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USGS2016

Quantifying the eroded volume of mercury-contaminated sediment using terrestrial laser scanning at Stocking Flat, Deer Creek, Nevada County, California, 2010–13

High-resolution ground-based light detection and ranging (lidar), also known as terrestrial laser scanning, was used to quantify the volume of mercury-contaminated sediment eroded from a stream cutbank at Stocking Flat along Deer Creek in the Sierra Nevada foothills, about 3 kilometers west of Nevada City, California. Terrestrial laser scanning was used to collect sub-centimeter, three-dimensional images of the complex cutbank surface, which could not be mapped non-destructively or in sufficient detail with traditional surveying techniques. The stream cutbank, which is approximately 50 meters long and 8 meters high, was surveyed on four occasions: December 1, 2010; January 20, 2011; May 12, 2011; and February 4, 2013. Volumetric changes were determined between the sequential, three-dimensional lidar surveys. Volume was calculated by two methods, and the average value is reported. Between the first and second surveys (December 1, 2010, to January 20, 2011), a volume of 143 plus or minus 15 cubic meters of sediment was eroded from the cutbank and mobilized by Deer Creek. Between the second and third surveys (January 20, 2011, to May 12, 2011), a volume of 207 plus or minus 24 cubic meters of sediment was eroded from the cutbank and mobilized by the stream. Total volumetric change during the winter and spring of 2010–11 was 350 plus or minus 28 cubic meters. Between the third and fourth surveys (May 12, 2011, to February 4, 2013), the differencing of the three-dimensional lidar data indicated that a volume of 18 plus or minus 10 cubic meters of sediment was eroded from the cutbank. The total volume of sediment eroded from the cutbank between the first and fourth surveys was 368 plus or minus 30 cubic meters.

California↗

USGS2019

Quantifying the eroded and deposited mass of mercury-contaminated sediment by using terrestrial laser scanning at the confluence of Humbug Creek and the South Yuba River, Nevada County, California, 2011–13

High-resolution, terrestrial laser scanning, also known as ground-based lidar (light detection and ranging), was used to quantify the volume of mercury-contaminated sediment eroded from an outcrop of historical placer-mining debris at the confluence of Humbug Creek and the South Yuba River in the Sierra Nevada foothills, about 17 kilometers northeast of Grass Valley, California, and delivered to a zone below an observed flood stage of the South Yuba River. Substantial quantities of mercury were used and lost to the environment from historical placer gold mining activities on the western slope of the Sierra Nevada, California, and recent studies have documented continued persistence of mercury and methylmercury concentrations in water, sediment, fish, and predatory invertebrates in the Yuba River drainage basin in relation to suspected mercury sources. To identify areas that have high levels of mercury contamination as possible remediation targets in the Yuba River drainage basin and other areas in the Sierra Nevada, the U.S. Geological Survey worked in cooperation with the Bureau of Land Management on this and other detailed studies. Malakoff Diggings, one of the largest hydraulic gold mines in the Sierra Nevada, is 3.5 kilometers north of the study site in the Humbug Creek subbasin. Terrestrial laser scanning was used to produce centimeter-scale, three-dimensional maps of the complex outcrop surface, which was composed of an upper erosional area (cliff and over-steepened slope) and a lower depositional area (colluvial slope). The outcrop could not be mapped non-destructively or in sufficient detail by traditional surveying techniques. The study site, which was approximately 70 meters long, 30 meters wide and 20 meters high, was surveyed four times in 2 years (December 15, 2011; October 25, 2012; January 4, 2013; and November 22, 2013) to determine volumetric differences in the upper erosional and lower depositional areas between surveys. Measured changes in volume for the upper erosional area and lower depositional area were multiplied by the corresponding sediment density so that a mass-balance relationship, between the eroded and deposited sediment during each period, could be used to estimate the amount of mercury-contaminated sediment that was transported to below the base of the colluvial slope, where it could be mobilized by the South Yuba River during a flood having a 5-to-10-year recurrence interval. On December 2, 2012, a flood of this estimated magnitude reached the base of the colluvial slope. Between the first and second surveys (December 15, 2011–October 25, 2012), an estimated mass of 18±9.2 kilograms of sediment was transported from steeper slopes to the gently sloping river bank below the base of the colluvial slope. Between the second and third surveys (October 25, 2012–January 4, 2013), an atmospheric river caused heavy precipitation at the study site during late November and early December 2012. This short-duration, high-intensity rain resulted in a large amount of erosion and deposition at the study site and also caused high streamflow (flood stage) in the South Yuba River. From October 2012 to January 2013, 51±31 kilograms of sediment was transported to below the base of the colluvial slope, that is, below the high-water mark of December 2, 2012. Between the third and fourth surveys (January 4, 2013–November 22, 2013), an additional 10±26 kilograms of sediment was transported to below the base of the colluvial slope. During the 24 months of the study, the total mass of sediment delivered below the base of the colluvial slope and the high-water mark of December 2, 2012, was 79±66 kilograms. In any given year there is a 10–20-percent chance (5-to-10-year recurrence interval) of a flood equal to or greater than that of the December 2, 2012, flood, which could transport mercury-contaminated sediment at the study site into the South Yuba River. Hydraulically modeled estimates of the South Yuba River stage during floods having a 50- and 100-year recurrence interval (2- and 1-percent annual exceedance probability, respectively) indicated that resulting river stages could be 2.2–3.0 meters above the base of the colluvial slope, or 2.2–3.0 meters above the high-water mark of December 2, 2012. Such high river stages would be likely to inundate the lower half of the colluvial slope and mobilize a substantial volume of mercury-contaminated sediment to downstream areas.

California↗

USGS1956

Rapid-scanning microphotometry

A rapid-scanning microphotometer is described with which a 10-inch spectrum may be scanned in two minutes. The resulting chart may be 60, 300, or 1,500 cm long (wavelength scale) and 4 cm high (intensity scale). Commercially available components are used.

Trace Elements Investigations↗

USGS2015

Can low-resolution airborne laser scanning data be used to model stream rating curves?

This pilot study explores the potential of using low-resolution (0.2 points/m 2 ) airborne laser scanning (ALS)-derived elevation data to model stream rating curves. Rating curves, which allow the functional translation of stream water depth into discharge, making them integral to water resource monitoring efforts, were modeled using a physics-based approach that captures basic geometric measurements to establish flow resistance due to implicit channel roughness. We tested synthetically thinned high-resolution (more than 2 points/m 2 ) ALS data as a proxy for low-resolution data at a point density equivalent to that obtained within most national-scale ALS strategies. Our results show that the errors incurred due to the effect of low-resolution versus high-resolution ALS data were less than those due to flow measurement and empirical rating curve fitting uncertainties. As such, although there likely are scale and technical limitations to consider, it is theoretically possible to generate rating curves in a river network from ALS data of the resolution anticipated within national-scale ALS schemes (at least for rivers with relatively simple geometries). This is promising, since generating rating curves from ALS scans would greatly enhance our ability to monitor streamflow by simplifying the overall effort required.

Krycklan catchment↗

USGS2011

Observations of debris flows at Chalk Cliffs, Colorado, USA: Part 2, changes in surface morphometry from terrestrial laser scanning in the summer of 2009

High resolution topographic data that quantify changes in channel form caused by sequential debris flows in natural channels are rare at the reach scale. Terrestrial laser scanning (TLS) techniques are utilized to capture morphological changes brought about by a high-frequency of debris-flow events at Chalk Cliffs, Colorado. The purpose of this paper is to compare and contrast the topographic response of a natural channel to the documented debris-flow events. TLS survey data allowed for the generation of high-resolution (2-cm) digital terrain models (DTM) of the channel. A robust network of twelve permanent control points permitted repeat scanning sessions that provided multiple DTM to evaluate fine-scale topographic change associated with three debris-flow events. Difference surfaces from the DTM permit the interpretations of spatial variations in channel morphometry and net volume of material deposited and eroded within and between a series of channel reaches. Each channel reach experienced erosion, deposition, and both net volumetric gains and losses were measured. Analysis of potential relationships between erosion and deposition magnitudes yielded no strong correlations with measures of channel-reach morphometry, suggesting that channel reach-specific predictions of potential erosion or deposition locations or rates cannot be adequately derived from statistical analyses of pre-event channel-reach morphometry.

Colorado↗

USGS1984

PROCESSING OF SCANNED IMAGERY FOR CARTOGRAPHIC FEATURE EXTRACTION.

Digital cartographic data are usually captured by manually digitizing a map or an interpreted photograph or by automatically scanning a map. Both techniques first require manual photointerpretation to describe features of interest. A new approach, bypassing the laborious photointerpretation phase, is being explored using direct digital image analysis. Aerial photographs are scanned and color separated to create raster data. These are then enhanced and classified using several techniques to identify roads and buildings. Finally, the raster representation of these features is refined and vectorized. 11 refs.

Conference Paper↗

USGS1984

TOPOLOGICAL STRUCTURING OF RASTER-SCANNED LINE MAP DATA.

The U. S. Geological Survey has a requirement for the collection of large amounts of digital map data from existing graphic map separates. Prototype production techniques have been developed to capture line data from the map separates using a raster-scanning input device. After minimal editing in raster form, the data are converted to 'unstructured' vector form. In order to be processed further, the line data must be topologically structured (nodes identified and start-node, end-node, area-left, and area-right tags associated with each line-segment chain). This paper describes the techniques which have been developed at the U. S. Geological Survey to topologically structure the raster-scanned line map data.

Conference Paper↗

USGS2007

Survey report of NOAA Ship McArthur II cruises AR-04-04, AR-05-05 and AR-06-03: habitat classification of side scan sonar imagery in support of deep-sea coral/sponge explorations at the Olympic Coast National Marine Sanctuary

Habitat mapping and characterization has been defined as a high-priority management issue for the Olympic Coast National Marine Sanctuary (OCNMS), especially for poorly known deep-sea habitats that may be sensitive to anthropogenic disturbance. As a result, a team of scientists from OCNMS, National Centers for Coastal Ocean Science (NCCOS), and other partnering institutions initiated a series of surveys to assess the distribution of deep-sea coral/sponge assemblages within the sanctuary and to look for evidence of potential anthropogenic impacts in these critical habitats. Initial results indicated that remotely delineating areas of hard bottom substrate through acoustic sensing could be a useful tool to increase the efficiency and success of subsequent ROV-based surveys of the associated deep-sea fauna. Accordingly, side scan sonar surveys were conducted in May 2004, June 2005, and April 2006 aboard the NOAA Ship McArthur II to: (1) obtain additional imagery of the seafloor for broader habitat-mapping coverage of sanctuary waters, and (2) help delineate suitable deep-sea coral-sponge habitat, in areas of both high and low commercial-fishing activities, to serve as sites for surveying-in more detail using an ROV on subsequent cruises, Several regions of the sea floor throughout the OCNMS were surveyed and mosaicked at 1-meter pixel resolution. Imagery from the side scan sonar mapping efforts was integrated with other complementary data from a towed camera sled, ROVs, sedentary samples, and bathymetry records to describe geological and biological (where possible) aspects of habitat. Using a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999), we created a preliminary map of various habitat polygon features for use in a geographical information system (GIS). This report provides a description of the mapping and groundtruthing efforts as well as results of the image classification procedure for each of the areas surveyed.

Washington↗

USGS1988

Using side scan sonar data in a geographic information system to locate and display lake trout spawning habitat in the Great Lakes

The National Fisheries Research Center-Great Lakes of the U.S. Fish and Wildlife Service has extensively used a side scan sonar to survey and pinpoint lake trout spawning grounds in the Great Lakes. The Geographic Information System (GIS) of the National Ecology Research Center produced maps from the side scan sonar data showing the exact location of the spawning grounds; this will enable current stocking programs to be carried out at those locations. These maps show the geographic position (latitude and longitude) of both the color-coded primary substrate types and the secondary substrate types, which are denoted by overstrikes. The maps must be supplemented with a Loran-C navigation grid for field use. The maps are proving useful to fishery managers by locating lake trout stocking areas in Lakes Michigan and Huron, as well as to researchers who investigate habitat quality on lake trout spawning grounds.

Conference Paper↗

USGS2022

Finalization of the Confocal Laser Scanning Microscopy (CLSM) working group

A working group in Commission II to investigate applications of confocal laser scanning microscopy (CLSM) for organic petrology investigations has finalized with publication of the manuscript “Characterization of bituminite in Kimmeridge Clay by confocal laser scanning and atomic force microscopy” in the International Journal of Coal Geology. The manuscript is available via Open Access from https://doi.org/10.1016/j.coal.2022.103927 and also from the Commission II working group (WG) webpage https://www.iccop.org/workinggroup/confocal-laser-scanning-microscopy-clsm/. A report detailing the full history and results from the WG also is available from the Commission II WG webpage. The working group investigated the application of CLSM to an organic-rich (44 wt.% TOC), thermally immature sample (VRo 0.42%) of the Kimmeridge Clay Formation. CLSM imaging and spectroscopy and atomic force microscopy (AFM) were used to characterize bituminite.

ICCP News↗

USGS2006

Rime and graupel: Description and characterization as revealed by low-temperature scanning electron microscopy

Snow crystals, which form by vapor deposition, occasionally come in contact with supercooled cloud droplets during their formation and descent. When this occurs, the droplets adhere and freeze to the snow crystals in a process known as accretion. During the early stages of accretion, discrete snow crystals exhibiting frozen cloud droplets are referred to as rime. If this process continues, the snow crystal may become completely engulfed in frozen cloud droplets. The resulting particle is known as graupel. Light microscopic investigations have studied rime and graupel for nearly 100 years. However, the limiting resolution and depth of field associated with the light microscope have prevented detailed descriptions of the microscopic cloud droplets and the three-dimensional topography of the rime and graupel particles. This study uses low-temperature scanning electron microscopy to characterize the frozen precipitates that are commonly known as rime and graupel. Rime, consisting of frozen cloud droplets, is observed on all types of snow crystals including needles, columns, plates, and dendrites. The droplets, which vary in size from 10 to 100 μm, frequently accumulate along one face of a single snow crystal, but are found more randomly distributed on aggregations consisting of two or more snow crystals (snowflakes). The early stages of riming are characterized by the presence of frozen cloud droplets that appear as a layer of flattened hemispheres on the surface of the snow crystal. As this process continues, the cloud droplets appear more sinuous and elongate as they contact and freeze to the rimed crystals. The advanced stages of this process result in graupel, a particle 1 to 3 mm across, composed of hundreds of frozen cloud droplets interspersed with considerable air spaces; the original snow crystal is no longer discernible. This study increases our knowledge about the process and characteristics of riming and suggests that the initial appearance of the flattened hemispheres may result from impact of the leading face of the snow crystal with cloud droplets. The elongated and sinuous configurations of frozen cloud droplets that are encountered on the more advanced stages suggest that aerodynamic forces propel cloud droplets to the trailing face of the descending crystal where they make contact and freeze.

Scanning↗

USGS2024

Side-scan sonar as a tool for measuring fish populations: Current state of the science and future directions

Side-scan sonar (SSS) is a powerful tool that can be used to address many key questions in fisheries science. In principle, SSS uses dual transducers to transmit a narrow-beam, wide-angle acoustic signal as the survey vessel transits an area. The intensity of reflected sound is recorded to generate an image mosaic comprised of benthic substrates and targets in the water column, including organisms such as fish. Although SSS has been around for decades, recent advancements have opened new opportunities to leverage this technology to directly measure fish populations. In this paper, we review the current state of the science and identify opportunities to further refine SSS for fisheries applications.

Fisheries↗

USGS2003

Collecting, shipping, storing, and imaging snow crystals and ice grains with low-temperature scanning electron microscopy

Methods to collect, transport, and store samples of snow and ice have been developed that enable detailed observations of these samples with a technique known as low-temperature scanning electron microscopy (LTSEM). This technique increases the resolution and ease with which samples of snow and ice can be observed, studied, and photographed. Samples are easily collected in the field and have been shipped to the electron microscopy laboratory by common air carrier from distances as far as 5,000 miles. Delicate specimens of snow crystals and ice grains survive the shipment procedures and have been stored for as long as 3 years without undergoing any structural changes. The samples are not subjected to the melting or sublimation artifacts. LTSEM allows individual crystals to be observed for several hours with no detectable changes. Furthermore, the instrument permits recording of photographs containing the parallax information necessary for three-dimensional imaging of the true shapes of snowflakes, snow crystals, snow clusters, ice grains, and interspersed air spaces. This study presents detailed descriptions of the procedures that have been used successfully in the field and the laboratory to collect, ship, store, and image snow crystals and ice grains. Published 2003 Wiley-Liss, Inc.

Microscopy Research and Technique↗

USGS2020

Surface elevation change evaluation in mangrove forests using a low‐cost, rapid‐scan terrestrial laser scanner

Mangrove forests have adapted to sea level rise (SLR) increases by maintaining their forest floor elevation via belowground root growth and surface sediment deposits. Researchers use surface elevation tables (SETs) to monitor surface elevation change (SEC) in mangrove forests, after which this information is used to assess SLR resiliency or to dictate active forest management for vulnerable systems. This method requires significant investments in terms of time and human resources and is limited in the number of points it can measure per plot. We use a low‐cost, portable terrestrial laser scanning (TLS) system to assess SEC for three mangrove forests on Pohnpei Island (Federated States of Micronesia). Cloth simulation filtering was used for ground detection, after which results were refined by filtering points using angular orientation. Digital elevation models then were generated via kriging interpolation for data collected in 2017 and 2019, after which the heights of corresponding points were compared across years. Extreme elevation changes, due to disturbances such as footprints or fallen logs, were removed using interquartile range analysis. The TLS‐obtained average SEC ranged between −6.92 and +6.01 mm, which exhibited an average consistency of 72% when compared to simultaneously collected SET data (root mean square error = 1.36 mm). We contend that this approach represents an improvement over the manual method, where very few points typically are used, that is, ≅ 36 points vs. ≅ 30,000 points in the case of TLS, and could contribute to improved monitoring and management of these rapidly changing forest environments.

Limnology and Oceanography Methods↗

USGS2019

Semiautomated process for enumeration of fishes from recreational-grade side-scan sonar imagery

The use of hydroacoustic techniques is increasing as scientists search for less invasive ways to monitor fish populations, and using recreational side‐scan sonar (SSS) imagery for monitoring has become more common in aquatic resource management over the last 15 years due in part to its low cost and user‐friendly interface. The time‐consuming nature of manually counting fish targets has limited the use of the data that is collected by these systems in research or management contexts. To reduce the time and effort that is required to enumerate acoustic targets that are presumed to be fish, we developed a semiautomated process that rapidly quantifies targets from recreational SSS imagery by using an open‐source image processing software. Perceived fish targets were enumerated using a set of macroinstructions that performed similarly to manual enumeration by three experienced assessors. This method reduced variation that arises from individual assessors and eliminated the prohibitive time constraints that are associated with manual processing. Herein, we describe how our semiautomated process could be used in fisheries management contexts after further research and development of sampling methods. Future research will focus on field validation, quantifying relative abundance, testing across a broader range of environmental conditions, and exploring other applications for fisheries management.N

North American Journal of Fisheries Management↗

USGS2022

Combination of acoustic telemetry and side-scan sonar advances suppression efforts for invasive lake trout in a submontane lake

Expansion of an invasive Lake Trout Salvelinus namaycush population in Swan Lake, Montana, threatens a core area population of Bull Trout S. confluentus . Given the recent development of novel suppression methods, such as use of carcass analog pellets to cause high mortality of embryos, there was a need to quantify spawning season aggregation sites, site use, and spawning habitat for Lake Trout in Swan Lake. Acoustic tags were implanted in 85 Lake Trout during the summer in 2018 and 2019. Nightly tracking efforts during autumn in both years resulted in 1,744 relocations for 49 individual Lake Trout. Kernel density analysis was used to evaluate Lake Trout aggregation sites, identifying 10 distinct sites. All spawning sites were located in the littoral zone along areas of steep bathymetric relief, and these sites composed 48% of total relocations during both spawning seasons. In 2019, side-scan sonar imaging was used to classify and quantify the total area of spawning substrate, which constituted 12.8% of the total surface area estimated for spawning sites 1, 6, and 9 and 11.4% of the total surface area for aggregation sites 2–5, 7, 8, and 10. Simultaneous treatment of all spawning sites would require 205,709 ± 86 kg of carcass analog pellet material, resulting in 370.4 ± 0.2 kg of phosphorus inputs and 7,487.9 ± 3.1 kg of nitrogen inputs to Swan Lake. Thus, pellet treatment would increase the Carlson's trophic state index (TSI) values from 20.8 to 27.7 for total phosphorus and from 22.1 to 26.2 for total nitrogen. Based on a TSI threshold of less than 40 for an oligotrophic lake, the use of carcass analog pellets could be feasible for supplementing the gill-netting suppression of Lake Trout in Swan Lake.

Montana↗

USGS1992

Interference fringes on GLORIA side-scan sonar images from the Bering Sea and their implications

GLORIA side-scan sonographs from the Bering Sea Basin show a complex pattern of interference fringes sub-parallel to the ship's track. Surveys along the same trackline made in 1986 and 1987 show nearly identical patterns. It is concluded from this that the interference patterns are caused by features in the shallow subsurface rather than in the water column. The fringes are interpreted as a thin-layer interference effect that occurs when some of the sound reaching the seafloor passes through it and is reflected off a subsurface layer. The backscattered sound interferes (constructively or desctructively) with the reflected sound. Constructive/destructive interference occurs when the difference in the length of the two soundpaths is a whole/half multiple of GLORIA's 25 cm wavelength. Thus as range from the ship increases, sound moves in and out of phase causing bands of greater and lesser intensity on the GLORIA sonograph. Fluctuations (or 'wiggles') of the fringes on the GLORIA sonographs relate to changes in layer thickness. In principle, a simple three dimensional image of the subsurface layer may be obtained using GLORIA and bathymetric data from adjacent (parallel) ship's tracks. These patterns have also been identified in images from two other systems; SeaMARC II (12 kHz) long-range sonar, and TOBI (30 kHz) deep-towed sonar. In these, and other cases world-wide, the fringes do not appear with the same persistence as those seen in the Bering Sea. ?? 1992 Kluwer Academic Publishers.

Marine Geophysical Research↗

USGS1991

Petrography of Permian “Gondwana” coals from boreholes in northwestern Bangladesh, based on semiautomated reflectance scanning

Drilling through Quaternary alluvium and Tertiary cover at low-gravity anomalies in northwestern Bangladesh showed the presence of Permian sedimentary rocks in depressions that may be as much as a thousand meters deep in the crystalline basement. These Permian strata include low-sulfur, high-volatile bituminous coals in beds as thick as 15 m. The maceral group composition of these coals was determined by semiautomated reflectance scanning with a motorized microscope stage, rather than by point counting. This method was chosen to give objectively recorded raw analytical data and to provide a graphical picture of each sample. The coals are mostly “Gondwana” type (poorly layered “plum pudding” with abundant minerals and inertinite in a vitrinite groundmass) that would be classed as semi-dull (inerto-gelitite) coals. However, six samples have more than 70% vitrinite. None of the samples would be classed as sapropelic (liptinitic). The upper, middle, and lower main seams in borehole GDH-45 were sampled in 10 benches (0.1–3 m thick) each. Inertinite ranges from 7 to 100 vol% (mineral free basis) in individual benches, but composite seam averages are 41, 54 and 67%. Inertinite increases toward the top of two main seams so the bottom would yield the most valuable first mine slices. Some benches with extremely high inertinite content, such as the top 7 m of the lower thick seam, might be mined specially for blending with foreign low-inert coals to increase coke strength. The free swelling index reaches 7.5 in several vitrinite-rich benches, which can indicate good coking coal. Much of the vitrinite is fluorescent, which indicates secondary bituminization characteristic of vitrinite in good coking coals. Ash yields range from 8 to 52%, with composite seam averages of 15, 14 and 24%. Rare visible pyrite is in veinlets or small nodules; framboids and dispersed pyrite are absent. In borehole GDH-40 near Barapukuria (200–500 m depth), the mean random reflectance of vitrinite “A” ranges from 0.60 to 0.80% R o and vitrinite “B” ranges from 0.55 to 0.65%. In borehole GDH-45 near Khalaspir (287–442 m), the reflectance of vitrinite ranges from 0.79 to 0.94%. In individual cases, the vitrinite is difficult to define because of semivitrinite at higher reflectance (forming a separate peak on several reflectograms) and because of surface bitumen films or resinous (?) inclusions at lower reflectance. On the basis of vitrinite reflectance, the coals can be considered to have entered the “main phase of bitumen generation” of organic thermal maturation as understood in petroleum geochemistry.

Organic Geochemistry↗