Professional Spotlight – Dr. Chris Harrod and Chilean Kelp Mapping

Professional Spotlight

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.

Continue reading “Professional Spotlight – Dr. Chris Harrod and Chilean Kelp Mapping”

Mapping and avoiding dense weed beds to get an edge while yacht racing

By Herb Garcia

Sailing enthusiast and BioBase Ambassador

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.

Continue reading “Mapping and avoiding dense weed beds to get an edge while yacht racing”

Mapping seagrass with BioBase and saving Florida Manatees

Guest Blog by Robert M. Baker, CPG, PG (a) and Penelope R. Baker (b)

(a) Professional geologist at RMBAKER LLC and Navico BioBase Ambassador

(b) Stanford University student, Ecology and Evolutionary Biology, Wildlife Photographer

BioBase is a cloud software that directly supports the preservation of our aquatic environments. Words like preservation and conservation directly imply things like careful planning, measuring and monitoring, treatment and rehabilitation – actionable strategies for the good of animals, plants and natural resources where BioBase can play an important role. BioBase offers an opportunity to observe natural systems, like seagrasses, not easily seen otherwise and does so effortlessly and affordably.

Continue reading “Mapping seagrass with BioBase and saving Florida Manatees”

Properly install your Lowrance/Simrad transducer and mapping is easy with BioBase.

Ray Valley

Aquatic Biologist and BioBase Product Expert

BioBase’s EcoSound is a powerful cloud platform for creating high definition lake or coastal maps of depth, aquatic vegetation (or seagrass), and bottom hardness from Lowrance® and Simrad®

sonar systems. For the user, the process of converting volumes of raw sonar and gps signals into an intuitive map is easy and requires very little input upfront. Record your sonar while out on the water to a microSD card, plug the card into your PC back at the office, log into your BioBase account and upload. Algorithms on remote servers do the rest of the work. However, one of the most frequently overlooked parts of this equation is careful attention to the proper installation of the transducer sensor that is pinging the bottom and collecting all the information below the boat. The importance of proper transducer installation cannot be overstated. If the transducer is not properly placed on the boat or not at the appropriate angle, your BioBase outputs could be inaccurate. Modelers have heard it said many times (sometimes in more colorful language), the quality of the output depends on the quality of the input.

Continue reading “Properly install your Lowrance/Simrad transducer and mapping is easy with BioBase.”

Social mapping of Australian bays and conservation of Fish Aggregating Bryozoans

Guest Blog By Dr. Adrian Flynn(a) and Dr. Travis Dutka(b)

(a) Marine Ecologist and Director at Fathom Pacific

(b) Senior Lecturer at La Trobe University Department of Ecology, Environment, and Evolution.

The waters of Western Port in southeastern Australia are a recreational fishing haven and hidden beneath its turbid waters, a unique fragile seafloor community has been newly described.  Here, bryozoans, skeleton-forming filter-feeding organisms also known as ‘lace corals’, form expansive areas of reef that support a high diversity and abundance of macroinvertebrates important to snapper and other prized recreational fish species.

Figure 1: Underwater imagery of the bryozoan reefs revealed remarkable biogenic reef structures with abundant invertebrate life surrounded by large areas of bare sediment.

Continue reading “Social mapping of Australian bays and conservation of Fish Aggregating Bryozoans”

Lowrance and BioBase informing Manatee Conservation in Lake Ossa, Cameroon Africa

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

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.

Lake Ossa Bathymetric Map
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 sonar do I need for BioBase mapping?

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

Continue reading “What sonar do I need for BioBase mapping?”

BioBase EcoSound Vegetation and Bottom Hardness Algorithms Improved

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

Continue reading “BioBase EcoSound Vegetation and Bottom Hardness Algorithms Improved”

New BioBase Feature Alert: Export Depth Contour Shapefiles

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.

DepthShapefileExportScreenShot
When viewing an EcoSound trip or merge of interest, select Export Data – Depth Shapefiles

Example from a big lake:

BlockFolders
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.”
BlockPolysinQGIS
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:

GolfCoursePondBioBase
5.8 acre (24,281 sq. m) pond as viewed in BioBase
GolfCoursePondQGIS
Exported 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)
GolfCoursePondDepthPolys
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.

Export BioBase EcoSound Maps as Lowrance Charts

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.)

SideBySideVegMaps

In the images and captions below, we’ll walk you through how to do this in your biobasemaps.com account.

  1. Register your Lowrance or Simrad Chartplotter in your BioBase Account
PlotterScreenshot
Assuming you have already recorded your sonar data and successfully uploaded to biobasemaps.com, log into your BioBase account. Click “Plotters”
AddDevice
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)
LowranceSystemAbout
Look in the “About” menu of your Chartplotter. Image above is from a Lowrance HDS Carbon.
SerialContentID
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.

ExportAT5
In the Export Data tool, select “GPS Chart Generation”
GPSChartGenerationModal
Export the desired layers

3. Unzip the downloaded file and save to a MicroSD card (<32 GB).

7-ZipAT5
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!

JosephineHeatMap
Insert the card with the saved AT5 chart files. Go to the Chart and select the appropriate Chart Source in Chart Options. Voilà!
JosephineCompositionAT5
Sample bottom hardness map from the same BioBase survey.
ChartCategories
If you want to view a blue- (or custom-) shaded contour map, simply uncheck the Vegetation/Composition categories in one of the Chart menus.
Screenshot_2020-05-18_14.11.44
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.

 

Translate »
%d bloggers like this: