Frequently Asked Questions

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.

Learn more here.

What kind of sonar is used with the BioBase EcoSound System?

BioBase 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. BioBase only requires logging of the 200 kHz downlooking broadband “Sonar” channel. However, optional StructureScan HD or StructureScan 3D provides high detail and crisp images of structures below (Downscan) and to the side (Sidescan) of your boat. Further, future BioBase release cycles may include processing StructureScan files. Better to have the data archived for potential future analyses.

What is Chirp and will it help me create better maps?

No, Chirp will not help you create better maps. 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.

Learn more here.

Can BioBase 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 BioBase 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.

Learn more here.

How can I create a custom poster-sized map that I can print?

BioBase is designed primarily to rapidly process large raw data files and create and archive informative aquatic maps for analysis. Still, a creating custom poster-sized maps is a desirable end product for many of our customers. High resolution BioBase imagery can be exported or grabbed via screenshots, but we offer affordable, optional GIS Services to create custom digital maps with your BioBase data exactly to your specifications.

Learn more here and here.

What is the accuracy of the GPS on Lowrance depth finders?

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 a Bing aerial image 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. Bottom line: we wouldn’t recommend Lowrance GPS for surveying the location of pylons for a new bridge, but for surveying the depth in a lake or pond, the accuracy and precision of a BioBase map will stand up to any equivalent with created with a survey-grade gps. Test it yourself!

Read more here and here.

How are vegetation and bathymetry maps created with sonar?

BioBase 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 BioBase 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, BioBase measures the strength of the acoustic returns which indicates 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. As your mapping paths (transects) get farther away and you increase your speed, you may miss detail and your interpolated predictions may be less reliable.

Learn more here.

How fast can I drive the boat when mapping?

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 have to 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.

Learn more here.

What is the minimum plant length that is detected by BioBase 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.

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 conforms to Lowrance specifications and is on the order to hundreds and even thousands of feet with the correct transducer. See Lowrance'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 BioBase 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 BioBase’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 EcoSound is produced from kriging grids.

There are two major considerations when deciding between using BioBase 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 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. A misaligned transducer can result inaccurate bathymetry, aquatic vegetation, and bottom hardness outputs. 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 BioBase EcoSound outputs will be.

Read more here.

Can BioBase 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 StructureScan technology, virtual images of plants can be captured and reproduced in BioBase EcoSound. 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
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?

Recommended:

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)

Read more here

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. 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 consumer product called C-MAP Genesis Social which combines anonymous sonar data from C-MAP Genesis and BioBase users and creates an aggregated online depth contour map (Social Map link). Users can create a free Genesis account and download a map encrypted for use in their Lowrance or Simrad Chartplotter.

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. 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 StructureScan or TotalScan 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.

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.

What Satellite Sensors does EcoSat use?

EOMAP algorithms were originally calibrated for Digital Globe WorldView 2 and 3, Airbus Pléiades, and European Space Agency (ESA) Sentinel 2 satellite sensors however algorithms and pricing can be adapted for any publically or commercially available sensor. Ask us about what sensor might be the best fit for your project.

Can you determine species cover from satellite images?

EcoSat uses tested algorithms to define discrete areas and boundaries of different vegetation communities. These polygon “objects” are automatically given unique classification numbers. The user has control over what to name the objects or whether to delete or lump classifications and reprocess the image and data with the new classifications.

How does cloud cover or haze affect satellite image quality?

Indeed, satellites can’t “see” through clouds and cloud cover (and haze) significantly impacts the availability of quality images in image archives. However, if customers choose to “task” a satellite during a 60 day window, then the upcharge ensures a guaranteed level of quality. Our satellite provider’s use sophisticated atmospheric forecasting tools and the satellite sensor angle is adjusted to capture the best possible image in the best possible weather conditions. Once the raw image is acquired EOMAP uses atmospheric correction filters to further sharpen the image and ready it for classification.

What is the minimum resolution that can be mapped with satellites?

Although it’s possible to get sub-meter resolution with satellite imagery, 2-m is the smallest resolution that EcoSat processes to balance cost, file size, and image quality. Sentinel 10-m archive images could be a low cost alternative for characterizing vegetation over very large areas while still retaining relatively high resolution.

How many spectral bands are analyzed?

Depending on the sensor, there could be four to ten spectral bands available to analyze. Different plant species may have different spectral “signatures” that can be differentiated and typed across the different bands.

I have an aerial drone equipped with a hyperspectral camera, why would I choose an image taken from Outer Space?

EcoSat is designed to automate the processing of imagery at scales greater than 25 km² to discern large-scale spatial patterns and trends in aquatic and wetland vegetation (e.g., system wide vegetation mapping). Hyperspectral aerial imagery acquired by drones or fixed-wing aircraft may be more suitable for small-scale aquatic or wetland vegetation restoration projects

Can I get the raw satellite image?

Yes, customers will have access to the true-color satellite imagery for download and internal use. Use and distribution of raw imagery is subject to copyright and terms provided here and by the satellite image provider.

What kind of certainty do you have about the quality of image and accuracy of the classifications?

What is a minimum mapping unit (MMU) and how does that affect EcoSat outputs?

Minimum mapping unit or MMU is the specific size of the smallest feature in the map. This can be controlled by the customer during the initial order request. The minimum MMU is the resolution of the satellite sensor (e.g., you cannot get finer detail than 2-m for Airbus Pléiades imagery). However, a 100 km² image packed with 2-m polygon objects might be too “busy” or “noisy” to clearly see patterns in vegetation communities. Adjusting the MMU upward will dissolve small vegetation patches within larger beds, thereby making the major vegetation community more distinct. Scientific research suggests 50-m MMU may give the best balance between detail and ability to visually discern vegetation patterns. By default EcoSat uses a 50-m MMU.

How does time of year affect outputs?

Time of year can have a significant effect on vegetation classifications. Accurate classification is most difficult during late and early times of the year when brown decayed vegetation is mixed with green vegetation. Investigators should target times of the year for acquisition when biomass is highest and color differentiation between species is greatest. Typically, this is during summer.

I see area summaries of classifications for “Satellite Vegetation” and for lakes intersected by the satellite image in the EcoSat automated report. What is the difference between these areas and how are they calculated?

EcoSat automatically calculates the area of each vegetation polygon object in the survey area using custom Microsoft SQL Geography scripts and sums the area across each classification (Satellite Vegetation). If a waterbody polygon stored in BioBase’s database is intersected by the survey area, A SQL script (STintersects) automatically calculates the overlap of the processed polygon objects and the waterbody boundary and sums the areas of all classifications. This process was designed specifically for complicated spatial datasets with 10’s of thousands of polygons within polygons.

BioBase does not share our administrative waterbody boundaries and they are subject to change depending on available imagery, water level, connections to other waterbodies, or changes in administrative boundaries. If they wish, users can export the processed polygon shapefile and intersect it with their own standard shapefile to regenerate area summaries.

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