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 90 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, as ESRI Silver Partners we offer basic support of viewing and analyzing BioBase data in ArcGIS 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 ciBioBase 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 ciBioBase to manage sedimentation in Arizona’s lifeblood 336-mile aqueduct.  Since then, CAP GIS Wizard Glenn Emanuel has worked some amazing magic on the ciBioBase 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, ciBioBase cloud processing software, and finally exported/imported into ArcScene.  Image courtesy of Scott Bryan and Glenn Emanuel, Central Arizona Project.

Any user of ciBioBase 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 ciBioBase users are interested in managing, protecting, and restoring.

ArcGIS Mapping Tutorials

ciBioBase is much more than a powerful data processing engine, it is also a complete data services package.  Contour Innovations’ Biologists and GIS Specialists on staff can help you get the data products you need to efficiently assess waterbodies and make sense of your output.

With your subscription to ciBioBase, you get access to basic GIS and survey tutorials and technical support for everything from suggested transect spacing to ways of analyzing ciBioBase outputs.

Access to ArcGIS Tutorials are available to all subscribers

Tutorial 1 covers converting ciBioBase grid point feature outputs into raster datasets (requires Spatial Analyst extension for ArcGIS).  Although many types of analyses can be done on the grid point data, converting to raster allows users to run a wider range of analyses, custom contouring and imagery, compare maps over time, and to create unique maps (e.g., plant canopy height grid).

Tutorial 2 covers a step-by-step process of creating transect lines in ArcGIS, converting the shapefile to a .gpx file, and then uploading as tracks/trails to your Lowrance HDS.

Transect lines can be created using an ArcGIS utility and converting the shapefile to a .gpx file for importing into your Lowrance HDS as a Trail.

Pre-planning transect coverage and following the lines on your HDS Chart ensures complete coverage of the area you intend to map.

ciBioBase provides all the tools and features necessary to users with no GIS experience to automatically create maps and data reports to carry out effective lake monitoring and management.  Nevertheless, CI supports a range of custom GIS and data analysis needs through these tutorials and help from technical support staff.  CI also has a range of contract offerings for bigger GIS or data analysis training needs or special jobs.  ciBioBase is more than an algorithm, it is a service that helps lake managers and researchers more efficiently and precisely measure the aquatic systems they are charged with understanding and managing.

Contour Innovations Becomes ESRI Partner!

Contour Innovations is excited to announce a new partnership with ESRI (Environmental Science Research Institute), the company that has set the global standard for GIS (Geographic Information Systems).  This direction and partnership allows us to continue to grow and provide the type of tools our customers need to get the most out of their time on the water.  Our partnership with ESRI also supports our ability to expand our offerings to better support the GIS needs of our clients through GIS training webinars or custom GIS analyses and layouts using ciBioBase datasets. 

Contour Innovations has automated the basic GIS mapping and analysis tools (e.g., exported imagery, polygon tool and automated reports) with ciBioBase to produce a fully functional geospatial data analysis and warehousing platform for users who need “turn-key” solutions for water resource assessments.

However, the true power of ciBioBase lies in its ability to rapidly produce high resolution spatial datasets that can be exported out of ciBioBase and brought into to third party software platforms such as ArcGIS.  Multiple layers such as hyperspectral imagery of floating-leaf or riparian vegetation, upland terrain, plant species survey points, land use, or other in-lake features can all be overlain onto one image (Figure 1).

Figure 1. Example layout of aquatic plant biovolume (% of water occupied by vegetation) collected with Lowrance HDS depthfinders, processed by ciBioBase and brought into ArcGIS.  Species sampling points, aerial photos, or other spatial data layers can be overlain and displayed together.

Or, one could explore a range of powerful spatial and image analysis tools and extensions such as Spatial Analyst, 3D Analyst, Geostatistical Analyst or ArcGIS for Maritime: Bathymetry.  For example, the raster calculator feature of Spatial Analyst is an amazingly simple and powerful tool for spatially comparing and visualizing differences between map outputs and the creation of unique maps.  For instance, by simply multiplying a ciBioBase bathymetry raster grid by the vegetation raster grid, you can create a plant height grid (Figure 2).

Figure 2. Plant canopy height grid created by multiplying the ciBioBase depth grid by the biovolume grid using the raster calculator in ArcGIS Spatial Analyst.  Plant canopy height ranged from 0 (blue) to 10 ft tall (red)

The sky is the limit with regard to what you can do with ciBioBase datasets to help managers and researchers better understand and manage water, aquatic plant and fisheries resources.  Contact rayv@contourinnovations if you are interested in learning more about how CI can help maximize the value of your ciBioBase outputs.

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 ciBioBase uniquely handles.

First, ciBioBase uniformly interprets acoustic signals and the output is the same regardless of the skill level of the individual collecting the data.  Second, ciBioBase 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.

Kriging takes irregularly spaced data points and creates a smooth GIS map (also called a raster grid) based on the geostatistical properties of the input data.  Generally, points close together are more related than points farther away but the precise relationship can vary from location to location.  Kriging uses the actual statistical relationship of neighboring data points to make predictions in unsampled locations.  Other popular methods such as Inverse-Distance-Weighted (IDW) interpolation make simple assumptions of relatedness and does not use actual data to influence predictions in unsampled locations.

Through its use of kriging, ciBioBase removes the concern of precisely following the same path from survey to survey; which is very difficult to do on moving water even for the most seasoned surveyor.  Further this process can leverage passive data collection while doing other survey work, fishing, or simply enjoying a pleasure cruise and turn it into useful information for water resource management and protection (Figures 1-4).



Figure 1. Fisheries biologists can collect fish habitat data passively while conducting electrofishing fish surveys.
Figure 2. Passively collect depth and vegetation abundance data while enjoying a pleasure cruise with the kids or fishing.
Figure 3. Result of merged ciBioBase trip path data from passive data collection (above) resulting in a uniform vegetation map (below).
Figure 4. Zoomed in area of Figure 4 showing merged trip paths (above) and the uniform map output (below).  The heat map represents density of aquatic vegetation.  Blue is no vegetation growth and red represents vegetation growth that is all the way to the water surface.

Revised ciBioBase automated summary reports 
At 15 pings per second coming out of Lowrance HDS depth finders, data quickly add up and without any help, users can be drowning in data and be worse off than when they started.  This issue was the topic of a previous blog post (What to do with all this data?). ciBioBase handles the data deluge by using kriging and creating automated summary reports.  Our recently revised summary reports now include statistics based on coordinate point data (i.e., your trip path) and data from the bathymetric and vegetation grids created by kriging (Figure 5).  When survey data collection is structured with straight transects of a uniform speed (as in the case with Figure 5), the differences between the point and grid summaries is small.

Figure 5. ciBioBase automated summary report excerpt showing both coordinate point and kriging grid summaries
In circumstances where lake managers are primarily interested in monitoring vegetation along standard transects, the point summaries may suit them best since the points are often uniformly spaced a part and along a straight path (Figure 6).
Figure 6. Example automated summary report showing results from a standard transect survey.  Because data lie along straight paths and are mostly uniformly spaced, point data summaries should be used.

However, if you idle for long periods time collecting samples on the lake or trying to entice finicky fish to bite, many data points amass in one location (Figure 6) and can bias the statistics from the point data (Figure 7).

Figure 7.  Vegetation point data along trip path (blue) exported from ciBioBase and displayed in GIS at two zoom levels overlayed on uniform kriging grid data (blue-red).  Notice the accumulation of data points over areas where the boat is only slightly moving.  Kriging creates a uniform grid of points no matter how the data are collected.

In the situation above, the differences between the point and grid data are larger and the grid data becomes more important to use for formal statistical summaries and reports (Figure 8).  The upshot is when in doubt, use the grid statistics for your data summaries.

Figure 8. Differences between point and grid statistical summaries when data along trip path are not uniform. In these situations, use the statistics from the uniform grid for report summaries and lake management decision making.

A better use of your time
By automating the complexities of creating maps, ciBioBase users do not need to spend precious time and money dealing with manual data collection with survey rods and hand held GPS’s, entering data with a pencil onto a datasheet, and then figuring out how to display the data in GIS and run Geostatistics models to get a map.  Before BioBase’s launch in 2011, bottom and vegetation mapping was a costly endeavor and often just wasn’t done.  ciBioBase is changing the game and is empowering all citizens regardless of technical expertise with the ability to see what is below the water’s surface, how it’s changing over time, and how to best manage that change.