Technology and Innovations: Data Collection, Analysis, & Reporting

SERCAL 2017 Technical Session, Davis

Chair: Allegra Bukojemsky, Landscape Architect

Lead presenters in alpha order

Measuring Milkweed: Quantifying restoration outcomes for the monarch butterfly
Erik Anderson
Environmental Incentives, LLC, 3351 Lake Tahoe Blvd, Suite 2, South Lake Tahoe,
Well-designed environmental metrics provide science-based, objective, and transparent assessments of ecological function. They allow for regulators, regulated entities, restoration designers, and landowners to understand a problem in the same way, communicate with a shared language, and work towards a common goal. Using these tools, the contribution of every action can be understood in a quantified way, fostering innovation and creativity to achieve habitat outcomes efficiently and with limited resources. This presentation will provide an example, using the recently-developed Monarch Butterfly Habitat Quantification Tool (HQT), of how environmental metrics and associated tools can be designed to meet the needs of the diverse stakeholders who use them. This design approach ensures that the HQT will: • Meet the requirements of pertinent regulatory authorities; • Provide precise estimates of habitat function or ecosystem service outputs in order to guide resource allocation decisions and incentivize desired behaviors; • Be applied in a reasonable amount of time; and • Generate consistent, repeatable results. Preservation of the monarch butterfly’s annual migration will require multi-national collaboration at an almost unprecedented scale. Well-designed environmental metrics can serve as the backbone of this collective effort, and can support restoration and recovery efforts for other imperiled resources and species as well.

Monitoring California’s Biodiversity through Environmental DNA
Emily Curd*1, Rachel Meyer2, Robert Wayne3
University of California Conservation Genomics Consortium, University of California, Los Angeles 90095: 14153 Terasaki Life Science Building,; 24153 Terasaki Life Science Building,; 34162 Terasaki Life Science Building,
A major challenge in conservation and restoration biology is effectively monitoring species distributions and establishing reliable baselines of a region’s biodiversity. This is particularly true for rare, cryptic, or hard-to-observe species (e.g. microorganisms) which may play critical roles in community stability. We introduce the CALeDNA citizen science-supported program by the University of California Conservation Genomics Consortium, which tackles biodiversity monitoring by sequencing DNA shed into the environment. As organisms live and die, they lose DNA to soils and sediments. We can collect these materials, and use metagenomic sequencing to reconstruct the biodiversity of a location. This initiative will generate a state-wide biodiversity baseline by recruiting 1,000 citizens to collect a total of 18,000 samples. These samples and sequencing data can be analyzed in multiple ways for basic and applied purposes. The kinks in metagenomics are far from worked out, and there are technical and theoretical challenges to doing such work, as well as challenges on the program operational front. However, this approach holds promise to identify entire communities from microbes to mammals, providing a community-oriented toolkit for managers. Our program demonstrates this value through additional targeted biodiversity projects aimed for conservation and restoration (e.g. pacific pocket mouse reintroduction, crayfish removal and restoration monitoring). We present the multiple angles of the CALeDNA approach to monitoring biodiversity, including technology developed to support citizen science, laboratory methods to generate data, accessibility of data and soil samples, and ways to involve conservation and restoration managers in our project.

The Promise of High-resolution Remote Sensing for Cost-effective and Coherent Wetland Restoration Monitoring Programs
Iryna Dronova* and Sophie Taddeo
202 Wurster Hall #2000, Department of Landscape Architecture & Environmental Planning, UC Berkeley, Berkeley 94720,,
Wetlands are important targets in ecological restoration due to their multiple ecosystem services — protection against coastal flooding, sequestration of greenhouse gases, pollution remediation, supporting biological diversity and various aesthetic and recreational qualities. However, measuring these benefits is difficult — wetland environments are often spatially complex, difficult to navigate, and often inhabited by sensitive plant and animal species easily disturbed by human presence. Very high-resolution remote sensing offers outstanding novel opportunities to monitor restored wetlands at spatial detail appropriate for small patches and microhabitats and at broad site extents where comprehensive field work may be logistically prohibitive and ecologically disruptive. Our study demonstrates the potential of such approaches across a chronosequence of 4 different-aged restored freshwater marshes in the Sacramento-San Joaquin Delta, where wetlands are actively explored as a target for carbon markets and emerging cap-and-trade programs. We discuss how remotely sensed information assists in detecting changes in ecosystem composition and structure and their sensitivity to site designs and how these outcomes may be used to assess whether restored sites follow their intended trajectories and with that to inform adaptive strategies to manage existing sites and design the future ones both in California and other similar regions.

Tracking Alluvial Floodplain Restoration Using UAV-derived Digital Surface Models and Imagery
Sundaran Gillespie
GISP, FAA Section 107 Pilot,, 415.524.7274
Munz Canyon is an alluvial fan restoration project within the boundaries of both the proposed San Andreas Rift Zone Significant Ecological Area and the Desert Renewable Energy Conservation Plan Area. The site is a component of the larger Petersen Ranch Wetland Mitigation Bank, the largest wetland bank in the state. Munz Canyon is topographically and biologically diverse with dominant vegetative communities including seasonal wetlands, ephemeral and desert washes, and alluvial floodplains. The project goal is to lower an existing dam and restore a large alluvial fan with re-introduced sediment deposition. As a pioneer in the field of restoration, WRA constantly employs new technologies. In order to save field-related costs and having a need for high accuracy data, WRA utilized an unmanned aerial vehicle (UAV) for analysis. WRA conducted several flights of the site at key points of interest to track change during restoration. Flights were performed prior to construction, directly after completion, and after all major rain events. With the 2016/17 rain season being one of the wettest in the last several years, it provides the perfect opportunity to track change. Aerial imagery from each flight was then processed into high resolution (2cm) orthomosaic imagery and a digital surface model. Utilizing both data products, change detection was performed through remote sensing, flow analysis, volumetric calculations, and visual interpretation comparing all of the datasets from each date. Success criteria are then addressed to confirm project goals are being met. The Petersen Ranch restoration project is ongoing for the next several years.

Photorealistic Geodesign
David Leonard
AICP, ASLA, GISP, LEED Green Associate, Senior Project Manager, Infrastructure and Planning Sector, PARSONS, 525 B Street, Suite 1600, San Diego 92101, 619.515.5153 office, 619.200.7309 cell,,
Accurate photorealistic depictions of habitats have not been feasible until now. In this presentation, we will explore software that provides the realism of Hollywood with GIS and CAD accuracy. We will demonstrate the workflow from concept to visualization rendering. This session will demonstrate how easy it is to depict habitats of all kinds, tidal inundations, sea level rise, and habitat migration. 3D visualization capability allows us to better explore our own designs, engage our clients and stakeholders, expedite decision-making, and view the site from many vantage points. The use of procedural vegetation increases the integrity of the renderings by not having repeating objects (all are unique). We will also explore how to generate custom plants for unique habitats to increase the accuracy of the site visualization.

Transforming Vegetation Data Collection & Analysis Through the Use of Digital Collection Methods
Eric Link* and Kristin Lantz* 
ICF, Sacramento,,
Botanical surveys incorporate many different methods to survey plant communities and habitat restoration areas for plant survival, percent cover and species composition and other metrics. These surveys typically include an on-the-ground assessment and “getting eyes” on your project site. These tried and true methods continue to be the best way to assess site conditions and progress toward meeting and achieving success criteria. However, the game is changing as it relates to data collection, management, and analysis. Recording field data has traditionally relied on the paper form followed by hours of data entry, but technological innovations are allowing us an opportunity to “upgrade our systems”. Incorporating digital data collection, storage, and transfer methods can improve the efficiency of data collection, management and analysis. We will discuss some of the options available for streamlining data collection, setting up project-specific electronic data collection forms, data transfer and management, and efficiencies in data analysis. We will provide some project-specific examples, as well as some lessons learned we have experienced.

A Habitat Quantification Tool: Case study and empirical ground truthing
Amy Merrill*1, Daniel Kaiser2, John Cain3, Nat Seavy4, Rene Henery5, and Scott Sellers2
1Stillwater Sciences, Berkeley,; 2Environmental Defense Fund, San Francisco,,; 3American Rivers, Berkeley,; 4Point Blue Conservation Science, Petaluma,; 5Trout Unlimited, Berkeley,
Land use conversion, drought, and climate change are conspiring against many native species once abundant in the Central Valley. Restoring and protecting habitat is critical for their recovery, and private lands, which make up over 80% of the Central Valley, are a necessary part of the solution. How do we engage private land owners in this effort to effectively address multiple species needs? As part of the Central Valley Habitat Exchange (CVHE), we developed and piloted a scientifically based and accessible “Multispecies Habitat Quantification Tool” (mHQT), to assess habitat quality and quantity, and to track conservation or mitigation outcomes for multiple native species in the Central Valley. To date, these species include riparian associated or dependent species: Swainson’s hawk, riparian landbirds, Chinook salmon, and giant garter snake. The mHQT incorporates information from the landscape and site-specific scales for site scoring, program tracking, and prioritization. The mHQT provides clear and concrete guidelines with response scores that private landowners can use to guide land management planning, implement conservation and mitigation projects, and demonstrate good stewardship. We present a case study for application of this tool to guide and initiate tracking restoration outcomes. We also present results from a ground-truthing study in which we compared tool scores against species occurrence data at 12 locations in the Delta and Central Valley using simple correlation analysis. Study results indicate the mHQT does reflect species use (R2=0.72) while sources of variation suggest the mHQT could be improved by addressing meso-scale site characteristics.

Intertidal Eelgrass Mapping in Humboldt Bay: Ultra-high resolution UAV imagery and GIS spectral classification
Greg O’Connell
SHN Engineers and Geologists, Inc., 812 W Wabash Ave, Eureka 95501, 707.441.8855,
Eelgrass (Zostera marina L.) is a native, perennial seagrass in the Zosteraceae family. Its rhizomatous growth pattern allows eelgrass to form dense, habitat-rich meadows in low-intertidal and shallow-subtidal portions of soft-bottomed estuaries and marine embayments. Accurate mapping of eelgrass has historically been challenging due to its patchy distribution in very soft substrates and access limited by infrequent negative tides during its growth period. Recent advancements in remote sensing technology allow for very precise mapping of intertidal eelgrass distribution when using ultra-high resolution imagery and spectral classification tools. In Humboldt Bay, we’ve used Unmanned Aerial Vehicles (UAVs; aka “drones”) to collect transects of ultra-high resolution aerial images (~3mm pixels). Individual photos were incorporated into large-scale mosaic images that are georeferenced and orthorectified. Supervised geographic information system (GIS)-based spectral classification of pixel color was used to create raster layers indicating presence/absence of eelgrass within each pixel. The classification output from mosaic images have resulted in reliable eelgrass classifications with accuracy assessments over 85%. Eelgrass classification is most accurate when eelgrass is above the tide line, lacks heavy epiphyte loads, occurs in dense clumps, and is not interspersed with algal macrophytes (e.g. Ulva spp.). In most instances, UAV-based imagery collection can map intertidal eelgrass faster, and more precisely than traditional ground-based global positioning system (GPS) surveys.  Lastly, mosaic images serve as preserved “snapshots in time”, allowing future comparisons within the same spatial area. The high accuracy of mosaic image eelgrass spectral classification is a perfect match with ongoing developments in UAV technology.

Two New Calflora Tools
Cynthia Powell* and John Malpas;
Calflora is a plant database containing over 2 million plant observations for over 10,000 species in California. We have two new features available: our planting guide and the ability to create history stacks to monitor and report on population changes over time. Use the Calflora Planting Guide for suggestions on which California native plants will likely grow well at a particular location. These suggestions are based on climate and soil suitability for that location, its elevation, as well as what other plants grow in that area. The occurrence data is only as good as what Calflora users submit, so we encourage all botanists to submit their wild plant data using a smart phone, spreadsheet, shapefile, or asking us for help. Many Calflora users need to monitor population changes over time, which can now be done within Calflora. This functionality might be used at a restoration site or within an invasive plant polygon over the course of several years. The ability to track and report on change over time, and create a so-called “history stack” allows effectiveness of restoration or treatment to be quantified. Using our free phone apps (on android or iOS), the blue GPS tracking dot can help data contributors find and visit previous Calflora plant assessments from past days, months, or years, which can be loaded on the phone to show on the maps. Then the new assessment may be added to the “root record,” thus creating a history stack.

3D Drafting for Design of Naturalistic Restoration Projects
Daniel Stratten*1 and Nic Truscott, EIT2
ICF:, 360.255.2522; 21108 11th Street, Bellingham, WA 98225,, 360.255.2307
Stream, floodplain, and wetland restoration projects require reliable prediction of the site’s hydraulic response to the proposed project. Having a reliable prediction allows designers and reviewers to have confidence the constructed project will function as intended. Modern computers and software allow restoration designers to more accurately develop and analyze complex design elements, which in turn leads to more informed design revisions, and ultimately better functioning projects. This presentation illustrates the application of 3-dimensional drafting and design using AutoCAD Civil 3D to design fish-passable roughened rock channels and complex large wood material habitat structures. We will illustrate methodology to simulate complex boulder/cobble/gravel streambeds, combining 3D objects with modelled channel corridors and topographic survey to develop a representative digital terrain model (DTM). The resultant DTM defines the streambed geometry for a 2D hydraulic model with much greater detail than a DTM from just channel breakline definitions and topo survey. The roughened channel bed definition leads to more detailed results from the hydraulic model to better inform design decisions. We will also demonstrate how 3D drafting can be used for the design of complex large wood material (LWM) habitat structures. Some projects include LWM structures created from dozens of individual logs. 3D drafting provides a better visualization of the LWM structures, and ensures the proposed design can be assembled using the specified materials, while providing means for more precise analysis to ensure long-term success.

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