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.
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
Users of BioBase may be interested to know you can view your location on a BioBase map on your mobile device if you allow your browser to access your location
Navigate to your browser settings and allow location. Screenshot is from Chrome on Samsung Galaxy
Then log into your account at https://www.biobasemaps.com and navigate to your waterbody of interest and view the trip/merge. The gray dot should show up automatically on your location. Users may find this useful to field verify mapped areas or navigate to areas of interest. However, downloadable full Lowrance/Simrad charts are also available for both EcoSound and EcoSat giving the user a bigger map screen and more navigation/waypoint features.
EcoSound Map with mobile location services enabled on ChromeEcoSat Map with mobile location services enabled on Chrome
Create detailed bathymetric, aquatic, and coastal habitat maps by recording sonar from Lowrance or Simrad sonar devices
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.
Please visit our plans page https://www.biobasemaps.com/Plans to see the full lst of plans, pricing, and features and download a brochure
Tamara Knudson
Limnologist
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.
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.
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.
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
Assuming you have already recorded your sonar data and successfully uploaded to biobasemaps.com, log into your BioBase account. Click “Plotters”Add unique details of your chartplotter. This feature is compatible with most newer (newer than 2014) Lowrance and Simrad GPS capable devices (e.g., Lowrance HDS, Elite Ti and Ti2, Simrad GO and Evo)Look in the “About” menu of your Chartplotter. Image above is from a Lowrance HDS Carbon.Look for the Serial Number and Content ID alphanumeric code. Enter these into the plotter form on biobasemaps.com
2. Export the GPS Chart file from the desired EcoSound Trip or Merge from BioBase.
In the Export Data tool, select “GPS Chart Generation”Export the desired layers
3. Unzip the downloaded file and save to a MicroSD card (<32 GB).
The layer will export as .zip with a random GUID name. The zip file must be unzipped (7-Zip is a great freeware for unzipping files) and the entire contents of the extracted zip file should be copied to a MicroSD card. The contents in the folder are propriety, encrypted files (.AT5) that are specific to the device you registered in your account. The chart file will not work in other non-registered devices. You can register multiple devices. One card can hold multiple AT5 folders (charts) and recorded sonar logs. Cards cannot be larger than 32 GB however.
4. View and Use in your Lowrance or Simrad!
Insert the card with the saved AT5 chart files. Go to the Chart and select the appropriate Chart Source in Chart Options. Voilà!Sample bottom hardness map from the same BioBase survey.If you want to view a blue- (or custom-) shaded contour map, simply uncheck the Vegetation/Composition categories in one of the Chart menus.Detailed, custom-made bathymetric chart. Note that prior to using for navigation, close attention by the user should be given to the quality of the sonar data recorded and resulting accuracy of the map.
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.
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.
