Verification of ciBioBase Depth Output

At Contour Innovations we are our own skeptics and constantly perform verification investigations of BioBase output for accuracy. 

As Chief Aquatic Biologist, I’ve been comparing bottom depths sampled with a survey rod with its corresponding depth derived from the automated depth outputs from the BioBase System.  In the figure below depths from Elk Lake (Clearwater Co. MN) are color coded from 1 – 50 ft with blue becoming more intense as depth increases.  The circles are depths recorded with a survey rod while the squares are ciBioBase depths.  Below is one visual representation of the high agreement between true depths and BioBase depths. This visual shows the symbol color agreement demonstrating accuracy in the output! 

True depth data come courtesy of Minnesota Dept. Natural Resources Fisheries Research Biologist Donna Dustin and are copyright of Minnesota DNR.

Ray Valley Joins Contour Innovations as Aquatic Biologist

Please join Contour Innovations in welcoming Ray Valley (RayV@ContourInnovations.com) to our team as Chief Aquatic Biologist. 

Previously employed by the Minnesota Department of Natural Resources as a Senior Research Biologist in the Section of Fisheries, Ray developed aquatic plant mapping protocols with acoustic technology and GIS, researched the link between aquatic plants and fish populations, and most recently chaired the successful launch of a collaborative and comprehensive long-term lake monitoring program called Sustaining Lakes in a Changing Environment (SLICE), Ray holds a B.S. degree in Fisheries from the University of Minnesota and a M.S. degree in Fisheries Ecology from Michigan State.

Ray brings a wide range of expertise to our team specifically related to aquatic vegetation mapping, GIS, and fisheries.   Our team is excited to have his deep technical background in aquatic habitat mapping using acoustics.  “We’ve only scratched the surface of what our platform can do both as a direct output and the benefit our users receive from a collaborative and uniform mapping effort,” said Matt Johnson, CEO of Contour Innovations.  “We will continue to add resources to ensure that Contour Innovations continues to push the boundaries in automated temporal and spatial mapping and Ray brings the expertise to go to the next level.”

Ray will be responsible for aquatic research using the ciBioBase System and providing technical mapping and research support for our empowered customers.    He will also be a keystone piece in designing and evaluating new features and valuable tools provided by the BioBase automated mapping system.  Ray will use his expertise to develop SOPs for and design mapping protocols for our customers’ unique mapping needs and to help maximize time on the water.
Ray has published the following selected list of articles related to submerged aquatic plant mapping and links to fish:

  • Valley, R.D. 2000. Effects of macrophyte structural heterogeneity and fish prey availability on age-0 largemouth bass foraging and growth. M.S. Thesis. Michigan State University, East Lansing.
  • Valley, R.D. and M.T. Bremigan. 2002.  Effects of macrophyte bed architecture on largemouth bass foraging: implications of exotic macrophyte invasions. Transactions of the American Fisheries Society 131(2):234-244
  • Valley, R.D. and M.T. Bremigan. 2002. Effects of selective removal of Eurasian watermilfoil on age-0 largemouth bass piscivory and growth in southern Michigan lakes. Journal of Aquatic Plant Management 40(2):79-87.
  • Valley, R.D., T.K. Cross, and P. Radomski 2004. The role of submersed aquatic vegetation as habitat for fish in Minnesota lakes, including the implications of non-native plant invasions and their management.  MN DNR, Division of Fish and Wildlife, Special Publication No. 160.
  • Valley, R.D., M.T. Drake, and C.S. Anderson. 2005. Evaluation of alternative interpolation techniques for the mapping of remotely-sensed submersed vegetation abundance. Aquatic Botany 81:13-25.
  • Valley, R.D., and M.T. Drake. 2005. Accuracy and precision of hydroacoustic estimates of aquatic vegetation and the repeatability of whole-lake surveys: field tests with a commercial echosounder. MN DNR, Division of Fisheries and Wildlife, Investigational Report No. 527.
  • Valley, R.D., W. Crowell, C. Welling, N. Proux. 2006. Effects of low dose applications of fluridone on submersed aquatic vegetation in a eutrophic Minnesota lake dominated by Eurasian watermilfoil and coontail. Journal of Aquatic Plant Management 44:19-25.
  • Valley, R.D. and M.T. Drake. 2007. What does resilience of a clear-water state in lakes mean for the spatial heterogeneity of macrophyte biovolume? Aquatic Botany 87:307-319.
  • Valley, R.D., M.D. Habrat, E. D. Dibble, and M.T. Drake. 2010. Movement patterns and habitat use of three declining littoral fish species in a north-temperate mesotrophic lake. Hydrobiologia 644:385-399.
  •  Beck, M.W., L. Hatch, B. Vondracek, and R.D. Valley. 2010. Development of a macrophyte-based index of biotic integrity for Minnesota lakes. Ecological Indicators 5:968-979.
  • Heiskary, S and Valley, R.D. In press. Curly-leaf pondweed and interrelationships with water quality. MN DNR Division of Fish and Wildlife, Investigational Report No. 557.
  • Valley, R.D. and Heiskary, S. In preparation. Short-term declines in curly-leaf pondweed across a network of sentinel lakes in Minnesota: potential influences of snow depth and water temperature. To be submitted to Lake and Reservoir Management.

Ray’s most research interests include lake ecology with specific emphasis on the interaction between aquatic plants and water quality regimes. 

He can be contacted at RayV@ContourInnovations.com

New Z-offset (depth offset) Feature

Some of our customers have requested the ability to make their maps even more accurate by eliminating the distance between their transducer and the bottom.  We listened! 
Depth calculations (z) using hydro acoustics are calculated from the source (transducer) to the bottom. Because a depth finder transducer is typically mounted below the water surface, depth readings are always off by the distance between the bottom of the transducer and the surface of the water . . . not anymore!   With the new z-offset feature, any user can now recalculate depths by entering this distance and reprocessing the trip.  For example, if your transducer is 6 inches below the surface, all of your depth readings should have a half foot added to them.  A 10 foot z should actually be 10.5” deep.  With a .5” z-offset, all of your depths will be reprocessed for better accuracy.  This is very important when calculating water volumes! 
The z-offset feature can also be used for calculations to high water marks or draw downs.  By using the z-offset for a 5 foot draw down scenario, our users can identify which bottom structures will be exposed as land (see below).  In addition, lake and pond managers can determine total water volumes at a high water mark by measuring this distance.  By simply offsetting all depth readings with a single z-coordinate offset, your trip will be reprocessed the way you want it.  Water volumes, blue scale, and plant biovolume will all be recalculated in your account.  Simple!
Below is an example of the z-offset in action for a simulated draw down.  We took an accurate trip from Trout Lake in Wisconsin and offest the z-coordinate by 20 feet to simulate a 20 foot draw down.  The new blue scale reflects the changes and displays the new land in green:

Auto Blue Scale Bathymetry Mapping

Contour Innovations (CI) is announcing the addition of a new feature of our BioBase System.  As many of you know, each trip uploaded to your account is processed for depths and plant canopy heights to automatically create maps and output the layered data in your interactive online account.  From now on, depth contours will be displayed in blue scale after launch of our new blue scale image feature.  When loading your vegetation layer, blue scale will disappear but transparent contour lines will display beneath the % biovolume output. 
This feature is great for lake and pond managers that are interested in getting a quick assessment of any sized water body to understand where the deep spots are for diffuser placement and overall management.  We still employ a TIN anlysis for accurately estimating total water volume.  On a pay per upload plan, our customers can get this data quickly for as little as $100 per water body and in as short as 10 minutes.   You collect the data with your low cost Lowrance HDS depth finder, upload it to a secure account from your computer, and the raw sonar is processed in the cloud in minutes.  Images of the blue scale can be exported with ease to be included in management plans (images in this blog are direct exports from the BioBase System).  State agencies are using the System for bathymetric output to update their existing lake maps provided to anglers.    This is just another great feature added to the powerful BioBase System.
To further demonstrate the power of automation and centralization anyone that has already uploaded trips to the BioBase System can now get blue bathymetry for those uploads with little effort.  To try it out, log into your account and click the interactive viewer for any trip.  Using the REPROCESS tab, check “contours” and resend the trip to our servers.  Within minutes you will get an email letting you know that your reprocess has been completed and blue scale will be provided for this trip.  Using an online account there are no software updates or manual processing of older trips.  Let our servers do the work.  That’s what they’re there for.  Anytime we add a new feature to BioBase, anything you’ve already uploaded to your account can be updated.   It’s pretty cool stuff!

Please contact us with any questions at matt@ContourInnovations.com or 715.864.9347.  Pond managers can contact our exclusive partner, Aquatic Eco-Systems (Orlando, FL) at mattr@aquaticeco.com or 407.462.4697.  Let us know what you think!

New BioBase Upload Tool

The Contour Innovations team has released a new and incredibly efficient upload tool for all BioBase users.  The new tool boasts enhanced performance, multi-select upload and automated upgrades for future revisions from Contour Innovations.  The following post goes through the procedure for obtaining the new tool and outlines some of the key functionalities of the latest release of the BioBase Upload Tool.

Downloading the New Upload Tool

Getting the new tool is as easy as logging into www.biobasemaps.com and clicking the download link found on your personal home page as seen in the following image.

After logging into BioBase, click on the “Download BioBase Upload Tool” link and the download process will begin.  This must only be done one time as future updates will be done automatically through the new tool.  After installing the new tool, if you get prompted with the following message when opening the application, click “Yes” to download and upgrade your upload tool to the latest release.

NOTE:  You will need Administrator rights on your local machine to install the tool.  If you are not an Administrator, please contact your internal IT Department for assistance with the installation.

We continue to plan enhancements to the upload tool.  Keeping it up to date will ensure your experience is as smooth as possible when uploading large amounts of data!

NOTE:  If you are currently running the previous version of the upload tool, please feel free to un-install it as it will no longer be needed after installing the new tool.

Getting Started

As an introduction to the new BioBase Upload Tool, we want to ensure you know the basics of how the tool works and where you can find certain information.  To start, everything was designed to be fast and easy to use.  The interface is light, but effective.  As shown in the figure below, there are only two areas of interaction.

1. The menu system is used for launching web pages, checking configuration information and exiting the application.  The key menu option to highlight, as shown below, is under “Help” >> “About…”, which will display a quick pop up window that contains 1. the current version of the tool, 2. the local directory used for staging pre-uploaded trips and 3. the location of the log file on your local machine.

If an error occurs, an entry is written to the Log File Location. This file is very important for troubleshooting potential issues that arise from the wide variety of network and local machine configurations. If an exception occurs and support is needed, check your “About…” menu option to find the location of the AppLog.log file and send the AppLog.log file to Contour Innovations at email@contourinnovations.com to ensure that any issue is resolved quickly!

2.  The content area contains two functionalities.  The first is the login area where you can specify your username and password to login to the client tool.  Once logged in, you will be able to start uploading your files.  Your username is stored locally in a configuration file, but for security purposes, you will be required to specify your password every time you launch the application.

After you have logged into the tool, you will be presented with the file upload and status content area as shown below.

To upload files simply click Select Files and select the Lowrance SLG and/or SL2 files you wish to upload.  A key feature to highlight is the multi-select capability in the Select Files browser window.  As shown in the following image, you can use the multi-select feature by holding CTRL while you select the individual files you want to upload, or you can select the first file in a larger file set then hold SHIFT and select the last file.  This will automatically select all files between the first and last file in your file set.

Once you have all of the files selected, click Open and they will be imported into the content area of the BioBase Upload Tool.  If you happen to select an invalid file type, the tool will notify you that a specific file is not the correct format and it will not be added to your local upload queue.  If you happen to select a file with the same name, the tool will ask you if you still want to add it.  You still have the option to add multiple files with the same name.  There is no reason to upload the same file twice, but in some cases, you may have different files with the same name that need to be uploaded.

Once you have all of the files ready to go in your queue, click the upload button, as shown below.  This will kick off the upload sequence and the tool will handle the rest.

At any point during the upload, if you decide that you do not want to upload a certain file, click the Red “X” on the right hand side of the file.  This will remove the file from your local queue.
Once the upload begins, feel free to monitor the status of your trip uploads or move on to some other work while the upload completes.  Your computer must remain on and an active Internet connection is required for files to complete the upload process.  The BioBase Upload Tool window must remain open while the upload progresses and, as shown in the following image, the upload tool will provide you with real time status updates of each file in your local queue.

1.  Files that complete will be represented with a green checkmark.  Once a file completes, the next file in the queue will begin to upload until all files have been completed.

2.  Other statuses include Compressing, Compressed, Uploading and Error.  If a file hits an unrecoverable error, the file record will be marked with an error and the exception will be written to your AppLog.log file (as discussed earlier in this post).  At that point, please send your AppLog.log file to email@contourinnovations.com for support and we will assist in resolving the error.

3.  If you decide to cancel the entire upload, click “Clear” on the bottom of the content area. This will cancel all file uploads and clear all files out of your local queue.

4.  A small summary is maintained throughout the entire upload process.  You can track your progress via this text and once complete you will see a message of:

“Upload complete with # error(s)”

If the # of errors does not equal 0 (zero), please send your AppLog.log file to email@contourinnovations.com to ensure that we can assist in resolving the error.

As always, the Contour Innovations team will continue to release updates and feature enhancements to the system as a whole while providing a high level support to BioBase users!  We welcome all feedback, questions and inquiries sent to email@contourinnovations.com!
We hope you find value and time savings in the new BioBase Upload Tool!

What is BioBase All About?

We’ve made historical bathymetry and aquatic habitat mapping quick and cost effective!

 BioBase has three main concepts: (1) Data Collection (2) Automated Data Processing and (3) Interactive Display. Acoustic data our subscribers collect using Lowrance HDS depth finders is automatically processed and warehoused online in a private account.

Our algorithms process for depths (bathymetry) and plant canopy height (sav abundance). By collecting data each time you or one of your colleagues are on the water, you are able to develop a historical database of aquatic habitats.

This powerful System uses the raw acoustic data you collect and sophisticated cloud based algorithm processing and GIS tools. Data collected on SD cards while on the water is uploaded to an online account where it is processed by our servers automatically. This innovative mapping solution has instantly made historical SAV and lake ecological habitat studies cost effective by reducing the technical skills, staff, and hours to produce vegetation abundance maps from raw sonar collection. The result a comprehensive and historical look at lake status and SAV changes over time in relation to important characteristics such as invasive species, herbicide performance, abundance, and resilience.

These historical maps can be used to monitor management successes, allocate efficient management, and provide detailed displays when reporting results.

One of the major benefits of cloud based software is that as we make changes to our algorithm or push out new features, everything is automatically associated to every trip you’ve uploaded to the System. For example: We recently pushed out a total water volume analysis tool in our standard reporting. Every trip uploaded to the System before this feature was available now has total water volume details.

CI BioBase also provides an objective output that is consistent from trip to trip. This provides objective uniform reporting for every trip uploaded to the System. We’ve removed the human element from the processing! Our servers don’t take breaks or vacations!

You can check out BioBase for yourself by logging in using our demo account:

You can log in here: www.biobasemaps.com
Username: demo@cibiobase.com
Password: demo

Since you no longer have to do the processing, the door is open to gathering data each time you’re on the water regardless of whether you’re actively managing a particular water body. The best time to plant a tree was 20 years ago; the second best time is now. Start building a historical database of the lakes you manage today with BioBase! Don’t wait until you have a project on a particular lake to gather historical data. Now anyone can map depths and vegetation every time they’re on the water!

Subscription required for each person collecting data. Unlimited subscriptions available!

www.biobasemaps.com

Water Volume Analysis

BioBase is powerful! The centralized (online) nature of our System allows us to offer new features to our customers and make them available to trips that have already been uploaded to the System. A perfect example is our recently pushed out water volume analysis feature that is included in the standard report generated from every trip.

We employ a TIN (triangulated irregular network) to provide total water volume of a water body in cubic meters. A TIN is a vector representation of a lake bottom produced with irregularly distributed lines and nodes with 3D coordinates arranged in a network of nonoverlapping triangles. Since the BioBase System already uses an X, Y, and Z coordinate system for bathymetry, we can use a TIN for water volume analysis. An advantage of using a TIN is that the points of a TIN are distributed variably using an algorithm to determine which points are most necessary for an accurate representation of the lake bottom.
Actual covered water volume is based on the surveyed area only. In addition to actual, we also offer the total water body water volume that is based on a universal kriging algorithm that estimates contours (using statistical analysis of actual data) to the shapefie boundary. TIN analysis will be more accurate with more data points gathered with you Lowrance HDS depth finder. However, we have found that there are diminishing returns when adding more data points to improving the accuracy of the water volume analysis. Here are a couple trips on a 3.2 acre lake for comparison:

Less data collected (1019 data points):
More coverage (1546 data points):
Both trips merged together:

“Actual” represents the total surface area of the water body sampled with your HDS sonar unit. Although we also show acres covered, “Total” represents total acreage of the shapefile. Total Lake Volume represents total volume using the TIN analysis with kriged estimates using the actual data points. More data points means more accurate contours and more accurate volume. More variability in the contours could mean more places for water to fit in the pond. All relative to the water body size, when data points increased from 1019 to 1546 and actual coverage increases from 59% to 90%, total volume increased by ~6k cu. m. However, when merged together (using our trip merge function) and data points increase from 1546 to over 2500, total water volume only increases by ~300 cu. m.

One way to potentially add more actual coverage to this trip would be to cross some of these with vertical zig zags. We provide the tools and allow you to decide how to maximize them.

Bathymetric and vegetation mapping is easy with the automated CI BioBase System. We’re changing perspectives on what it mean to map and who can do it.

If you have any questions about BioBase, give us a call or email us at info.biobase@navico.com.