Professional Spotlight: Santa Cruz Harbor Sediment Mapping

Blake Anderson is the harbormaster at the Santa Cruz Harbor in California. As harbormaster he oversees all the operations of the harbor, harbor patrol staff, which includes search and rescue, law enforcement and public safety. He also oversees administration of about 1000 boat slips and day to day operations of the harbor. 6 years ago, Blake was faced with the challenge of rapidly mapping the constant shifting sand shoals in the harbor and turned his attention to BioBase as a potentially rapid mapping system

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BioBase Paper Published: Accuracy and Precision of Low-Cost Echosounder and Automated Data Processing Software for Habitat Mapping in a Large River

We are grateful to the aquatic research community who continue to verify and validate Consumer Sonar Technologies (Lowrance) and BioBase automated mapping platform to produce scientifically valid outputs that benefit aquatic conservation.  We are excited to see the recent publication of research out of the University of New Brunswick that evaluated the accuracy and precision of Lowrance and BioBase’s EcoSound depth and vegetation outputs.  The research is published in the open access journal Diversity and can be downloaded here. Below is the abstract

The development of consumer hydroacoustic systems continues to advance, enabling the use of low-cost methods for professional mapping purposes. Information describing habitat characteristics produced with a combination of low-cost commercial echosounder (Lowrance HDS) and a cloud-based automated data processing tool (BioBase EcoSound) was tested. The combination frequently underestimated water depth, with a mean absolute error of 0.17 ± 0.13 m (avg ± 1SD). The average EcoSound bottom hardness value was high (0.37–0.5) for all the substrate types found in the study area and could not be used to differentiate between the substrate size classes that varied from silt to bedrock. Overall, the bottom hardness value is not informative in an alluvial river bed setting where the majority of the substrate is composed of hard sands, gravels, and stones. EcoSound separated vegetation presence/absence with 85–100% accuracy and assigned vegetation height (EcoSound biovolume) correctly in 55% of instances but often overestimated it in other instances. It was most accurate when the vegetation canopy was ≤25% or >75% of the water column. Overall, as a low-cost, easy-to-use application EcoSound offers rapid data collection and allows users with no specialized skill requirements to make more detailed bathymetry and vegetation maps than those typically available for many rivers, lakes, and estuaries.

EcoSound vs Manual Measures Vegetation Helminen et al 2019

ciBioBase Vegetation Mapping

We love to show off the accuracy of our submerged vegetation mapping algorithm.  Check out this break in the weeds that was picked up and clearly displayed in the ciBioBase vegetation layer:

The BioBase vegetation layer is automatically generated by powerful cloud computers so you receive an objective output every time.  The white line on the right and red dot on the left show the boat position as a cross section and aerial view of the water column respectively. 

Submerged vegetation is displayed as percent biovolume (BV%) which represents the percent of the water column occupied by plants.  This provides a clear picture of total plant abundance from each trip on the water.  Data can be passively logged because none of our users have to do any of the processing when they get back to the office.  Do what you were already planning to do and our automated system will take care of the rest.

Let us know if you have any questions about how this process works!

Assessing Fish Habitat in Rivers

BioBase is not just a lake vegetation mapping tool, it also can help Fisheries managers and researchers assess, monitor, and simulate fish habitat conditions in large rivers.  We demonstrated this application on a trip to the Mississippi River Pool 2 in St. Paul, MN on 4/27/2012.  Just downstream of the Lock and Dam, we used a Lowrance HDS sounder and the automated processing of BioBase to map the bathymetry of a pool where a range of fish species often congregate (Figure 1).

Figure 1.  Bottom mapping with a Lowrance HDS-5 on Pool 2 of the Mississippi R. just downstream of the Lock and Dam on 4/27/2012.


The raw pool elevation on 4/27/2012 was 4.27 feet; still within the range of moderate drought according to the US Drought Monitor but 1.7 feet higher than the most recent low on 12/10/2011. Coincidentally, these drought levels follow historic flood levels just one year earlier (Figure 2). To demonstrate BioBase’s utility as a fish habitat assessment tool, we compared sizes and volumes of our mapped pool under the hydrologic conditions experienced on Pool 2 during the last year.

Figure 2. Hydrograph for the Mississippi River at St. Paul, MN (DNR ID# 20088002; USGS ID# 05331000; Data and figure courtesy of the MN DNR).

On 4/27/2012, we mapped and analyzed a 15-ft pool using the ciBioBase polygon creation tool and determined that the max depth was 17 ft, surface area was 317 m2 and the volume was 1508 m3 (Figure 3).

Figure 3.  Diagnostics of a pool of interest using BioBase’s polygon tool.

In order to reconstruct changes to this pool under the recent low flow on December 10th 2011, we used the Z-depth Offset feature iniBioBase to drop the elevation down 1.7 feet.  In Figure 4, you can see the striking difference this reduction has on the size of this pool and consequently the amount of available fish habitat.  The area on December 10th 2011 was estimated to be 3.1 m2 and volume was 9.4 m3; 100 times smaller in size and 161 times smaller in volume than on 4/27/2012. If we increase the offset by the peak flood elevation on March 30th 2011, the 15-foot hole becomes a 30-foot hole (Figure 5).


Figure 4. Polygon overlay in BioBase demonstrating the difference in size and volume of a 15-ft deep hole between the yearly low elevation on 12/10/2011 (pink) and during data collection on 4/27/12 (green).


Figure 5. Polygon overlay of drought elevations in 2012 (green and pink) overlain onto simulated peak flood bathymetry on 3/30/2011.
This demonstrates one potential application of BioBase for fish habitat studies in large rivers.  We presented three striking contrasts in fish habitat conditions within one year’s time with data that took 20 minutes to collect and an hour to analyze in BioBase. Different hydrological scenarios can be modeled in BioBase and thus could be used in predictive fisheries habitat models or to reconstruct habitat conditions over some period of time.

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:

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