Frequently Asked Questions

How does the ciBioBase System Work?

CI BioBase is cloud based software that automates processing of Lowrance™ depth finder sonar log files to make aquatic vegetation and bathymetric maps. We make aquatic plant and lake habitat studies cost effective by reducing the equipment costs, technical skills, staff, and hours normally required to produce bathymetric and vegetation maps.

With CI BioBase you collect data using high-tech, low-cost Lowrance™ HDS depth finders (starting at $689.00) and record your raw sonar and GPS to an SD card in the unit. These files can then be uploaded to your CI BioBase account online using our file upload tool. All of the work is then done for you by our servers. The output is available in your account and can be viewed online or exported to third party GIS or statistical software.

What depth finders are used with the ciBioBase System?

CI BioBase is compatible with Lowrance™ brand depth finder that have .SLG and .SL2 (Structure Scan) log file recording capability. We currently recommend the HDS line. Navico, Inc. can provide the HDS models at a discounted price or as part of your subscription package. Please contact us for more information.

What is the accuracy of the GPS on Lowrance HDS fish finders?

Lowrance™ GPS receivers come equipped with Wide Area Augmentation System (WAAS) that utilizes a ground-based network of reference stations to measure small variations in the GPS satellites' signals. These corrections are then sent to the Lowrance GPS receiver and the position is corrected. Accuracy varies depending on location and presence of nearby obstructions. Lowrance™ discusses this topic at and cites accuracy values of 5 meters (15 ft) or less with WAAS enabled. Actual accuracy is typically better than this conservative estimate and users can tell by examining the smoothness and placement of their trip path. You can be assured you have a highly accurate signal if your trip path is smooth and precisely falls within known boundaries (e.g., a shoreline). Ensure that WAAS is enabled in the GPS Configuration screen within the HDS unit. Satellite reception and estimated precision accuracy can be monitored by selecting the "Satellite" screen within the System submenu of the the main menu on your HDS unit.

In addition, we put the HDS units to the test and our results can be viewed here.

How are vegetation and bathymetry maps created?

ciBioBase applies well-studied concepts of hydroacoustic theory to interpret bottom signals and incorporates a mult-step process of analyzing the raw acoustic and coordinate data. The geostatistical procedure, kriging, is applied to the interpreted data in order to create a smooth, interpolated map of bottom and the vegetation within a buffer (typically 25-m on both sides) of your trip track. Kriging is important for addressing statistical issues and bias with uneven sampling.

How accurate are bottom and vegetation maps?

See for yourself! A key feature of ciBioBase is the ability for users to verify automated map outputs through the software's Trip Replay feature. This feature couples a scrolling sonar chart overlain onto your actual trip path and map output. You can stop the chart at any point and see if the automated output matches what you see on your sonar screen. In the rare instances of map errors (perhaps due to an interrupted transducer signal), users can delete points and reprocess the map. Because ciBioBase is a cloud-based centralized database, our Quality Control team continually reviews data coming into the system and works with Biologists across the country and globe to ensure accurate outputs in almost every possible aquatic system imaginable from water supply canals, to condominium water features, to deep glacial lakes. No other system or software, even with narrowly published accuracy measures in a few cherry-picked environments can come close to the robustness of ciBioBase algorithms!

What is the minimum plant length that is detected by ciBioBase?

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 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 ciBioBase 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. ciBioBase produces a visually intuitive map and data that can help manage lakes for multiple uses.

How many people do I need in the boat to map a lake?

Just yourself! If you just want to gather data to upload to your BioBase account, you just need someone to drive the boat. There's nothing to hold onto, no computers in the boat, and no manual controls. If your HDS unit and transducer are mounted to the boat, there is nothing required other than pressing record when you want to log sonar. CI BioBase does all the processing for you when you get your SD card back to your computer. This is very different than existing techniques and that's why we feel our product will change the way we gather and processes sub-surface data.

How does the mapping feature work?

Each time you gather data and upload it to the system, the raw acoustics will be processed and displayed in your account. We currently process the raw acoustics for bottom and plant canopy height to display bathymetric data as well as % biovolume, or the % of the water column taken up by vegetation (sometimes referred to as Percent Volume Infested or Percent Volume Inhabitat-PVI). If the distance between transects exceeds our recommended distances, the System will automatically blank out those areas so as to eliminate bad data or high variability estimations from your output. In addition to the % biovolume display, we also provide a vegetation standard deviation map which shows the variability of data points used to estimate data between transects.

We use a kriging algorithm to "estimate" the depths and plant canopy height in the areas where you didn't collect actual data. However our default feature is to only display bathymetric data around a 25-m buffer where actual data is collected.

Using our accurate and highly detailed bathymetric mapping System, our software automatically provides a water volume analysis (in cubic meters) for the actual area covered and total water body as long as you have over 60% coverage in actual data.

What is an Area of Interest (AOI) in summary reports and how is that controlled?

Often, service providers and biologists monitor aquatic plants along study transects or plots and require summary statistics broken down by these areas. Therefore, in order to create separate AOI's in a merged trip, users' should allow more than 2 minutes to elapse between logged files collected in respective AOI's. Files separated by shorter times will be considered all part of the same trip and the merged output will lumped as one AOI. Regardless, a full trip summary is displayed at the top of the report.

I see "Point" and "Grid" statistics in the summary report, why are there two sets of different numbers?

ciBioBase analyzes sonar and GPS signals and outputs a file of a large number of geographical coordinate points with a number of physical attributes including bottom depth and vegetation height and percent biovolume. The "Point" statistical summaries represent simple summary statistics pooling these coordinate data points into various classes (e.g., depth or biovolume categories). These summaries are appropriate for summarizing findings where survey protocols are standardized and highly repeatable (e.g., long straight transects traveled at uniform speed). ciBioBase uniquely takes these coordinate data to the next step by feeding them into a kriging interpolation algorithm that analyzes the relationship between neighboring points and makes quantitative predictions in unsampled locations at uniform intervals of a specified grid cell size. This addresses statistical biases associated with unevenly spaced data points (e.g., idling, driving variable speeds, variable transect design and spacing). Thus in most cases, the "Grid" summary statistics should be used for characterizing depth and vegetation growth.

Why should I use the ciBioBase System?

We believe lake service providers can provide more efficient and effective results for their customers while providing them with objective and intuitive images and reports. ciBioBase provides the accuracy to offer more features in less time. Our imagery export and layered mapping make it very easy to recommend management techniques with valuable metrics from third party output.

Fisheries and aquatic invasive species (AIS) management professionals can create a historical database of bathymetry and vegetation to monitor lake performance and changes over time. This is the first System to create this opportunity with rapid assessment tools and a database warehousing function.

Does heavy algae growth in the lake affect the acoustic signal and map outputs?

We have trips in system from a wide range of water quality conditions ranging from "gin clear" to "pea soup." We have rarely encountered problems with floating algae obscuring acoustic signals.

Can ciBioBase 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 advent of Lowrance's StructureScan technology (a $700 add on to any HDS unit), virtual images of plants can be captured and reproduced in ciBioBase. Thus, given some ground-truth samples that confirm certain growh 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 ciBioBase allows GIS layers of plant abundance to be exported and overlain with species presence/absence surveys conducted simultaneously.

We do rake surveys and tracing of beds with GPS, how is ciBioBase any better?

Three words: Abundance, Objectivity, and Repeatability. Abundance: rake surveys are great for telling lake managers what species are present in a lake but tell very little about the actual abundance of plants in the lake. Invasive plant species, fish habitat, water quality, recreational quality all hinge on the state of vegetation abundance in a lake. Thus, for effective lake management the state of vegetation abundance must be known. Objectivity: ciBioBase algorithms remove the human error element. Instead of developing criteria for how to rank the abundance of a gob of vegetation pulled up on a rake, ciBioBase algorithms use acoustic signal characteristics to make objective, quantitative estimates of plant abundance. Repeatability: How does one define what a "bed" of vegetation is and where does one end and the other begin? How confident are you that this can be repeated by someone else on your team? This is another human error element that is removed with ciBioBase. If vegetation is longer than 5% of the water column depth, as long as you passively drive over it while logging data, it's mapped and after processing by ciBioBase, anyone can clearly see exactly where vegetation grows and it's density. These features make ciBioBase an invaluable tool for lake monitoring and evaluating lake management actions.

What are the suggested Lowrance HDS unit settings?

After a lot of trial and error, we have determined the following settings to provide the best or most efficient data collection:

Fishing Mode = Shallow Water
Ping Rate = 15-20
Range = Auto
Frequency = 200 khz
Speed = 1-7 mph

Please refer to your HDS user manual for details on how to configure these settings. Further, when you open a ciBioBase account you will have access to updated ciBioBase user reference guides

Do you have suggested transect spacing?

Yes, we recommend no more than 1/5th of interpolated grid cell size. CI BioBase's default gridding is 5 m for most water bodies over 30 acres so we recommend 25 m maximum transect spacing for best performance of kriging algorithms. If you are gathering data on water bodies less than 30 acres in total size please use the following chart for your maximum transect spacing:

Less than 5 total Acres 5 meters
More than 5 acres but less than 10 total Acres 10 meters
More than 10 acres but less than 20 total Acres 15 meters
More than 20 acres but less than 30 total Acres 20 meters
More than 30 acres but less than 10 total Acres 25 meters

This dynamic gridding chart has allowed us to minimize error coefficients and thereby provide the most accurate data for each file upload depending on a wide range of scenarios.

Where should I mount the my Lowrance™ unit?

Since the HDS unit has 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 antennae 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.

What do I need to use the System?

In addition to an HDS depth finder, you will need an account at Most of our users have purchased an annual subscription for an account. Most annual subscriptions provide unlimited uploads to any lake. Each person that collects data must have a subscription.

We also have packages available for Lake Associations, Service Providers (that provide CI BioBase data gathering and processing on behalf of another), or local units of government that are only interested in uploading data from one or more specific lakes (both unlimited and per upload pricing based on lake acreage available). Please contact Navico, Inc. for more info.

Can I view data of another user and can they view mine?

No, you cannot view the data of another user without their permission. Data uploaded to the System 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.

What Lakes are covered by the database?

Our database has been designed using lake shape files for over 9,000,000 lakes. To narrow this size to a manageable number, the database includes all inland waters (not including river systems) of 30 acres or more. Please contact us if you would like to determine if a lake you plan to collect data on is available in the database.

We don't claim to have every lake, but any water body can be added. We also provide custom shapefile development for water bodies that are less than 30 acres. Contact us for more information on this!

What do I need to do if I plan to upload data on a water body smaller than 30 acres in surface area?

We can quickly create shapefiles for these water bodies in advance of your upload to be sure that there is no delay in you receiving your processed data. Please send the name of the water body, the GPS location of the center (in decimal format) and date you plan to gather and upload. This information can be sent to the ciBioBase staff.

Is ciBioBase just for lakes?

NO! ciBioBase processes data in any waterbody greater than 1.2 feet deep. The range of systems successfully mapped with ciBioBase include deep glacial lakes, karst seepage lakes, shallow lakes, stormwater ponds, water supply canals, dredged townhome water features, large river systems, dammed reservoirs, and brackish estuaries. Essentially, if you can float a boat on it, ciBioBase can map it!

How long can I collect data in a single file?

In order to prevent "mapping" for a full day only to discover that you never hit record, we recommend that your files be approximately 1-2 hours of collection each. There is no additional charge for uploading more than one file (subject to and aggregate 8 hour "trip" rules for service providers paying on a per upload basis)

What if I collected 2 hours files, but I want a full lake map from 10 hours of data?

We offer a merge function that allows you to merge post processed data from more than one file to create a total lake map. Your account will still have each individual file but a new "merged" file will be created in your account based on the data from the files you combined.

If I upload information, what defines a "TRIP"?

A Trip is defined as all log files recorded on the same lake and same day (midnight to midnight) that in aggregate do not add to more than 8 hours of total data collection time. This typically applies to service providers that have a per upload arrangement to use the CI BioBase System. In a chain of lakes, multiple lakes will appear in the same trip if multiple lakes are visited with less than 15 minutes from the time you leave one lake before recording on another.

Our database has been designed to show individual lakes of any chain, but when each lake is accessible to the point where you can visit multiple lakes with less than 15 minutes in between taking records on two lakes all visits are considered one Trip. In a lake chain, the boundary of one lake can be touching the boundary of another. By crossing this line, both lakes will be included in a single Trip. The Trip will end as soon as records are no longer taken for at least 4 hours.

Can I Export the Raw Data?

Yes. We provide an export tool with full delimiter control in your account. You can export the bathymetric bottom data, vegetation data, or both. The data is exported in a text file that can then be used in your own GIS software.

What hardware/computer requirements do I need to use the website and upload data from my depth finder?

Navico, Inc. and its affiliate websites are designed to work with any browser. If you have Chrome, IE, Firefox, or Safari, it's no problem! Using the latest versions of each browser is recommended. You'll also need to have Microsoft Silverlight 3.0 or newer to view and interact with the site and your content. Cookies must be enabled.

Download Silverlight at

You must download our upload client tool to upload your data to your account. The client tool can be downloaded to your local computer desktop. We currently do not support Apple's™ Operating System. Data upload into the client also requires at least a USB 2.0 Drive.

Do service providers using the BioBase System work for Navico, Inc.?

NO! Navico, Inc. merely provides the BioBase System to process, interpret and warehouse the data. Products or services offered using the BioBase System are solely created and controlled by service provider. Assessments and recommendations based on interpreted data is not a service offered by Navico, Inc. at this time. We leave it up to the service provider to make an independent assessment and/or recommendation for their clients using objective data from CI BioBase

What if I survey a waterbody that is not in your database?

No problem, we have an autoshapefile generating feature that buffers your trip path. Our Quality Control Team is alerted each time a new waterbody is uploaded to the system and we quickly adjust the shapefile to conform with the most recent aerial imagery. We also will accept user shapefiles if they have been personally verified and we can be assured of their accuracy.

Is Navico done innovating?

Never! We promise to stay true to our name and continue to innovate. Our team is an extremely talented group and we've stayed lean so our development cycles are incredibly short. We are easy to get a hold of and we are passionate about changing the way our customers collect and map. Our products will always empower our customers.

A major benefit to our System is the centralization aspect of warehousing your data in the cloud. As we make new features available, they are automatically associated to previously uploaded files. Data you uploaded 2 years ago will have features and outputs that we develop today! The idea of Clean Web is alive and well with Navico and we are changing the way we look at, study, and assess lakes on a global level.

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