Mapping Hidden Channels with Genesis Live

River channel thalwegs (the line of lowest elevation within a valley or watercourse) are often dynamic, and sometimes hidden features of large river systems.  Especially low slope or impounded systems.  The thalweg is a critical geomorphological feature of river and reservoir systems and affects everything from sediment transport, to fisheries habitat, to algae or invasive plant control.

Thus a good bathymetric contour map is a necessary pre-requisite for effective river and reservoir management.  Here, we walk you through how to use new real time technologies (C-MAP’s Genesis Live) to produce smooth, precise, and accurate maps of hidden river thalwegs all within one trip to the site and with automated post-processing with BioBase’s EcoSound.  We’ll use an annotated image gallery to take you through this process.

Continue reading “Mapping Hidden Channels with Genesis Live”

BioBase Paper Published: Estimation of paddlefish (Polyodon spathula Walbaum, 1792) spawning habitat availability with consumer-grade sonar.

We’re excited to see another publication demonstrating another novel use of BioBase EcoSound technology for Fisheries Science. For a complete list of pubs see hereContact us to get a copy of any of these publications

Estimation of paddlefish (Polyodon spathula Walbaum, 1792) spawning habitat availability with consumer-grade sonar
Jason D. Schooley
Oklahoma Department of Wildlife Conservation
Ben C. Neely
Kansas Department of Wildlife, Parks, and Tourism
Journal of Applied Icthyology 2017
The paddlefish (Polyodon spathula Walbaum, 1792) is a springtime migrant that requires discrete abiotic conditions such as water temperature, discharge, and substrate composition for successful spawning and recruitment. Although population declines have prevailed throughout much of the species range, Oklahoma paddlefish are abundant and support popular recreational snag fisheries – most notably in Grand Lake. This stock utilizes the Grand Lake’s two primary headwaters, the Neosho and Spring rivers, with only episodic recruitment success. However, relationships between suitable spawning habitat and water level have not been evaluated in this system. Using consumer-grade sonar equipment, this study identified and quantified hard river substrates (such as cobble and bedrock) and investigated proportional habitat availability at a variety of simulated river conditions. Sonar data were used to construct 49-m2 grids of depth and bottom hardness (H) ranging from 0.0 (soft) -0.5 (hard). Ground-truthing samples of bottom composition were collected with a grab sampler and by visual identification. Substrate types were pooled into two categories: soft substrates (H < 0.386) and spawning substrates (H ≥ 0.386) allowing for estimation of available spawning habitat in each river. Spawning habitat comprised 69% of total available habitat for the Neosho River (6.5 ha/km) and 58% for the Spring River (7.9 ha/km). Estimated spawning habitat was simulated over a range of river stages and predictive models were developed to estimate proportional spawning habitat availability (PHA). Although the Spring River contains more concentrated spawning habitat in closer proximity to Grand Lake, the Neosho River contains a greater quantity over nearly twice the distance to the first migration barrier, has a larger watershed, and demonstrates greater PHA at lower river stages. Model results were validated in context of known high and low recruitment years, where a greater frequency and duration of days with ≥90% PHA were observed in good recruitment years, particularly in the Neosho River. In total, results suggest the Neosho River has greater value for paddlefish reproduction than the Spring River. Research-informed harvest management will remain critical to the conservation of wild-recruiting stocks for continued recreational use in Oklahoma.
Average Neosho and Spring river substrate hardness index (H) for substrate classification groups across pooled methods (grab samples and visual samples). Cobble/Rock includes fine, medium, and coarse cobble pooled with bedrock. Substrates represented by H ≥ 0.386 were regarded as paddlefish spawning habitat. Sample size is noted at the base of each column and error bars indicate 95% confidence intervals
Schooley JD, Neely BC. Estimation of paddlefish (Polyodon spathula Walbaum, 1792) spawning habitat availability with consumer-grade sonar. J Appl Ichthyol. 2017;00:1–9.

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.

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 or 715.864.9347.  Pond managers can contact our exclusive partner, Aquatic Eco-Systems (Orlando, FL) at or 407.462.4697.  Let us know what you think!