New BioBase Website including new DIY GIS tutorials

We’re excited to announce the launch of the new biobasemaps.com website! You’ll find an image-rich professional look and feel as well as information segmentation into solutions and features that speak directly to the markets we serve (Aquatic Plants, Fisheries, Water Resources, Private Ponds, Coastal).

New visitors to biobasemaps.com will also see more information about our optional GIS Services that can take your BioBase maps and tailor them to your precise needs regarding image size, contour interval, custom legend, logos, etc.

GISServices_EMULAKE200DPI
Sample custom map created by our GIS staff from BioBase EcoSound outputs. 

Dabbling in GIS? We can help you get started in QGIS

Many of you also come to us with questions about how to do more with your BioBase outputs (e.g., custom contouring, water volume calculations, spatial data analyses). To empower you to fully leverage the potential of BioBase outputs we have prepared several step-by-step QGIS tutorials to get you the outputs you require for your work. See our Support Resources page for these tutorials along with other useful self help resources

Training EcoSat Vegetation Classifications: User tips

What is EcoSat?
EcoSat delivers a one-of-it’s-kind semi-automated cloud processing of very high resolution satellite imagery to map nearshore vegetation and coastal benthic habitats.  EcoSat uses the latest multi-spectral imagery from reputable providers such as Digital Globe (World View 2,3 and 4), Airbus Defence and Space (Pleiades), and ESA’s Sentinel program and industry standard image processing techniques.  Sophisticated Amazon Web Service cloud infrastructure rapidly processes imagery, creates reports and imagery tiles, and delivers detailed habitat maps to user’s BioBase dashboard where it can be analyzed and shared.  Average turnaround time from imagery tasking order to delivery of results is 60 days.  The rapid and standard processing methods are allowing entities like the Florida Fish and Wildlife Conservation Commission to establish regular monitoring programs for emergent vegetation.  The extremely long and expensive one-off nature of conventional remote sensing mapping projects using non-repeatable tailored techniques has prevented natural resource entities from assessing the degree that habitats are changing as a result of environmental stressors such as invasive species invasions and climate change.

Continue reading “Training EcoSat Vegetation Classifications: User tips”

FAQ of the year: Does BioBase EcoSound Map Sediment Depth?

Thanks to advances in physical, chemical and biological technologies and funding that are focused on reducing sedimentation or muck depth in waterways, many water resource practitioners are eager to determine how much sediment is in a waterway of interest and how much could be removed. As such, we frequently are asked: “Will BioBase tell you how deep the sediment is?”

Continue reading “FAQ of the year: Does BioBase EcoSound Map Sediment Depth?”

Need a Custom Map? We’ll make you one!

BioBase’s primary strength is an automated map creation engine designed to take thousands raw of data signals from your Lowrance and rapidly summarize them into informative maps.  These maps have helped aquatic resource professionals throughout the globe make more informed aquatic management decisions.

But BioBase also creates maps that are rather pleasing to the eye and many have asked how they might be able to create customized digital or print maps for their clients.  We offer two solutions that will help you create professional quality maps. First, we offer basic support of viewing and analyzing BioBase data in QGIS and have produced several do-it-yourself tutorials that are available in your BioBase Support & Resources.  Second, we offer GIS Services to BioBase customers who lack expertise in GIS or the proper software licenses.  Below we present a gallery of images from these projects.  Identities and locations of projects have been changed or omitted to protect the privacy of the customers.

We’ll create a map for you!
Navico offers custom GIS services where interested customers fill out an order form specifying their needs.  Navico GIS staff will transfer the appropriate BioBase data to ArcMap 10.x and any ancillary GIS shapefiles (e.g., sampling waypoints or other points of interest) and produce a custom-sized, high resolution digital map that you can have printed online or at a local print shop.  Email us at info.biobase@navico.com to get print and pricing details.

Multiple BioBase maps can be combined into one map and exported as any image format and custom sized.  Send us your logo and we’ll add it to the map.
Request transparency to the image to show floating leaf vegetation in the aerial imagery.
Send us points of interest to add to the map.  In this case, navigation hazards in front of a land owner’s property
Send us sediment depth point data and if sufficient, we’ll interpolate and create a sediment depth map (left) and pare it with other BioBase maps (in this case aquatic vegetation biovolume).
Would you like to add water body statistics? We’ll add full lake summaries or summaries by depth.  You tell us the contour interval and units.
An example where a customer desired to simulate the pond depth at a significantly higher water elevation than when mapped with BioBase. Customer used survey-grade GPS to generate precise land elevation data while walking along the soon-to-be-inundated shore.  Customer submitted these point elevation data to Navico along with a high-water shoreline for incorporation into the lake map.
If you have any custom mapping or presentation needs with your BioBase data contact us today at info.biobase@navico.com and we’ll provide you with an order form and generate a quote and delivery timeline for your map.

 

New Survey Findings: Use of Geographic Information Systems by Fisheries Management Agencies

Recently Brandon Eder from the Nebraska Game and Parks Commission and Ben Neely from the Kansas Department of Wildlife, Parks, and Tourism published some interesting findings in Fisheries pages 491-495 regarding the use of GIS in fisheries management agencies in the US and Canada (see abstract below).  Technology is opening horizons and aquatic resource practitioners now have a variety of intuitive tools at their disposal to characterize and describe the complex spatial environments they are charged with managing.

Better characterization and description of aquatic environments leads to better management decisions and public welfare.  How can we promote more academic training and utilization of GIS tools for aquatic resource practitioners?  Eder and Neely have some advice that is worth a read.

ABSTRACT: Use of geographic information systems (GIS) in fisheries science has increased in prevalence since its introduction in the late 1980s, but use among and within fisheries management agencies has not been quantified. We surveyed 89 administrators of fisheries management agencies in the United States and Canada to determine the current status of GIS in fisheries management and received 54 responses (61% return rate). Survey respondents indicated that GIS was used to help manage fish populations, and 63% of respondents believed that GIS was either “very useful” or “extremely useful” for meeting agency objectives. However, most GIS work conducted by fisheries management agencies was executed by few individuals within the agency or by contracted service. Barriers preventing more widespread use by managers within agencies included lack of knowledge or training and limited time to use GIS in job duties. Our results suggest that GIS is an important tool for fisheries management. Further, GIS use within an agency might be increased by focusing on increased biologist participation in training exercises, integration with existing job duties, and recognizing diversity among GIS software.

Amendment to BioBase Guest Blog: GIS Tools helping CAP manage sedimentation

Earlier this year, Senior Biologist Scott Bryan from the Central Arizona Project (CAP) blogged about how the CAP is using BioBase to manage sedimentation in Arizona’s lifeblood 336-mile aqueduct.  Since then, CAP GIS Wizard Glenn Emanuel has worked some amazing magic on the BioBase grid exports using Spatial and 3D Analyst Extensions for ArcGIS (Figure 1).

Central Arizona Project, sedimentation, Lowrance, ciBioBase, BioBase, sonar, mapping, acoustics
Figure 1. Images showing the change in sediment volume prior to and after experimental dredging activities in a Forebay of the CAP canal.  The Raster Calculator in ArcGIS’s Spatial Analyst was used to subtract a “current” bathymetry from a baseline bathymetry (e.g., “as built”) to estimate sediment height and volume.  Images are 3-dimensionally enhanced using 3D Analyst for ArcGIS. Image courtesy of Scott Bryan and Glenn Emanuel, Central Arizona Project

The data and images allow CAP to make informed decisions regarding the efficiency of sediment removal operations.  In addition, ArcScene was used to produce a 3D scene of the forebay (Figure 2), which can then be animated with a video fly-through.

Central Arizona Project, sedimentation, ciBioBase, ArcScene, Lowrance, BioBase, sonar, mapping, acoustics
Figure 2. “Fly-through” images of sediment height  in Little Harquahala Forebay in the CAP Canal collected by Lowrance HDS sonar and GPS, BioBase cloud processing software, and finally exported/imported into ArcScene.  Image courtesy of Scott Bryan and Glenn Emanuel, Central Arizona Project.

Any user of BioBase properly equipped with the proper third party GIS software can create these amazing map products that are more than just pretty pictures.  They create a real-life, tangible perspective of aquatic resource conditions that BioBase users are interested in managing, protecting, and restoring.

Mapping is Easier with Passive Collection

I remember the days when you had to schedule an hour out of your field day to “set up” and “take down” your mapping set-up.  Wires, an echosounder, a transducer, a GPS, a PC to run everything all had to be set up and configured (Figure 1).  Most importantly, equipment had to be secured by creatively fashioned brackets, booms, and working platforms so you didn’t lose a $4,000 part.  Many horror stories over the years have been told by colleagues who forgot “Righty” was “Tighty” and as a result dropped an expensive piece of fish structure in the drink!

Figure 1.  Elaborate set up of wires, brackets, and working platforms needed to operate the  hydroacoustic systems of yesterday

Needless to say, life during this period was about dedication.  A dedicated survey boat.  Dedicated surveys.  Dedicated staff to run the equipment.  Dedicated staff to analyze the data.  Dedicated staff to oversee that “Righty” made “Tighty” (ok, maybe not that bad).  But still, the expense and logistics of such dedication kept hydroacoustic mapping out of the reach of most water and fisheries resource entities.

With advances in consumer sonar technology, GIS and cloud-computing, now anyone can create high quality bathymetry, vegetation, and bottom hardness maps and datasets with a $700 Lowrance Depth finder, a canoe, and access to the internet with a subscription to ciBioBase (Figure 2).

Figure 2. A 3.6-acre storm water retention pond mapped in 30-min (upload processing time = 10-min) using a canoe and a portable Lowrance HDS-5.  Red lines are the actual traveled track along which data were collected and uploaded to ciBioBase for the generation of the bathymetric map.

Who needs dedication anyway?

No needs for a dedicated boat. The unit can be made portable with no larger than a 12” by 8” footprint (Figure 3).  The transducer(s) and optional GPS can be mounted on a bracket available from Cabelas (Figure 4).  This set up can then be put on a range of vessels from a canoe to a large cabin cruiser.  It can be checked out and passed around by lake association subscribers taking turns mapping the lake on which they live if they don’t already have an HDS.

Figure 3.  Lowrance HDS units can be made portable a variety of different ways to fit your budget and  sampling needs.
Figure 4. Example portable mounts for transducers 
No needs for dedicated surveys. Whether you are a lake association member drinking cocktails (while staying under the legal limit of course) on pleasure cruise on your pontoon or a biologist going point-to-point sampling species of plants, passively recording sonar data requires no work outside of hitting “record,” inspecting the screen for signal quality (i.e., a clear picture), and uploading the data when you return from the field.  ciBioBase algorithms rigorously evaluate the quality of each signal and filter poor outputs (Figure 5).  Back in the day, the staff hydroacoustician had to do this.  Computers do this now.

Figure 5.  Example of automated data quality filtering by ciBioBase.  In the top example, bass tournament anglers were rapidly hopping from spot to spot.  Vegetation detection becomes unreliable at speeds greater than 12 mph.  Consequently, outputs are not generated at speeds that exceed this threshold.  In the bottom example, depths were shallower than 2.4 feet and thus not mapped because of detection errors in depths shallower than this threshold.  However, manual waypoints can be added in these locations within users’ ciBioBase account.

No need for dedicated staff trained in hydroacoustics and GIS.  Although ciBioBase offers much for the Hydroacoustic and GIS aficionados via data exporting and importing into their favorite data analysis software, training in hydroacoustics and GIS is not a prerequisite for creating good outputs and datasets.  Hydroacoustics and Geostatistics are not new or “soft” sciences that are so variable and complex that they can’t be automated (i.e., ecology).   The basic physics of sound traveling through water and reflecting off of various objects has been well understood for decades.  Concepts and applications of kriging (originally developed in the gold mining industry) are almost as old and well understood.  Accordingly, ciBioBase automates the interpretation of acoustic signals, creation of a GIS map layers, and standard summary reports.

Dedication in almost every aspect of life is an admirable virtue for which we all should strive.  However, when it comes to mapping lakes, rivers, or ponds, ciBioBase lowers the prestige of this virtue.  Indeed, there will always be a well-placed need for dedicated mapping.  However, we feel opportunities for understanding the dynamic nature of aquatic habitats will be missed if data are not logged while engaging in other activities on the water.  This is non-dedication at its finest!

Precision Management-Time to Quantify

Lake Harriet Monitoring Before and After Harvester. . .

A multitude of factors impact the health of aquatic systems creating a need to monitor lakes’ “vital signs”.  In the same way it is expected that a medical doctor will do more than glance at a patient and say: “you look fine” the same is needed for our lakes.  A number of different vital signs are necessary to give a precise assessment of human health and our aquatic systems are no different, they are complex biological systems.  ciBioBase provides many “unchecked” parameters that have not been assessed until now in an automated processing system.  Two trips on a small section of Lake Harriet in Minneapolis collecting “vital signs data” have already told a story about big changes in the aquatic community.  What more can we learn about this complex ecosystem by simply monitoring with ciBioBase on an ongoing basis?
A data collection trip with ciBioBase in late June on Lake Harriet revealed what you might expect from an unseasonably warm spring in a lake infested with Eurasian watermilfoil(EWM).  Aquatic plant growth was several weeks ahead of schedule with EWM dominating the sample area on north shore and already being matted on the surface.  The majority of near-shore areas sampled exhibited near 100 % EWM biovolume (% water column occupied).  In fact, in the far east and west reaches of the sample area our survey-boat was skirting matted EWM too dense to navigate through.  Wherever vegetation occurred (percent area coverage) on the June 18th survey the biovolume average was very high, due to it being composed primarily of EWM (average of 54.4%).  
BEFORE:
 

In late August a comparison trip was completed, navigating the same transect line from the June trip using ciBioBase following the Lowrance HDS track overlay on the unit.  A striking feature noticed shortly after getting on the water was…..Where was all the topped-out vegetation?  The transect sampled on June 18th skirted topped-out EWM, but on August 22nd no topped-out vegetation occurred in the same sampling area.  This excerpt from the Star Tribune written by Bill McAuliffe on June 10th explains: “The Minneapolis Park Board’s milfoil harvest began with a single mower.  . The harvesting each year generally requires at least two passes through each lake. Cedar Lake was scheduled for mowing Friday. After that, Lake Harriet is on the schedule.” (View the article by clicking here).  That would explain the drop in average biovolume in vegetated areas from 54.4% to 16% and overall average biovolume for the entire sampled area from 28.3 to 5.1%.

AFTER:
*Automated Reports Generated for Each Trip Uploaded to ciBioBase

ciBioBase not only displays that the average biovolume in vegetated areas for this study site dropped from 54.4% to 16% and overall average biovolume for the entire sampled area from 28.3 to 5.1%, but it also outlines vegetation distribution.  Spatial characteristics such as the shift from about 30% of the sampled area having a biovolume of  >80% to 0.34% of the sampled area having a biovolume >80% after the EWM harvest are also a part of the ciBioBase data output.

ciBioBase has enabled users to precisely compare changes in biovolume and spatial distribution of vegetation; pinpointing changes and quantifying their outputs.  This means precision monitoring and management using quantifiable target goals while leveraging objective “before and after” monitoring data that is easily collected, processed, and viewed with the ciBioBase system.

Knowing precisely “where and how much” are critical components to knowing if management plans are effective.  Another excerpt from Bill McAuliffe’s Star Tribune article states: “The Lake Minnetonka Conservation District launched its two mowers Thursday, about on schedule because it uses school teachers to run them, said Judd Harper, who manages the district’s milfoil removal. But weed growth on the lake is “a lot worse than it was last year,” Harper said.”  ciBioBase provides numbers behind “a lot worse”.

Using the ciBioBase system and historical database comparison, it is now possible to quantitatively identify year to year and other temporal trends.  Managers can now implement corresponding management based on sound scientific data and quantitative metrics.  ciBioBase is the key to precision management!

TRIP COMPARE FEATURE IN CIBIOBASE

* %BV (% of the water column filled with plants)
ANOTHER SHOT OF BAIT FISH PICKED UP BY STRUCTURE SCAN

 

ABOUT CIBIOBASE:

ciBioBase removes the time and labor required to create aquatic maps! The System was engineered to provide automated cloud based bathymetric and aquatic vegetation mapping and historical trend tools for aquatic habitat analysis. ciBioBase leverages log file formats recorded to SD cards using today’s Lowrance™ brand depth finders and chart plotters. Data you collect while on the water is uploaded to an online account where it is processed by our servers automatically! We rely on automation to make vegetation mapping cost effective by reducing the technical skills, staff, and hours to produce vegetation abundance maps from raw sonar collection. With the human element gone, you get accurate and objective mapping at lightening speeds! The result is a uniform and objective output all over the world!

What’s this Kriging Business?!

Thanks to advances in Geographic Information Systems (GIS) computing technology, evaluating changes to lake bottoms over time has gotten much easier!  Prior to GIS, biologists and surveyors would go through great pains to ensure that repeated data collection in study areas of interest would precisely fall on the same area or transect.  If this condition was not met, data would have to be thrown out because biologists could never be sure that the difference seen between two time periods was real, an artifact of sampling a different area, or a product of sampling in a different way.  Consequently, efforts from multiple groups collecting similar data in the same system but in a slightly different way could not be leveraged.  This is an unfortunate missed opportunity that BioBase uniquely handles.

First, BioBase uniformly interprets acoustic signals and the output is the same regardless of the skill level of the individual collecting the data.  Second, BioBase employs kriging to create a statistically robust uniform map output that figuratively turns Survey 1 by Bob Smith from an orange into an apple and Survey 2 by Amy Johnson in the same area from a grapefruit into an apple.  This is unique to kriging which is a geostatistical procedure.  All other standard interpolation methods are simply 3D representations of the input data and each map will look different depending on the precise location of your survey points.  Only kriging turns different fruits into apples.

Continue reading “What’s this Kriging Business?!”

Bathymetry Mapping with ciBioBase!

At Contour Innovations, we often preach the importance of aquatic plant mapping and monitoring, but of equal importance and capability is ciBioBase bathymetric mapping features.  ciBioBase comes with many features that automate the tedious, mundane, yet highly technical GIS processes associated with creating a bathymetric map.  Water resource and lake managers and researchers should be spending their time and talents focusing on thorny management problems, not compiling and managing volumes of data and trying to map them in GIS.  The science of acoustic bottom detection and GIS mapping has been extensively tested, verified, and proven with standard methods.  We automate this.

Because ciBioBase maps only areas you cover up to a 25-m buffer outside of your track, you are assured that maps do not include extrapolated data.  40-m spacing of transects with a criss-cross design assures you that you will get complete coverage and smooth contours (Figure 1). 

Figure 1. Transect coverage showing a “criss-cross” design to assure a high quality bathymetric map.

The Trip Replay feature in ciBioBase further allows you to see disruptions in the contours (Figure 2).  As in the case with Figure 2, there was a temporary disruption in the transducer signal, thus giving an erroneous depth (Figure 2 and 3).  In ciBioBase, these erroneous depths can be edited out; thus creating a smoother, more accurate bathymetric map and associated statistics.

Figure 2. Desktop verification of bathymetric outputs with ciBioBase’s Trip Replay feature.
Figure 3. Areas of disrupted signal can be deleted and the trip reprocessed for a more accurate and smooth bathymetric map.

Other times, these little “donuts” occur because depths temporarily enter a different contour level (e.g., 3ft contours with series depths = 5.99, 6.0, 5.99, 5.98, etc).  Although the 6.0 depth is likely legit, it may be more aesthetically pleasing to remove the 6.0 depth to prevent the creation of a 6ft donut hole.

Once you are happy with the output with individual trips, you can merge them in ciBioBase to create a uniform output (Figure 4).

Figure 4.  Merging function in ciBioBase that allows users to merge individual files or trips into a single, uniform map.

Tying Bathymetry to a Benchmark Elevation
When mapping bathymetry, it may be important to tie the water level to a benchmark water level elevation.  In our Minnesota Lake example, we went to the Minnesota Department of Natural Resource’s Lakefinder website and found important water level information (Figure 5).  On 6/5/2012, we surveyed McCarron’s Lake in Ramsey County, MN.  On 6/7/2012, the elevation-corrected water level reported by citizen volunteers was  840.84 ft above sea level.  The Ordinary High Water Level  (OHW) benchmark for McCarron’s is 842.21 ft (Figure 5).  Using the Data Offset feature in ciBioBase (Figure 6), we can simply add 1.37 ft (elevation correction) plus 1 ft (transducer correction) to get a bathymetric map that is corrected to the OHW (Figure 7).  This eliminates water level as a confounding variable with repeated bathymetric surveys on the same waterbody.  The final products are high resolution, blue-scale imagery as seen in Figure 7 (up to 1-ft contours) or the actual point and grid data that can be imported into any third party GIS or statistical software (Figure 8).

Figure 5. Water level information for McCarron’s Lake in Ramsey County, Minnesota USA.
Figure 6. Data Offset feature in ciBioBase that allows users to correct their bathymetric data to a benchmark water level and transducer depth.
Figure 7. Bathymetric imagery with resolution (both bottom and pixel) that can be controlled by the user.
Figure 8. Export point data along your traveled path or the kriging interpolated grid for use in third party GIS or statistical software.

Life is good in the cloud…

Because of the centralized, cloud-based platform of ciBioBase, we see trip uploads into the system from all types of lakes, ponds, and reservoirs throughout the country and even abroad; so our acoustic and geostatistic algorithms have seen it all!

See for yourself in our demo account at ciBioBase.com.  In the login page, enter demo@cibiobase.com and “demo” for the password.  Operators are standing by to answer any questions you may have!