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Integrating GIS and Fluorometry For Real-Time mapping of Coastal Systems


In VivoChlorophyll, Dye Tracing


About Cawthron Institute
Cawthron Institute provides science and technology solutions to enable the sustainable management and development of New Zealand’s coastal and freshwater resources for the benefit of the region and the nation. Cawthron has been operating in Nelson, New Zealand for over 80 years and is owned by a trust that represents the local community and employs over 150 scientific and technical staff.

Within Cawthron, the Coastal Group provides expert scientific advice in both commercial and research settings in the fields of resource management, coastal ecology, fisheries and aquaculture sustainability, environmental effects of waste discharges and oil spills, biosecurity and environmental modelling. 

This article focuses on our integration of the 10-AU and SCUFA fluorometers with desktop Geographical Information System (GIS) software for real-time mapping and data collection. To demonstrate this, we have highlighted two case studies: (i) tracking effluent dispersion/dilution from coastal outfall (using Rhodamine® WT dye) and (ii) mapping chlorophyll-a depletion around marine mussel farms.

The Monitoring Dilemma
While monitoring dye in effluent plumes or in-situ chlorophyll-a using fluorometers is by no means new, one of the biggest dilemmas is incorporating the data collected with positional data to create maps and/or charts. Historically, this was done in the field by writing down position and fluorescence readings or entering them into a laptop. However, manual data collection can be both tedious and fraught with potential transcription errors.

The change from analog to digital instruments has greatly enhanced the ability to collect and log fluorescence data, but that’s only half the story, since position data are also required. The advent of Global Positioning Systems (GPS), and the subsequent removal of selective availability, has meant that accurate (i.e. ± 2-5 m) real-time position data are now both readily available and affordable. Also, along with the improvements in instrumentation, the ability to run desktop GIS has been rapidly improving. Therefore, in order to create real-time maps, these three components: GPS, GIS, and fluorometry need to be combined. 

The Solution
Cawthron has created a custom add-on to Arcview ® 8.3 GIS that connects to the different simultaneous serial data streams of the instrumentation in the field (i.e. GPS, SCUFA, 10-AU), combines the incoming data and maps the fluorescence in real-time as graduated dots. The fluorescence data are overlaid on a rectified nautical chart or aerial photograph so that the actual position of each fluorescence reading in relation to the area being studied (e.g. outfall or mussel farm) can be determined. This approach has numerous benefits, including the ease of use, time-saving, the ability to collect large amounts of data, and the ability to view and make decisions in the field regarding the data collected. 

The Arcview® add-on was written in Visual Basic for Applications (VBA®) and enables the user to select which serial port the instruments are connected to (Figure 1), the frequency with which data are to be collected (the capture interval) and the file name to log the data to. In addition, there is a real-time window that displays current position and fluorescence.

Integrating GIS and Fluorometry For Real-Time mapping of Coastal Systems
Figure 1. Screen shot of Arcview® serial data capture form.

Once a connection is made the incoming data are parsed into individual variables. For general monitoring, much of the GPS data is extraneous and just the position and time data are required. This includes Latitude, Longitude, Speed, Direction, and Time. Therefore, only certain GPS sentences are used in the add-on and are converted on the fly to local New Zealand Map Grid coordinates. All GPS and fluorometric data are parsed and logged in Arcview® as individual fields within a shapefile.

A screen shot of the 4,300 data points collected on the four hour ebb tide study is presented in Figure 3. Receiving water dilutions of each data point were calculated from the effluent concentrations measured in the grab samples. Contours of these dilution factors were manually digitized using the GIS software to better illustrate the dispersion and dilution pattern of the effluent (Figure 4).

Case Study 1: Mapping Dye from a Coastal Outfall using a 10-AU Fluorometer
This integrated logging system was used for a recent study on the south coast of New Zealand’s North Island, to study dye dispersion from a nearshore coastal outfall discharging tertiary treated wastewater. 

Rhodamine® WT dye was injected into the wastewater at a constant rate (Figure 2) and effluent dilution and dispersion were mapped on both an ebb and flood tide. Continuous fluorescence readings were taken from a vessel using a 10-AU field fluorometer set up for flow-through measurements and linked to a portable PC and GPS. Data were collected by running a series of transects through the effluent plume both perpendicular to and along the effluent plume path. To verify effluent concentrations, grab samples were collected every 15 minutes using a sequential autosampler positioned downstream of the injection point.

Case Study 2: Mapping chlorophyll-a around a mussel farm
Another example of the application of this integrated GIS-fluorometry system is the real-time mapping of chlorophyll-a depletion around coastal mussel farms. In order to assess the sustainability of mussel farms around New Zealand’s coast, the concentrations of chlorophyll-a (which represents phytoplankton) are measured at 3m (i.e. the active feeding depth) and incorporated into modelled predictions of sustainability. This information can then also be used by the farmer to optimise farm management.

The SCUFA can be employed in a similar way to the 10-AU in outfall dye studies, providing continuous measurements of chlorophyll-a (post-calibrated) through and around mussel farms (Figure 5). Typically, currents are also collected simultaneously with the GPS positions and fluorometry data, to give insight into the patterns of water movement around the farms. 

In the example below (Figure 5), two synoptic snap-shots were taken in a bay containing four small farms (delineated by black dotted lines). The data were then plotted in 2-dimensional colour contours using an appropriate interpolation method. Depletion areas (blue regions) are evident in the vicinity of the farms, allowing the magnitude of depletion to be assessed and the behaviour of the water through the bay to be observed. The results are then compared against outputs from various models to improve our confidence in their predictive capabilities.

Integrating GIS and Fluorometry For Real-Time mapping of Coastal Systems
Figure 2. Configuration of dye injection system in relation to autosampler and outfall.


Cawthron’s integration of Turner fluorometers with GPS and GIS for real-time mapping has had major benefits in the way we use these instruments. The efficiency with which data are collected ensures research is conducted in a cost effective manner. Further, field data can be tracked visually and any anomalies in spatial distribution are immediately apparent. This helps ensure data validation and overall data integrity.

Integrating GIS and Fluorometry For Real-Time mapping of Coastal Systems
Figure 3. Graduated symbols of all data points collected for mapping dye dilution/dispersion.
Integrating GIS and Fluorometry For Real-Time mapping of Coastal Systems
Figure 4. Post-generated dilution contours of ebb tide data points.
Figure 5. Subsurface (3m) contours of Chlorophyll-a concentration in the vicinity of four mussel farms under two different tidal states.


  • Author: Paul Barter
  • E-Mail: This e-mail address is being protected from spambots. You need JavaScript enabled to view it


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