- What is BioBase?
BioBase is a cloud based platform that automates processing and map creation of spatial data. Currently, BioBase is composed of two products, EcoSound and EcoSat. EcoSound processes sonar log files (.slg, .sl2, or .sl3 file formats) from off-the-shelf Lowrance™ or Simrad sonar/gps chartplotters to create detailed bathymetric, submerged aquatic vegetation, and bottom hardness maps. Through a partnership with EOMAP, EcoSat processes high-resolution satellite imagery in a user’s area of interest and delineates beds of wetland, riparian, floating-leaf or near-surface aquatic vegetation. Maps and reports from both EcoSound and EcoSat can be analyzed by non-GIS trained professionals in BioBase with automated tools. If GIS experts want to go deeper, any BioBase map can be exported for detailed analysis or overlays with other spatial datasets in any third party GIS.
- What kind of sonar is used with the BioBase EcoSound System?
EcoSound is compatible with only Lowrance or Simrad brand Sonar/Chartplotter that have .slg, .sl2, and .sl3 log file recording capability.
- Do you need StructureScan to create maps?
No. EcoSound only requires logging of the 200 kHz downlooking broadband “Sonar” channel (sometimes branded by its chirp capability and called “low/high” or “mid/high” but select 200 kHz for EcoSound processing). Optional “scanning” transducer elements within many available transducers provides high detail and crisp images of structures below (Downscan) and to the side (Sidescan) of your boat. Scanning transducers maybe branded as StructureScan HD, StructureScan 3D, TotalScan, or Active Imaging. Future BioBase release cycles may include processing scanning sonar files so record all sonar channels as .sl2 if possible.
- What is Chirp and will it help me create better maps?
No, Chirp will not help you create better maps of bottom habitats. Chirp signals from a Chirp-enabled sounder sweep many short pulses of a range of frequencies within a relative long pulse burst. It’s designed for better noise rejection and target separation of suspended targets (i.e., fish). Chirp is not recommended for bottom mapping and users should select the 200 kHz broadband frequency.
- Can BioBase’s EcoSound tell me how thick the sediment is?
Not really. The bottom hardness algorithm analyzes the acoustic reflectivity of the bottom. Hard bottoms “echo” more than soft bottoms. The EcoSound output is simply a relative “echo” measure. Some studies have found correlation of bottom hardness with sediment thickness, but the relationship is often variable. If you have a good understanding of the desired bathymetry, BioBase provides you a near real-time snapshot of current bathymetry and simple subtraction of the current bathymetric map from the desired or historical map will inform sediment thickness studies.
- What is the accuracy of the GPS on Lowrance or Simrad chartplotters?
There is a big difference between published accuracy by some certified board of survey engineers and actual accuracy that the user achieves for their local application. BioBase bathymetric maps are created by roving surveys over a flowing medium (water in a pond, lake, or river). Lowrance GPS uses WAAS/EGNOS real-time differential correction (if available) and will track up to 32 satellites. Positions are refreshed 10 times a second with newer generation Lowrance chartplotters. This often results in actual accuracy of less than 1 m. Further, users can replay their track over the top of the embedded aerial image within BioBase and qualitatively verify the accuracy of their track. What most users find is a smooth track that matches their recollection of where they actually surveyed. Still, if your survey work requires DGPS, you can network real-time DGPS positions from third-party receivers into Lowrance or Simrad sonar files via NMEA 0183 or NMEA 2000.
- How are vegetation and bathymetry maps created with sonar?
EcoSound algorithms process the 200 kHz broadband down-looking signal. The echosounder in the head unit sends 10-20 signals or “pulses” or “pings” per second through a transducer to the bottom and EcoSound evaluates each signal. Some signals are obviously wrong (e.g., lost depth) and they are automatically discarded. Good signals are retained and the sound wave is interpreted by an algorithm that determines the location of bottom, if there is vegetation present, and if so, where the canopy intercepts the acoustic cone (e.g., plant height which then is summarized as percent biovolume or percent of water column depth with vegetation present). Finally, EcoSound measures the strength of the acoustic returns which gives a measure of bottom hardness. Signals are aggregated and summarized for unique gps locations and stored as coordinate points along your trail. Finally, these points are passed to a kriging interpolation algorithm that predicts depth, vegetation biovolume, and bottom hardness between your sampled trails. The spacing of your transects and speed at which you travel will affect the level of detail in the map. The implications of missing a unique bottom/habitat feature between sampled transects or local imprecisions because of too fast of a survey speed must be assessed by the surveyor. It’s often not feasible to map every inch of water and some tradeoffs must be acceptable in order to complete surveys in a time efficient and economic matter.
Maximum mapping speeds (hard threshold that if exceeded will result in no output)
- Depth – 20 mph (32 km/h)
- Vegetation – 12 mph (19 km/h)
- Composition – 10 mph (16 km/h)
We caution users against pushing these limits and rather consider the objectives of your mapping exercise. The appropriate speed depends greatly on the study or management objectives. Users might be able to use painting as a useful analogy for a starting place to guide transect spacing decisions. For instance, if you are painting a large flat wall, you use a large roller and your objective is to get the best coverage as fast as possible. Similarly, if you are mapping a large lake or bay with gently changing bottom features, you can drive a modest speed (e.g., 8 mph or 12 km/h) if you have a good install with your transducer. In contrast, if you are painting an ornate cabinet with detailed carvings, then you must use a small brush and spend a lot of time getting that small brush into all cracks and crevices. Hastily slapping some paint on with a brush will miss lot of detail. Likewise a similar loss of detail will occur if you drive 19 mph over a small midwater hump or dip. The quality of the output you get out depends on the quality of the data collection going in.
- What is the minimum plant length that is detected by BioBase’s EcoSound?
Debris near lake bottoms can often acoustically mimic aquatic plants. In order to prevent false detections of aquatic plants, signals that resemble plants must be longer than 5% of the water column in order to be classified as plants. In other words, in 10 ft of water plants must be longer than 6 in. In 4 ft of water, plants must be longer than 2.4 in. However, if local survey conditions require greater sensitivity and lower plant detection thresholds, we can adjust this setting.
- What are the depth limits for accurate BioBase EcoSound map outputs?
Depth is accurately mapped in depths as shallow as 1.2 ft below the transducer. A little more space is needed for accurate vegetation detection and BioBase does not produce vegetation outputs in depths less than 2.4 feet. The deeper range of outputs will conform to Lowrance or Simrad specifications and is on the order to hundreds and even thousands of feet with the correct transducer. See Lowrance or Simrad’s website for their hardware specifications.
- What is Percent Biovolume and why does BioBase EcoSound map it?
Percent biovolume (otherwise known as Percent Volume Inhabited or PVI) represents the percent of the water column occupied by plant matter at each GPS location. It's a simply plant height divided by water depth multiplied by 100 for the collection of pings bound to each GPS location along a traveled path. Biovolume ranges from 0% (bare bottom) to 100% (vegetation growth to the surface). In addition to being visually intuitive, biovolume is an indicator of recreation nuisance conditions (e.g., surface growth), changes due to invasive species introductions (which typically grow closer to the surface than native species), and fish habitat conditions. Numerous research studies have demonstrated that fish feeding success and prey availability depends on how much visual barriers are present in the water column. Some biovolume is needed to support prey communities and water quality (50% is a good rule of thumb), but too much (>80%) can promote overly abundant and stunted fish communities and create recreational nuisances. BioBase EcoSound produces a visually intuitive map and data that can help manage lakes for multiple uses.
- I see "Point" and "Grid" statistics in the BioBase EcoSound summary report, why are there two sets of different numbers and which one should I use?
Point data statistics are calculated from the X-Y-Z coordinates translated from the sonar log during EcoSound processing. They contain the GPS coordinates as they are recorded on the water and each point's associated depth, biovolume, or composition value for that location.
Grid data statistics are calculated from the raster grid values produced by EcoSound’s kriging interpolation model which is driven by the point data and the waterbody shapefile. X-Y coordinates from grid outputs are the raster cells' centroids. The Z-value (depth, biovolume, or composition) associated to each point is the geostatistical result of the kriging model that uses information about neighbor values to make predictions in unsampled locations. All of the layer imagery shown in BioBase is produced from kriging grids.
There are two major considerations when deciding between using EcoSound point stats or grid stats. The objective of your analysis will help determine which data set is more applicable. Analysis of grid stats is more appropriate if your survey and analysis area encompasses an entire waterbody or transects were irregularly spaced with varying speeds of data collection. Analysis driven by point stats is more suited to specific areas of interest or uniform data sets. Either idling in one spot while logging, or driving faster over some areas and not others, will result in unbalanced point data sets. Kriging uses geostatistics to balance out biased data. Still, users should exercise caution when comparing outputs from repeated surveys using different transect designs that do not precisely cover the same area.
- Does heavy algae growth or turbidity in lakes or rivers affect the acoustic signal and map outputs?
Any hard object or turbulence in the water with any amount of gas is generally acoustically reflective. Most floating algaes are so small and do not have significant amounts of gas as part of their composition. Thus, they do not affect acoustic signals. However, active photosynthesis, sediment resuspension and turbidity, turbulence caused by wind or boats can create acoustically “noisy” environments and can affect vegetation detection. Bottom depth and hardness outputs are more robust to acoustic noise.
- I received a Quality Control email that stated my transducer was tilted. What does this mean and how can I prevent this problem in the future?
An angled, or misaligned transducer is the most common oversight of users. A misaligned transducer will result in weak return signals over flat bottoms or slopes where the beam is pointed away from the slope. In contrast, if the beam is pointed toward the slope, the signal return will be much stronger than normal. Also, a misaligned transducer will cause cavitation (air bubbles) to circulate around the transducer face and you will lose depth tracking at even modest speeds. A transom mounted transducer must be straight, level, and height perfectly aligned with a smooth hull of the boat (e.g., don’t place in front of ribs or rivets). Flow of water must be laminar across the transducer face. A misaligned transducer can result inaccurate bathymetry, aquatic vegetation, and bottom hardness outputs. We recommend that once you find the best transducer mounting location, either locking down the transducer mount or very carefully noting the precise location of a portable mount so that exact spot can be achieved repeatedly. There are a wealth of online resources about properly mounting your transducer. The more meticulous you are about getting the transducer installed correctly, the higher quality your EcoSound outputs will be.
- Can BioBase’s EcoSound map individual species of plants?
Indeed, different species of aquatic plants have different acoustic signatures or "fingerprints," however the technology to confidently classify different species of plants in an automated fashion with minimal error is still a ways out. Still, with the Lowrance's scanning technology, virtual images of plants can be captured and reproduced in BioBase. Thus, given some ground-truth samples that confirm certain growth types, researchers or lake managers can use the Trip Replay feature in BioBase to produce maps of individual species or communities. Further, the export function in BioBase allows GIS layers of plant abundance to be exported and overlain with species presence/absence surveys conducted simultaneously.
- What are the suggested Lowrance or Simrad unit settings?
- Fishing Mode = Shallow Water if less than 60 ft, Freshwater if less than 400 ft, General Use if less than 1000 ft
- Ping Rate = 15-20
- Range = Auto, unless mapping shallow ponds, then set range 2x the max depth
- Noise Rejection = Low
- Surface Clarity = Off
- Frequency = 200 kHz
- Speed = 1-7 mph
Please refer to your user manual for details on how to configure these settings. Further, when you open a BioBase account you will have access to updated BioBase user reference guides.
- How far apart should I space my transects?
- Lakes < 1000 acres – 40-m spaced; perpendicular to the longest shoreline
- Lakes > 1000 acres – 100-300-m spaced; perpendicular to the longest shore
- Ponds < 30 acres – Concentric Circle
- Best Bathymetric Map – Transects parallel to major features (e.g., shoreline, channel)
- Where should I mount my Lowrance™ or Simrad unit?
Since the Lowrance and Simrad Sonar/Chartplotters have an internal GPS, you should mount the unit as near to the transducer as possible such that your GPS and bottom locations match up. Alternatively, you can purchase an external GPS antenna to mount near the transducer if you would like to have the display near a console operator. Having the antenna distant from the transducer can lead to positional bias of the pings. This bias will change depending on the geographical direction of your boat.
- Will BioBase work on my Mac or is it compatible with PC’s only?
BioBase EcoSound performs optimally on a PC using updated Chrome or Firefox Internet Browsers. However, Mac users can upload sonar logs via Safari or Chrome directly from their BioBase dashboard. If your mobile device reads MicroSD, you can also upload via the web upload tool directly. PC users also have the option of uploading using a desktop client tool which generally performs better with slow internet connections.
- Can I view data of another user and can they view mine?
Only if you allow it. You cannot view the data of another user without their permission. Data uploaded to BioBase is private to the account user that uploaded it. However, we do have an organization sharing feature that allows you to link accounts with associates or other account holders within your organization. This will allow them to see your uploads while you can see their uploads.
- I see a map very similar to the one I made on Genesis Social Map. There is no other map on this lake that I know of. How is this possible?
We have another recreational product called C-MAP Genesis Social Map which combines anonymous sonar data from C-MAP Genesis and BioBase users and creates an aggregated online depth contour map. Users can log on to genesismaps.com with their BioBase account and download a map encrypted for use in their Lowrance or Simrad Chartplotter. BioBase users can elect whether to contribute their aggregated data to Social Map (no track, timestamp or personal data is shared) or keep their data private.
- I am mapping a small stormwater retention pond, how does BioBase know what the pond is named or where the boundary is?
Quality Control staff review every uploaded sonar log overlain on top of Bing Satellite imagery (the same as what you see in your dashboard). If Bing names it, that’s the name we give it. If Bing is wrong, you can send us an email and have us correct it. Further, we rely on our users to communicate to us names of ponds that do not have a public name. Finally, Quality Control staff will adjust the waterbody boundary to precisely conform to the shoreline. Each vertex is a zero depth value thus creating smooth, closed contours near shorelines.
- In what kind of aquatic systems does BioBase EcoSound work?
BioBase EcoSound processes data in any waterbody greater than 1.2 feet deep. The range of systems successfully mapped with BioBase include deep glacial lakes, karst seepage lakes, shallow lakes, stormwater retention ponds, water supply canals, private ponds, large river systems, dammed reservoirs, and brackish estuaries. Essentially, if you can float a boat on it, BioBase EcoSound can map it!
- How large are the sonar data files?
Sonar files can be large and the size depends on the file format and other devices on the network. The minimum required for EcoSound outputs is the broadband 200 kHz sonar only recorded as .slg. At 15 data points per second (Ping rate), .slg 2.7 MB of data are are recorded every minute. If a scanning transducer is installed, two side- and one additional down-scanning channel is added for each ping increasing the file size to approximately 5.1 MB per minute when recorded as .sl2. Finally, StructureScan 3D recorded as .sl3 additional data to the file and file sizes are approximately 7.2 MB per minute. Generally, file size is not a great issue since large capacity microSD cards are low cost and fast broadband internet access is common. We recommend using a 16 GB or 32 GB card. Some Lowrance and Simrad devices are not compatible with larger storage media.
- Can I Export the Raw Data?
Yes. We provide an export tool in your account. You can export all layers for both EcoSound and EcoSat for local archiving and analysis in a range of third party programs.
- What hardware/computer requirements do I need to use the website and upload data from my depth finder?
BioBase works best with up to date Chrome or Firefox internet browsers and fast internet connections (greater than 5 mb/sec download and 1 mb/sec upload speed).
- Does C-MAP provide mapping field services?
No. We provide mapping software services to on the ground service providers. We have a large global network of providers and we could help you find one who use the BioBase service.
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