey methods using the rake method are used to collect submerged plants, but the patches need to be located first. Bathymetric maps used previously were limited and we were looking for a good way to locate and map distribution of vegetation throughout the reservoir. Identification of the vegetation patches would allow us to target specific locations for invasive plant monitoring and inform fish surveys. To accomplish this, we used the Lowrance HDS12 with side and down scan capability. We made several tracks throughout the reservoir to maximize coverage and recorded all our movements on the Lowrance unit. The process was fairly simple…as we drove the boat around the reservoir, we recorded our tracks and saved the files as .sl3 files on the Lowrance unit, and uploaded them to the BioBase website. Once BioBase received the upload, they processed the data and we were then able to obtain bathymetric and vegetation heat maps that included vegetation percent biovolume such as the one shown below.
Since I was new to this product, I had a bit of a steep learning curve. [BioBase Product Expert] Ray Valley provided exceptional technical support in helping resolve challenges we faced during the initial setup and navigating the BioBase output. The outputs that we obtained from BioBase using the data (tracks) we recorded included bathymetry and aquatic distribution heat maps that provided a baseline for future invasive plant monitoring in this reservoir. Since we recorded several tracks, Biobase processed them individually which provides the user with the ability to look at smaller sections or to combine areas into a larger picture. The user should check the outputs to confirm the information provided in the outputs matches known site conditions. This information will be used to guide fish surveys and inform invasive species management in the reservoir. This product performed as promised by BioBase and met our expectations. We found this to be a valuable tool that we will continue to use for additional vegetative mapping and delineation to inform management of invasive species.
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).
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 ArcToolbox > Conversion Tools > From KML > KML to Layer
Input KML File
Toggle to saved .KML file Lake_Kerr_Biobase.kml (example) > Open
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.
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.
We were excited to see another great paper published by researchers in an esteemed peer-reviewed journal (Aquatic Botany) using BioBase’s EcoSound to demonstrate patterns in aquatic vegetation growth in Idaho’s beautiful Coer d’Alene basin. In addition to being novel work showing how aquatic vegetation rises and falls throughout the year, this work is a precursor to understand how heavy metal contaminants are absorbed and released into waterways. BioBase is a key technology for these researchers to explore this important environmental topic! The paper is referenced online here.
See here for a complete list of peer-reviewed papers using BioBase technology.
Fisheries Scientist Jim Lyons from the UK’s Environment Agency has been in action over the last few months introducing Yorkshire Fisheries Officers to the benefits of the BioBase system. Following two days of survey work on a couple of gravel pit fisheries in the area the team received a report less than a week later. Mike Lee from the local team and the angling clubs who manage the waters, were very impressed with the technique and the report generated. They have come away with a host of ideas about how to further use Lowrance Fish Finders and the Biobase System across their catchment in both river and Stillwater fisheries.
Further Mr. Lyons, recently presented to aquatic plant specialists from the Environment Agency, Natural England and Natural Resources Wales at Preston Montford Field Studies centre as part of the relaunch of the aquatic plant specialist’s network.
Area specialist are responsible for the technical lead for aquatic plant survey delivery within their Area, ensuring that all aquatic plant surveyors are suitably trained and have the relevant support to deliver their surveys. The specialists also play a key role in underpinning the delivery of the quality assurance programme.
Mr. Lyons talked about ‘Using acoustics and cloud-based technology to monitor aquatic weed.’He shared with the group the benefits of using BioBase to inform weed management programmes. Enthusiastic feedback from the group has provided a number of potential new applications for this technology from across the Department of Environment, Food, and Rural Affairs (DEFRA) family organisations present.
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!
EcoSat is a first of its kind semi-automated satellite imagery processing tool that’s part of the BioBase cloud mapping platform (Figures 1 and 2). EcoSat is helping several US states and countries map and monitor the status of shallow growing aquatic vegetation and benthic habitats. In this blog, we discuss several tips and tricks about how practitioners can maximize the accuracy and precision of their EcoSat vegetation maps.