Monday, February 25, 2013

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.

Wednesday, February 13, 2013

Legacy applications of commercial sonar

At Contour Innovations we stand on the shoulders of giants who proved commercial depthfinders are precise scientific instruments for the measurement of aquatic plant abundance and distribution in lakes.   As early as 1980, researchers saw the potential for fathometers/chart recorders/depth finders/sonar/echosounders - whatever you want to call them - to substantially reduce time, effort, and cost in assessing aquatic plant communities in lakes (Maceina and Shireman 1980).

The commercial sounders of the 1980's had only a fraction of the power and resolution of what Lowrance manufactures today (not to mention integration with GPS) and investigators still boasted of the quality and cost-effectiveness of the data acquired.  Here are some excerpts:

Maceina and Shireman (1980): "The principle advantage of utilizing a recording fathometer for vegetation surveys is that savings in time and manpower can be accomplished.  In Lake Baldwin, 14 transects covering a total distance of 11.3 km were completed in three hours." p 38.

Duarte (1987): "Direct harvesting is an expensive and time-consuming procedure (see Downing and Anderson 1985).  Two SCUBA divers require 20 min on average to harvest the biomass of six replicate quadrats at a single depth.  In contrast, six replicate echosounder transects require only 8-35 min to obtain biomass estimates for all depths, with the actual time required dependent on the littoral slope and the depth to which the plants grow.  Additional advantages of the echosounder method are (1) a continuous record of the vegetation, rather than at discrete depths only, with the latter resulting in inaccuracies when the mean biomass values are estimated, (2) nondestructive sampling, which allows monitoring of the growth of stands over time and (3) simultaneous recording of other variables such as percent cover (Stant and Hanley 1985), volume occupied by the submerged vegetation, and littoral slope (Duarte and Kalff 1986), which influences macrophyte biomass." p. 734

In fact, Duarte (1987) publishes biomass prediction equation from acoustic estimates of plant height (a ciBioBase output) for 22 aquatic plant species.

Thomas et al. (1990): "Fortunately, shallow range (0-7 m) chart recorders are standard on many low cost (less than $400) commercial echosounders, so the data acquisition equipment costs are relatively low with respect to fisheries acoustic assessments, which makes this procedure relatively nontechnical and very cost effective" p. 810

The concept of using commercial acoustics for mapping lake bottoms is established and proven.  Contour Innovations has refined, streamlined, and automated the methodology with ciBioBase and delivers an intuitive visualization of the complex underwater world we call littoral zones.
A Raytheon DE-719 "fathometer" relic when plant biovolume was measured on paper charts with the use of planimeters.  Photo from

Paper chart from a Raytheon DE-719 displaying dense hydrilla canopies and bottom in a central Florida lake.  Reproduced from Maceina and Shireman 1980; J. Aquat. Plant Manage.

Classic Literature
Duarte, C.M. 1987. Use of echosounder tracings to estimate the aboveground biomass of submerged plants in lakes. Canadian Journal of Fisheries and Aquatic Sciences 44: 732-735

Maceina, M and Shireman, J. 1980. The use of a recording fathometer for determination of distribution and biomass of Hydrilla. Journal of Aquatic Plant Management 18:34-39.

Maceina, M.J., Shireman, J.V., K.A. Langland, and D.E. Canfield Jr. 1984. Prediction of submerged plant biomass by use of a recording fathometer.  Journal of Aquatic PlantManagement 22: 35-38.

Stent, C.J. and Hanley, S. 1985. A recording echosounder for assessing submerged aquatic plant populations in shallow lakes. Aquatic Botany 21: 377-394

Thomas, G.L., Thiesfeld, S.L., Bonar, S.A., Crittenden, R.N., and Pauley, G.B. 1990. Estimation of submergent plant bed biovolume using acoustic range information. Canadian Journal of Fisheries and Aquatic Sciences 47: 805-812.

Thursday, February 7, 2013

Is StructureScan worth it? You be the judge

Debating whether it's worth the upgrade to the new HDS7 Gen2 Touch StructureScan bundle?  Outside of the bigger screen and more intuitive touch technology than its older generation HDS5 sibling, the imagery produced by StructureScan should be reason enough!

Below are the same areas of a lake in Minnesota using the traditional 200 khz signal (top) and the 455 khz DownScan add-on (bottom).  A school of fish hovering over Eurasian watermilfoil plants is clearly resolved in the bottom image.  The wider cone angle of the traditional signal cannot adequately resolve these minute features.  BioBase leverages both signals to produce accurate map data sets and reproduce spatially explicit imagery for plant cover typing.  Contact us if you would like to know more about HDS features or are interested in purchasing a unit

Waypoint Upload Feature

We tout the power of passive acoustic data collection while on the water for other reasons.  Those other reasons may include sampling plant species, water quality, substrate composition, or marking other points of interest.  Now ciBioBase allows you to upload up to 1000 points of interest, where they can be viewed on your ciBioBase maps and in the automated reports (Figure 1)!
Figure 1. Waypoint upload feature that allows basic uploads and overlays of comma-delimited .csv waypoint files

Its Beauty is its Simplicity
ciBioBase's waypoint feature is not intended to be a waypoint file manager and advanced analysis tool but rather an easy way for users to incorporate spatial samples into their ciBioBase maps and reports for viewing and sharing needs.

Figure 1. shows how multiple waypoint "layers" can be filtered from one grand spreadsheet of point-intercept survey points.  Only points of interest can be uploaded as individual files (a max of 4 data columns are allowed) and easily deleted if needed.  Figure 1. shows Eurasian watermilfoil survey points in yellow and non-milfoil points in blue.  Without going to any other lengths to combine these data layers as mentioned in previous posts, you can already see that the dense bed in the NW bay of McCarron's Lake is probably mostly Eurasian watermilfoil.

Made for Easy Data Sharing Through a Link
After a .csv waypoint file is successfully uploaded, users must reprocess their report by clicking on the lower right icon in their waypoint viewer (Figure 1).  After less than 5 minutes, you'll receive an email saying the report is done reprocessing.  Figure 2 is an excerpt showing how the various layers are incorporated into the reports and have collapsible views.  Click here to get this exact report.  Try highlighting the data and pasting into Excel.  Now you have all the data that was in the report and you can do your own analysis on the data.  Large file attachments of spreadsheets are no longer needed with this feature.  Just send your partners or clients the link to the report or embed it in your lake survey report.

Figure 2.  Excerpt from a reprocessed automated report with waypoints from a point-intercept  plant species survey incorporated into the report.  Highlighting the data and pasting into MS Excel allows for quick sharing of data.
Some additional notes about use
This waypoint feature is in the beta stage of development.  We encourage its use by our clients and appreciate feedback on its utility and suggested improvements.  As mentioned above, the aim of this tool is not to be an alternative to GIS or other waypoint management programs but rather a way of quickly integrating waypoints into ciBioBase for viewing and sharing.

Pay careful attention to the file prerequisites (e.g., header names, decimal degree coord. system) as files will not load if they are not met.  Contact CI if you need assistance using the tool.

Friday, February 1, 2013

Lowrance GPS Accuracy: Seeing is believing!

A quick post to demonstrate the precision of Lowrance's internal WAAS corrected GPS antennae is in a variety of open water environments.  Docks? Boat lifts? Overhanging trees?  No problem.  WAAS correction in North America is explained here.  Have a look at a couple examples in ciBioBase:
GPS Track from a Lowrance HDS on Newport Bay, California overlain onto a bathymetry map created by automated processing of the Lowrance .sl2 log file by ciBioBase.  This trip was used for water volume calculations, bathymetry, and vegetation mapping

GPS tracks and ciBioBase derived bathymetry map in a 3-acre pond in a wooded valley in a metropolitan area of Minnesota, an example of retention pond volume monitoring.

GPS tracks and ciBioBase derived contour map of a 3-acre pond in Illinois for water
volume and aquatic vegetation analysis

GPS tracks around docks and boat lifts and ciBioBase derived contour map on Grand Lake O the Cherokees near Tulsa  Oklahoma.  The satellite even shows data collection in an area where a boat can be moored next to the dock.  That's close!