USE OF UNMANNED AERIAL VEHICLES (UAV) FOR URBAN TREE INVENTORIES

In contrast to standard aerial imagery, unmanned aerial systems (UAS) utilize recent technological advances to provide an affordable alternative for imagery acquisition. Increased value can be realized through clarity and detail providing higher resolution (2-5 cm) over traditional products. Many natural resource disciplines such as urban forestry will benefit from UAS. Tree inventories for risk assessment, biodiversity, planning, and design can be efficiently achieved with the UAS. Recent advances in photogrammetric processing have proved automated methods for three dimensional rendering of aerial imagery. Point clouds can be generated from images providing additional benefits. Association of spatial locational information within the point cloud can be used to produce elevation models i.e. digital elevation, digital terrain and digital surface. Taking advantage of this point cloud data, additional information such as tree heights can be obtained. Several software applications have been developed for LiDAR data which can be adapted to utilize UAS point clouds. This study examines solutions to provide tree inventory and heights from UAS imagery. Imagery taken with a micro-UAS was processed to produce a seamless orthorectified image. This image provided an accurate way to obtain a tree inventory within the study boundary. Utilizing several methods, tree height models were developed with variations in spatial accuracy. Model parameters were modified to offset spatial inconsistencies providing statistical equality of means. Statistical results (p = 0.756) with a level of significance (α = 0.01) between measured and modeled tree height means resulted with 82% of tree species obtaining accurate tree heights. Within this study, the UAS has proven to be an efficient tool for urban forestry providing a cost effective and reliable system to obtain remotely sensed data

Forestry and Arboriculture Applications Using High-Resolution Imagery from Unmanned Aerial Vehicles (UAV)

Forests cover over one-third of the planet and provide unmeasurable benefits to the ecosystem. Forest managers have collected and processed countless amounts of data for use in studying, planning, and management of these forests. Data collection has evolved from completely manual operations to the incorporation of technology that has increased the efficiency of data collection and decreased overall costs. Many technological advances have been made that can be incorporated into natural resources disciplines. Laser measuring devices, handheld data collectors and more recently, unmanned aerial vehicles, are just a few items that are playing a major role in the way data is managed and collected. Field hardware has also been aided with new and improved mobile and computer software. Over the course of this study, field technology along with computer advancements have been utilized to aid in forestry and arboricultural applications. Three-dimensional point cloud data that represent tree shape and height were extracted and examined for accuracy. Traditional fieldwork collection (tree height, tree diameter and canopy metrics) was derived from remotely sensed data by using new modeling techniques which will result in time and cost savings. Using high resolution aerial photography, individual tree species are classified to support tree inventory development. Point clouds were used to create digital elevation models (DEM) which can further be used in hydrology analysis, slope, aspect, and hillshades. Digital terrain models (DTM) are in geographic information system (GIS), and along with DEMs, used to create canopy height models (CHM). The results of this study can enhance how the data are utilized and prompt further research and new initiatives that will improve and garner new insight for the use of remotely sensed data in forest management

KOLAM : human computer interfaces fro visual analytics in big data imagery

In the present day, we are faced with a deluge of disparate and dynamic information from multiple heterogeneous sources. Among these are the big data imagery datasets that are rapidly being generated via mature acquisition methods in the geospatial, surveillance (specifically, Wide Area Motion Imagery or WAMI) and biomedical domains. The need to interactively visualize these imagery datasets by using multiple types of views (as needed) into the data is common to these domains. Furthermore, researchers in each domain have additional needs: users of WAMI datasets also need to interactively track objects of interest using algorithms of their choice, visualize the resulting object trajectories and interactively edit these results as needed. While software tools that fulfill each of these requirements individually are available and well-used at present, there is still a need for tools that can combine the desired aspects of visualization, human computer interaction (HCI), data analysis, data management, and (geo-)spatial and temporal data processing into a single flexible and extensible system. KOLAM is an open, cross-platform, interoperable, scalable and extensible framework for visualization and analysis that we have developed to fulfil the above needs. The novel contributions in this thesis are the following: 1) Spatio-temporal caching for animating both giga-pixel and Full Motion Video (FMV) imagery, 2) Human computer interfaces purposefully designed to accommodate big data visualization, 3) Human-in-the-loop interactive video object tracking - ground-truthing of moving objects in wide area imagery using algorithm assisted human-in-the-loop coupled tracking, 4) Coordinated visualization using stacked layers, side-by-side layers/video sub-windows and embedded imagery, 5) Efficient one-click manual tracking, editing and data management of trajectories, 6) Efficient labeling of image segmentation regions and passing these results to desired modules, 7) Visualization of image processing results generated by non-interactive operators using layers, 8) Extension of interactive imagery and trajectory visualization to multi-monitor wall display environments, 9) Geospatial applications: Providing rapid roam, zoom and hyper-jump spatial operations, interactive blending, colormap and histogram enhancement, spherical projection and terrain maps, 10) Biomedical applications: Visualization and target tracking of cell motility in time-lapse cell imagery, collecting ground-truth from experts on whole-slide imagery (WSI) for developing histopathology analytic algorithms and computer-aided diagnosis for cancer grading, and easy-to-use tissue annotation features.Includes bibliographical reference

14th Annual Research in the Capitol [Program], April 1, 2019

Program of research presentations given at the Capitol by students from the University of Northern Iowa, Iowa State University, and the University of Iowa.https://scholarworks.uni.edu/programs_rcapitol/1012/thumbnail.jp

The pitfalls of platform comparison: DNA copy number array technologies assessed

<p>Abstract</p> <p>Background</p> <p>The accurate and high resolution mapping of DNA copy number aberrations has become an important tool by which to gain insight into the mechanisms of tumourigenesis. There are various commercially available platforms for such studies, but there remains no general consensus as to the optimal platform. There have been several previous platform comparison studies, but they have either described older technologies, used less-complex samples, or have not addressed the issue of the inherent biases in such comparisons. Here we describe a systematic comparison of data from four leading microarray technologies (the Affymetrix Genome-wide SNP 5.0 array, Agilent High-Density CGH Human 244A array, Illumina HumanCNV370-Duo DNA Analysis BeadChip, and the Nimblegen 385 K oligonucleotide array). We compare samples derived from primary breast tumours and their corresponding matched normals, well-established cancer cell lines, and HapMap individuals. By careful consideration and avoidance of potential sources of bias, we aim to provide a fair assessment of platform performance.</p> <p>Results</p> <p>By performing a theoretical assessment of the reproducibility, noise, and sensitivity of each platform, notable differences were revealed. Nimblegen exhibited between-replicate array variances an order of magnitude greater than the other three platforms, with Agilent slightly outperforming the others, and a comparison of self-self hybridizations revealed similar patterns. An assessment of the single probe power revealed that Agilent exhibits the highest sensitivity. Additionally, we performed an in-depth visual assessment of the ability of each platform to detect aberrations of varying sizes. As expected, all platforms were able to identify large aberrations in a robust manner. However, some focal amplifications and deletions were only detected in a subset of the platforms.</p> <p>Conclusion</p> <p>Although there are substantial differences in the design, density, and number of replicate probes, the comparison indicates a generally high level of concordance between platforms, despite differences in the reproducibility, noise, and sensitivity. In general, Agilent tended to be the best aCGH platform and Affymetrix, the superior SNP-CGH platform, but for specific decisions the results described herein provide a guide for platform selection and study design, and the dataset a resource for more tailored comparisons.</p

Use of multi-spectral imagery and LiDar data to quantify compositional and structural characteristics of vegetation in red-cockaded woodpecker (Picoides borealis) habitat in North Carolina

This study evaluated habitat parameters for the red-cockaded woodpecker (RCW; Picoides borealis) on three tracts in Hoke County, North Carolina. Multi-spectral imagery was used to classify shadow, non-vegetation, herbaceous, hardwoods, and loblolly and longleaf pine trees. Field data were collected for image classification training and validation. Overall classification accuracy for separating hardwood from pine trees, was 80.8%. When separating longleaf (Pinus palustris Mill.) and loblolly (Pinus taeda L.) pine from hardwoods the accuracy was 73.7%. Field-based height/diameter relationships were applied to LiDAR-identified trees to predict diameter classes. Due to differences in management regimes and site conditions, each tract had different majority pine diameter classes. Average height, diameter, basal area, and stem density per plot were reported from matched, unmatched, and total LiDAR trees to field trees. Differences between the height, diameter, basal area, and stem density values occurred between the matched and unmatched LiDAR- and field-identified trees

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1–2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks

Characterization and Application of Angled Fluorescence Laminar Optical Tomography

Angled fluorescence laminar optical tomography (aFLOT) is a modified fluorescence tomographic imaging technique that targets the mesoscopic scale (millimeter penetration with resolution in the tens of microns). Traditional FLOT uses multiple detectors to measure a range of scattered fluorescence signals to perform 3D reconstructions. This technology however inherently assumes the sample to be scattering. To extend the capability of FLOT to cover the low scattering regime, the oblique illumination and detection was introduced. The angular degree of freedom for the illumination and detection was theoretically and experimentally investigated. It was concluded that aFLOT enhanced resolution 2.5 times and depth selectivity compared to traditional FLOT, and that it enabled the stacking representation, a process that skips the computationally-intensive reconstruction usually needed to render the tomogram. Because stacking is enabled, the necessity of a reconstruction process is retrospectively discussed. aFLOT systems were constructed and applied in tissue engineering. Phantoms and engineered tissue models were successfully imaged. The aFLOT was shown to perform non-invasive in situ imaging in biologically relevant samples with 1mm penetration and 9-400 micron resolution, depending on the scattering of samples. aFLOT illustrates its potential for studying cell-cell or cell-material interactions