CyVerse: Cyberinfrastructure for open science.

CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and open-source software.

Integrating drone imagery with existing rangeland monitoring programs.

The recent availability of small and low-cost sensor carrying unmanned aerial systems (UAS, commonly known as drones) coupled with advances in image processing software (i.e., structure from motion photogrammetry) has made drone-collected imagery a potentially valuable tool for rangeland inventory and monitoring. Drone-imagery methods can observe larger extents to estimate indicators at landscape scales with higher confidence than traditional field sampling. They also have the potential to replace field methods in some instances and enable the development of indicators not measurable from the ground. Much research has already demonstrated that several quantitative rangeland indicators can be estimated from high-resolution imagery. Developing a suite of monitoring methods that are useful for supporting management decisions (e.g., repeatable, cost-effective, and validated against field methods) will require additional exploration to develop best practices for image acquisition and analytical workflows that can efficiently estimate multiple indicators. We embedded with a Bureau of Land Management (BLM) field monitoring crew in Northern California, USA to compare field-measured and imagery-derived indicator values and to evaluate the logistics of using small UAS within the framework of an existing monitoring program. The unified workflow we developed to measure fractional cover, canopy gaps, and vegetation height was specific for the sagebrush steppe, an ecosystem that is common in other BLM managed lands. The correspondence between imagery and field methods yielded encouraging agreement while revealing systematic differences between the methods. Workflow best practices for producing repeatable rangeland indicators is likely to vary by vegetation composition and phenology. An online space dedicated to sharing imagery-based workflows could spur collaboration among researchers and quicken the pace of integrating drone-imagery data within adaptive management of rangelands. Though drone-imagery methods are not likely to replace most field methods in large monitoring programs, they could be a valuable enhancement for pressing local management needs.

Considerations for Achieving Cross-Platform Point Cloud Data Fusion across Different Dryland Ecosystem Structural States.

Remotely sensing recent growth, herbivory, or disturbance of herbaceous and woody vegetation in dryland ecosystems requires high spatial resolution and multi-temporal depth. Three dimensional (3D) remote sensing technologies like lidar, and techniques like structure from motion (SfM) photogrammetry, each have strengths and weaknesses at detecting vegetation volume and extent, given the instrument's ground sample distance and ease of acquisition. Yet, a combination of platforms and techniques might provide solutions that overcome the weakness of a single platform. To explore the potential for combining platforms, we compared detection bias amongst two 3D remote sensing techniques (lidar and SfM) using three different platforms [ground-based, small unmanned aerial systems (sUAS), and manned aircraft]. We found aerial lidar to be more accurate for characterizing the bare earth (ground) in dense herbaceous vegetation than either terrestrial lidar or aerial SfM photogrammetry. Conversely, the manned aerial lidar did not detect grass and fine woody vegetation while the terrestrial lidar and high resolution near-distance (ground and sUAS) SfM photogrammetry detected these and were accurate. UAS SfM photogrammetry at lower spatial resolution under-estimated maximum heights in grass and shrubs. UAS and handheld SfM photogrammetry in near-distance high resolution collections had similar accuracy to terrestrial lidar for vegetation, but difficulty at measuring bare earth elevation beneath dense herbaceous cover. Combining point cloud data and derivatives (i.e., meshes and rasters) from two or more platforms allowed for more accurate measurement of herbaceous and woody vegetation (height and canopy cover) than any single technique alone. Availability and costs of manned aircraft lidar collection preclude high frequency repeatability but this is less limiting for terrestrial lidar, sUAS and handheld SfM. The post-processing of SfM photogrammetry data became the limiting factor at larger spatial scale and temporal repetition. Despite the utility of sUAS and handheld SfM for monitoring vegetation phenology and structure, their spatial extents are small relative to manned aircraft.

Modeling vegetation heights from high resolution stereo aerial photography: an application for broad-scale rangeland monitoring.

Vertical vegetation structure in rangeland ecosystems can be a valuable indicator for assessing rangeland health and monitoring riparian areas, post-fire recovery, available forage for livestock, and wildlife habitat. Federal land management agencies are directed to monitor and manage rangelands at landscapes scales, but traditional field methods for measuring vegetation heights are often too costly and time consuming to apply at these broad scales. Most emerging remote sensing techniques capable of measuring surface and vegetation height (e.g., LiDAR or synthetic aperture radar) are often too expensive, and require specialized sensors. An alternative remote sensing approach that is potentially more practical for managers is to measure vegetation heights from digital stereo aerial photographs. As aerial photography is already commonly used for rangeland monitoring, acquiring it in stereo enables three-dimensional modeling and estimation of vegetation height. The purpose of this study was to test the feasibility and accuracy of estimating shrub heights from high-resolution (HR, 3-cm ground sampling distance) digital stereo-pair aerial images. Overlapping HR imagery was taken in March 2009 near Lake Mead, Nevada and 5-cm resolution digital surface models (DSMs) were created by photogrammetric methods (aerial triangulation, digital image matching) for twenty-six test plots. We compared the heights of individual shrubs and plot averages derived from the DSMs to field measurements. We found strong positive correlations between field and image measurements for several metrics. Individual shrub heights tended to be underestimated in the imagery, however, accuracy was higher for dense, compact shrubs compared with shrubs with thin branches. Plot averages of shrub height from DSMs were also strongly correlated to field measurements but consistently underestimated. Grasses and forbs were generally too small to be detected with the resolution of the DSMs. Estimates of vertical structure will be more accurate in plots having low herbaceous cover and high amounts of dense shrubs. Through the use of statistically derived correction factors or choosing field methods that better correlate with the imagery, vegetation heights from HR DSMs could be a valuable technique for broad-scale rangeland monitoring needs.

Spatial patterns of grassland­shrubland state transitions: a 74­year record on grazed and protected areas.

Tree and shrub abundance has increased in many grasslands causing changes in ecosystem carbon and nitrogen pools that are related to patterns of woody plant distribution. However, with regard to spatial patterns of shrub proliferation, little is known about how they are influenced by grazing or the extent to which they are influenced by intraspecific interactions. We addressed these questions by quantifying changes in the spatial distribution of Prosopis velutina (mesquite) shrubs over 74 years on grazed and protected grasslands. Livestock are effective agents of mesquite dispersal and mesquite plants have lateral roots extending well beyond the canopy. We therefore hypothesized that mesquite distributions would be random on grazed areas mainly due to cattle dispersion and clustered on protected areas due to decreased dispersal and interspecific interference with grasses; and that clustered or random distributions at early stages of encroachment would give way to regular distributions as stands matured and density-dependent interactions intensified. Assessments in 1932, 1948, and 2006 supported the first hypothesis, but we found no support for the second. In fact, clustering intensified with time on the protected area and the pattern remained random on the grazed site. Although shrub density increased on both areas between 1932 and 2006, we saw no progression toward a regular distribution indicative of density-dependent interactions. We propose that processes related to seed dispersal, grass­shrub seedling interactions, and hydrological constraints on shrub size interact to determine vegetation structure in grassland-to-shrubland state changes with implications for ecosystem function and management.