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Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

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At least 919 records · Page 51Linked to original sources
USGS2006

Northern Florida reef tract benthic metabolism scaled by remote sensing

Holistic rates of excess organic carbon production (E) and calcification for a 0.5 km 2 segment of the backreef platform of the northern Florida reef tract (NFRT) were estimated by combining biotope mapping using remote sensing with community metabolic rates determined with a benthic incubation system. The use of ASTER multispectral satellite imaging for the spatial scaling of benthic metabolic processes resulted in errors in E and net calcification (G) of 48 and 431% respectively, relative to estimates obtained using AISA hyperspectral airborne scanning. At 19 and 125%, the E and G errors relative to the AISA-based estimates were less pronounced for an analysis that used IKONOS multispectral satellite imagery to spatially extrapolate the chamber process measurements. Our scaling analysis indicates that the holistic calcification rate of the backreef platform of the northern Florida reef tract is negligible at 0.07 g CaCO 3 m -2 d -1 . All of the mapped biotopes in this reef zone are net heterotrophic, resulting in an estimated holistic excess production rate of -0.56 g C m -2 d -1 , and an overall gross primary production to respiration ratio of 0.85. Based on our finding of ubiquitous heterotrophy, we infer that the backreef platform of the NFRT is a sink for external inputs of suspended particulate organic matter. Further, our results suggest that the inward advection of inorganic nutrients is not a dominant forcing mechanism for benthic biogeochemical function in the NFRT. We suggest that the degradation of the northern Florida reef tract may parallel the community phase shifts documented within other reef systems polluted by organic detritus.

Florida↗
USGS2022

Forecasting explosions at Sinabung Volcano, Indonesia, based on SO2 emission rates

Dome-building volcanic eruptions are often associated with frequent Vulcanian explosions, which constitute a substantial threat to proximal communities. One proposed mechanism driving such explosions is the sealing of the shallow volcanic system followed by pressurization due to gas accumulation beneath the seal. We investigate this hypothesis at Sinabung Volcano (Sumatra, Indonesia), which has been in a state of eruption since August 2010. In 2013, the volcano began erupting a lava dome and lava flow, and frequent explosions produced eruptive columns that rose many kilometers into the atmosphere and at times sent pyroclastic density currents down the southeast flanks. A network of scanning Differential Optical Absorption Spectrometers (DOAS) was installed on the volcano’s eastern flank in 2016 to continuously monitor SO 2 emission rates during daytime hours. Analysis of the DOAS data from October 2016 to September 2017 revealed that passive SO 2 emissions were generally lower in the 5 days leading up to explosive events (∼100 t/d) than was common in 5-day periods leading up to days on which no explosions occurred (∼200 t/d). The variability of passive SO 2 emissions, expressed as the standard deviation, also took on a slightly wider range of values before days with explosions (0–103 t/d at 1-sigma) than before days without explosions (43–117 t/d). These observations are consistent with the aforementioned seal-failure model, where the sealing of the volcanic conduit blocks gas emissions and leads to pressurization and potential Vulcanian explosions. We develop a forecasting methodology that allows calculation of a relative daily explosion probability based solely on measurements of the SO 2 emission rate in the preceding days. We then calculate forecast explosion probabilities for the remaining SO 2 emissions dataset (October 2017—September 2021). While the absolute accuracy of forecast explosion probabilities is variable, the method can inform the probability of an explosion occurring relative to that on other days in each test period. This information can be used operationally by volcano observatories to assess relative risk. The SO 2 emissions-based forecasting method is likely applicable to other open vent volcanoes experiencing dome-forming eruptions.

Frontiers in Earth Science↗
USGS2023

A novel non-destructive workflow for examining germanium and co-substituents in ZnS

A suite of complementary techniques was used to examine germanium (Ge), a byproduct critical element, and co-substituent trace elements in ZnS and mine wastes from four mineral districts where germanium is, or has been, produced within the United States. This contribution establishes a comprehensive workflow for characterizing Ge and other trace elements, which captures the full heterogeneity of samples through extensive pre-characterization. This process proceeded from optical microscopy, to scanning electron microscopy and cathodoluminescence (CL) imaging, to electron microprobe analysis, prior to synchrotron-based investigations. Utilizing non-destructive techniques enabled reanalysis, which proved essential for verifying observations and validating unexpected results. In cases where the Fe content was <0.3 wt% in ZnS, cathodoluminescence imaging proved to be an efficient means to qualitatively identify trace element zonation that could then be further explored by other micro-focused techniques. Micro-focused X-ray diffraction was used to map the distribution of the non-cubic ZnS polymorph, whereas micro-focused X-ray fluorescence (μ-XRF) phase mapping distinguished between Ge 4+ hosted in primary ZnS and a weathering product, hemimorphite [Zn 4 Si 2 O 7 (OH) 2 ·H 2 O]. Microprobe data and μ-XRF maps identified spatial relationships among trace elements in ZnS and implied substitutional mechanisms, which were further explored using Ge and copper (Cu) X-ray absorption near-edge spectroscopy (XANES). Both oxidation states of Ge (4+ and 2+) were identified in ZnS along with, almost exclusively, monovalent Cu. However, the relative abundance of Ge oxidation states varied among mineral districts and, sometimes, within samples. Further, bulk XANES measurements typically agreed with micro-focused XANES (μ-XANES) spectra, but unique micro-environments were detected, highlighting the importance of complementary bulk and micro-focused measurements. Some Ge μ-XANES utilized a high energy resolution fluorescence detector, which improved spectral resolution and spectral signal-to-noise ratio. This detector opens new opportunities for exploring byproduct critical elements in complex matrices. Overall, the non-destructive workflow employed here can be extended to other byproduct critical elements to more fully understand fundamental ore enrichment processes, which have practical implications for critical element exploration, resource quantification, and extraction.

Frontiers in Earth Science↗
USGS2019

Soil aggregates as a source of dissolved organic carbon to streams: An experimental study on the effect of solution chemistry on water extractable carbon

Over the past two decades, headwater streams of the northern hemisphere have shown increased amounts of dissolved organic carbon (DOC), coinciding with decreased acid deposition. The exact nature of the mechanistic link between precipitation composition and stream water DOC is still widely debated in the literature. We hypothesize that soil aggregates are the main source of stream water DOC and that DOC release is greater in organic rich, riparian soils vs. hillslope soils. To test these hypotheses, we collected soils from two main landscape positions (hillslope and riparian zones) from the acid-impacted Sleepers River Research Watershed in northeastern Vermont. We performed aqueous soil extracts with solutions of different ionic strength (IS) and composition to simulate changes in soil solution. We monitored dynamic changes in soil particle size, aggregate architecture and composition, leachate DOC concentrations, dissolved organic matter (DOM) characteristics by fluorescence spectroscopy and trends in bioavailability. In low IS solutions, extractable DOC concentrations were significantly higher, particle size (by laser diffraction) was significantly smaller and organic material was separated from mineral particles in scanning electron microscope observations. Furthermore, higher DOC concentrations were found in Na + compared to Ca 2+ solutions of the same IS. These effects are attributed to aggregate dispersion due to expanding diffuse double layers in decreased IS solutions and to decreased bridging by divalent cations. Landscape position impacted quality but not quantity of released DOC. Overall, these results indicate that soil aggregates might be one important link between Critical Zone inputs (i.e., precipitation) and exports in streams.

Vermont↗
USGS2015

Characterization of pH dependent Mn(II) oxidation strategies and formation of a bixbyite-like phase by Mesorhizobium australicum T-G1

Despite the ubiquity of Mn oxides in natural environments, there are only a few observations of biological Mn(II) oxidation at pH < 6. The lack of low pH Mn-oxidizing bacteria (MOB) isolates limits our understanding of how pH influences biological Mn(II) oxidation in extreme environments. Here, we report that a novel MOB isolate, Mesorhizobium australicum strain T-G1, isolated from an acidic and metalliferous uranium mining area, can oxidize Mn(II) at both acidic and neutral pH using different enzymatic pathways. X-ray diffraction, Raman spectroscopy, and scanning electron microscopy with energy dispersive X-ray spectroscopy revealed that T-G1 initiated bixbyite-like Mn oxide formation at pH 5.5 which coincided with multi-copper oxidase expression from early exponential phase to late stationary phase. In contrast, reactive oxygen species (ROS), particularly superoxide, appeared to be more important for T-G1 mediated Mn(II) oxidation at neutral pH. ROS was produced in parallel with the occurrence of Mn(II) oxidation at pH 7.2 from early stationary phase. Solid phase Mn oxides did not precipitate, which is consistent with the presence of a high amount of H 2 O 2 and lower activity of catalase in the liquid culture at pH 7.2. Our results show that M. australicum T-G1, an acid tolerant MOB, can initiate Mn(II) oxidation by varying its oxidation mechanisms depending on the pH and may play an important role in low pH manganese biogeochemical cycling.

Frontiers in Microbiology↗
USGS2024

Particle morphology and elemental analysis of lung tissue from post-9/11 military personnel with biopsy-proven lung disease

The relationship between exposure to inhaled inorganic particulate matter and risk for deployment-related lung disease in military personnel is unclear due in part to difficulties characterizing individual exposure to airborne hazards. We evaluated the association between self-reported deployment exposures and particulate matter (PM) contained in lung tissue from previously deployed personnel with lung disease (“deployers”). The PM in deployer tissues was compared to normal lung tissue PM using the analytical results of scanning electron microscopy and inductively coupled plasma mass spectrometry. The majority of PM phases for both the deployers and the controls were sub-micrometer in size and were compositionally classified as aluminum and zirconium oxides, carbonaceous particles, iron oxides, titanium oxides, silica, other silicates, and other metals. The proportion of silica and other silicates was significantly higher in the retained dust from military veterans with biopsy-confirmed deployment-related lung disease compared to the control subjects. Within the deployer population, those who had combat jobs had a higher total PM burden, though the difference was not statistically significant. These findings have important implications for understanding the role of inhaled inorganic dusts in the risk for lung injury in previously deployed military veterans.

International Journal of Enviornmental Research an↗
USGS2026

The USGS Rotating X-ray Computed Tomography (RXCT) Coral-Core Archive: Scope, access, and standardization

We announce the U.S. Geological Survey (USGS) Rotating X-ray Computed Tomography (RXCT) Coral-Core Archive, a digital resource derived from ~400 coral reef cores curated at the USGS Pacific and St. Petersburg Coastal and Marine Science Centers. The archive de-livers calibrated 3-D image volumes that enable reproducible values of skeletal density, linear extension, and calcification from decadal-to-centennials scale records of coral growth and bioerosion. Cross-study comparability within the archive is supported by a unified RXCT workflow that minimizes imaging artifacts. This includes rejecting im-age-intensity–density regressions with r² < 0.95, back-calculating standard densities to verify a ±10% target precision, and confirming that band-averaged density values fall within published species- and site-specific ranges. Given global coral-reef decline and the rarity of physical archives, we release data under FAIR (Findable, Accessible, Interopera-ble, Reusable) principles. Calibrated imagery and scan metadata are distributed through CoralCache/CoralCT for analysis (DeCarlo et al., 2025), while core locations and collection metadata are published through the USGS Geologic Core and Sample Database (DOI: 10.5066/F7319TR3) with links to CT slice imagery in a USGS ScienceBase repository (DOI: 10.5066/P139Y9H4). This archive provides a powerful dataset for evaluating environ-mental controls on coral growth, establishing restoration baselines, and improving coastal-hazard assessments in the face of global coral-reef declines.

American Somoa, Guam, Florida, Hawaii, U.S. Virgin↗
USGS2019

sUAS-based remote sensing of river discharge using thermal particle image velocimetry and bathymetric lidar

This paper describes a non-contact methodology for computing river discharge based on data collected from small Unmanned Aerial Systems (sUAS). The approach is complete in that both surface velocity and channel geometry are measured directly under field conditions. The technique does not require introducing artificial tracer particles for computing surface velocity, nor does it rely upon the presence of naturally occurring floating material. Moreover, no prior knowledge of river bathymetry is necessary. Due to the weight of the sensors and limited payload capacities of the commercially available sUAS used in the study, two sUAS were required. The first sUAS included mid-wave thermal infrared and visible cameras. For the field evaluation described herein, a thermal image time series was acquired and a particle image velocimetry (PIV) algorithm used to track the motion of structures expressed at the water surface as small differences in temperature. The ability to detect these thermal features was significant because the water surface lacked floating material (e.g., foam, debris) that could have been detected with a visible camera and used to perform conventional Large-Scale Particle Image Velocimetry (LSPIV). The second sUAS was devoted to measuring bathymetry with a novel scanning polarizing lidar. We collected field measurements along two channel transects to assess the accuracy of the remotely sensed velocities, depths, and discharges. Thermal PIV provided velocities that agreed closely (R^2 = 0.82 and 0.64) with in situ velocity measurements from an acoustic Doppler current profiler (ADCP). Depths inferred from the lidar closely matched those surveyed by wading in the shallower of the two cross sections (R^2 = 0.95) but the agreement was not as strong for the transect with greater depths (R^2 = 0.61). Incremental discharges computed with the remotely sensed velocities and depths were greater than corresponding ADCP measurements by 22% at the first cross section and < 1% at the second.

Colorado↗
USGS2019

Geometric targets for UAS Lidar

Lidar from small unoccupied aerial systems (UAS) is a viable method for collecting geospatial data associated with a wide variety of applications. Point clouds from UAS lidar require a means for accuracy assessment, calibration, and adjustment. In order to carry out these procedures, specific locations within the point cloud must be precisely found. To do this, artificial targets may be used for rural settings, or anywhere there is a lack of identifiable and measurable features in the scene. This paper presents the design of lidar targets for precise location based on geometric structure. The targets and associated mensuration algorithm were tested in two scenarios to investigate their performance under different point densities, and different levels of algorithmic rigor. The results show that the targets can be accurately located within point clouds from typical scanning parameters to <2 cm &#x3C3; , "> σ , and that including observation weights in the algorithm based on propagated point position uncertainty leads to more accurate results.

Remote Sensing↗
USGS2020

Positional accuracy assessment of lidar point cloud from NAIP/3DEP pilot project

The Leica Geosystems CountryMapper hybrid system has the potential to collect data that satisfy the U.S. Geological Survey (USGS) National Geospatial Program (NGP) and 3D Elevation Program (3DEP) and the U.S. Department of Agriculture (USDA) National Agriculture Imagery Program (NAIP) requirements in a single collection. This research will help 3DEP determine if this sensor has the potential to meet current and future 3DEP topographic lidar collection requirements. We performed an accuracy analysis and assessment on the lidar point cloud produced from CountryMapper. The boresighting calibration and co-registration by georeferencing correction based on ground control points are assumed to be performed by the data provider. The scope of the accuracy assessment is to apply the following variety of ways to measure the accuracy of the delivered point cloud to obtain the error statistics. Intraswath uncertainty from a flat surface was computed to evaluate the point cloud precision. Intraswath difference between opposite scan directions and the interswath overlap difference were evaluated to find boresighting or any systematic errors. Absolute vertical accuracy over vegetated and non-vegetated areas were also assessed. Both horizontal and vertical absolute errors were assessed using the 3D absolute error analysis methodology of comparing conjugate points derived from geometric features. A three-plane feature makes a single unique intersection point. Intersection points were computed from ground-based lidar and airborne lidar point clouds for comparison. The difference between two intersection points form one error vector. The geometric feature-based error analysis was applied to intraswath, interswath, and absolute error analysis. The CountryMapper pilot data appear to satisfy the accuracy requirements suggested by the USGS lidar specification, based upon the error analysis results. The focus of this research was to demonstrate various conventional accuracy measures and novel 3D accuracy techniques using two different error computation methods on the CountryMapper airborne lidar point cloud.

Remote Sensing↗
USGS2021

Geometric calibration updates to Landsat 7 ETM+ instrument for Landsat Collection 2 products

The Landsat 7 (L7) spacecraft and its instrument, the enhanced thematic mapper plus (ETM+), have been consistently characterized and calibrated since its launch in April of 1999. These performance metrics and calibration updates are determined through the U. S. Geological Survey (USGS) Landsat image assessment system (IAS), which has been performing this function since launch. Starting in 2016, the USGS adopted a tiered collection management structure for its Landsat data products that ensures a consistent method of processing for the Landsat archive within a given collection while allowing a set of calibration updates to be performed between any two given collections. The time frame between 2016 and the end of 2020 was part of the Landsat data Collection 1, in the middle of 2020 was the start of the Landsat Collection 2 data products. The start of a given collection initiates the reprocessing of the Landsat archive, which may involve one or more of a set of updated calibration parameters, improvements in the support data needed for product generation, and improved algorithms used in both the processing flow of products along with the characterization and calibration of the Landsat instruments and spacecraft. This paper discusses only the ETM+ geometric spacecraft and instrument calibration improvements for Collection 2. Three ETM+ calibration updates were made for the ETM+; updates to the thermal band odd-to-even detector alignment, sensor to attitude control system (ACS) alignment, and a cold-to-warm focal plane alignment adjustment. The sensor alignment updates impact only the accuracy of the systematic terrain products (L1GT), which are the products generated before applying any corrections based on the ground control used in registration. The band alignment changes impacted only bands 5, 6, and 7 within the focal plane. Other geometric calibration updates, such as scan mirror alignment, are done on a routine basis and are not part of the Collection 2 updates due to their more dynamic characteristics.

Remote Sensing↗
USGS2024

Hyperspectral Image Transects during Transient Events in Rivers (HITTER): Framework development and application to a tracer experiment on the Missouri River, USA

Rivers convey a broad range of materials, such as sediment, nutrients, and contaminants. Much of this transport can occur during or immediately after an episodic, pulsed event like a flood or an oil spill. Understanding the flow processes that influence the motion of these substances is important for managing water resources and conserving aquatic ecosystems. This study introduces a new remote sensing framework for characterizing dynamic phenomena at the scale of a channel cross-section: Hyperspectral Image Transects during Transient Events in Rivers (HITTER). We present a workflow that uses repeated hyperspectral scan lines acquired from a hovering uncrewed aircraft system (UAS) to quantify how a water attribute of interest varies laterally across the river and evolves over time. Data from a tracer experiment on the Missouri River are used to illustrate the components of the end-to-end processing chain we used to quantify the passage of a visible dye. The framework is intended to be flexible and could be applied in a number of different contexts. The results of this initial proof-of-concept investigation suggest that HITTER could potentially provide insight regarding the dispersion of a range of materials in rivers, which would facilitate ecological and geomorphic studies and help inform management.

Remote Sensing↗
USGS2014

Remote sensing of Sonoran Desert vegetation structure and phenology with ground-based LiDAR

Long-term vegetation monitoring efforts have become increasingly important for understanding ecosystem response to global change. Many traditional methods for monitoring can be infrequent and limited in scope. Ground-based LiDAR is one remote sensing method that offers a clear advancement to monitor vegetation dynamics at high spatial and temporal resolution. We determined the effectiveness of LiDAR to detect intra-annual variability in vegetation structure at a long-term Sonoran Desert monitoring plot dominated by cacti, deciduous and evergreen shrubs. Monthly repeat LiDAR scans of perennial plant canopies over the course of one year had high precision. LiDAR measurements of canopy height and area were accurate with respect to total station survey measurements of individual plants. We found an increase in the number of LiDAR vegetation returns following the wet North American Monsoon season. This intra-annual variability in vegetation structure detected by LiDAR was attributable to a drought deciduous shrub Ambrosia deltoidea, whereas the evergreen shrub Larrea tridentata and cactus Opuntia engelmannii had low variability. Benefits of using LiDAR over traditional methods to census desert plants are more rapid, consistent, and cost-effective data acquisition in a high-resolution, 3-dimensional context. We conclude that repeat LiDAR measurements can be an effective method for documenting ecosystem response to desert climatology and drought over short time intervals and at detailed-local spatial scale.

Arizona↗
USGS2017

Fine-resolution repeat topographic surveying of dryland landscapes using UAS-based structure-from-motion photogrammetry: Assessing accuracy and precision against traditional ground-based erosion measurements

Structure-from-motion (SfM) photogrammetry from unmanned aerial system (UAS) imagery is an emerging tool for repeat topographic surveying of dryland erosion. These methods are particularly appealing due to the ability to cover large landscapes compared to field methods and at reduced costs and finer spatial resolution compared to airborne laser scanning. Accuracy and precision of high-resolution digital terrain models (DTMs) derived from UAS imagery have been explored in many studies, typically by comparing image coordinates to surveyed check points or LiDAR datasets. In addition to traditional check points, this study compared 5 cm resolution DTMs derived from fixed-wing UAS imagery with a traditional ground-based method of measuring soil surface change called erosion bridges. We assessed accuracy by comparing the elevation values between DTMs and erosion bridges along thirty topographic transects each 6.1 m long. Comparisons occurred at two points in time (June 2014, February 2015) which enabled us to assess vertical accuracy with 3314 data points and vertical precision (i.e., repeatability) with 1657 data points. We found strong vertical agreement (accuracy) between the methods (RMSE 2.9 and 3.2 cm in June 2014 and February 2015, respectively) and high vertical precision for the DTMs (RMSE 2.8 cm). Our results from comparing SfM-generated DTMs to check points, and strong agreement with erosion bridge measurements suggests repeat UAS imagery and SfM processing could replace erosion bridges for a more synoptic landscape assessment of shifting soil surfaces for some studies. However, while collecting the UAS imagery and generating the SfM DTMs for this study was faster than collecting erosion bridge measurements, technical challenges related to the need for ground control networks and image processing requirements must be addressed before this technique could be applied effectively to large landscapes.

Remote Sensing↗
USGS2025

A real-time fish detection system for partially dewatered fish to support selective fish passage

Recent advances in fish transportation technologies and deep machine learning-based fish classification have created an opportunity for real-time, autonomous fish sorting through a selective passage mechanism. This research presents a case study of a novel application that utilizes deep machine learning to detect partially dewatered fish exiting an Archimedes Screw Fish Lift (ASFL). A MobileNet SSD model was trained on images of partially dewatered fish volitionally passing through an ASFL. Then, this model was integrated with a network video recorder to monitor video from the ASFL. Additional models were also trained using images from a similar fish scanning device to test the feasibility of this approach for fish classification. Open source software and edge computing design principles were employed to ensure that the system is capable of fast data processing. The findings from this research demonstrate that such a system integrated with an ASFL can support real-time fish detection. This research contributes to the goal of automated data collection in a selective fish passage system and presents a viable path towards realizing optical fish sorting.

Michigan↗
USGS2006

Storm-induced redistribution of deepwater sediments in Lake Ontario

High-resolution seismic reflection profiles, side-scan sonar profiles, and surface sediment analyses for grain size (% sand, silt & clay), total organic carbon content, and carbonate content along shore-perpendicular transects offshore of Olcott and Rochester in Lake Ontario were utilized to investigate cm-thick sands or absence of deep-water postglacial sediments in water depths of 130 to 165 m. These deepwater sands were observed as each transect approached and occupied the "sills," identified by earlier researchers, between the three deepest basins of the lake. The results reveal thin (0 to 5-cm) postglacial sediments, lake floor lineations, and sand-rich, organic, and carbonate poor sediments at the deepwater sites (> 130 m) along both transects at depths significantly below wave base, epilimnetic currents, and internal wave activity. These sediments are anomalous compared to shallower sediments observed in this study and deeper sediments reported by earlier research, and are interpreted to indicate winnowing and resuspension of the postglacial muds. We hypothesize that the mid-lake confluence of the two-gyre surface current system set up by strong storm events extends down to the lake floor when the lake is isothermal, and resuspends and winnows lake floor sediment at these locations. Furthermore, we believe that sedimentation is more likely to be influenced by bottom currents at these at these sites than in the deeper basins because these sites are located on bathymetric highs between deeper depositional basins of the lake, and the bathymetric constriction may intensify any bottom current activity at these sites.

Journal of Great Lakes Research↗
USGS2011

Hyperkyphosis in longnose gar ( Lepisosteus osseus ) of North Central Texas

Two mature female longnose gar ( Lepisosteus osseus ) exhibiting severe hyperkyphotic spinal deformities were captured during the 2010 spring spawn at Lake Arrowhead, Clay County, Texas. Yet, despite their deformities and impaired motility, both longnose gar were in overall good condition. Hyperkyphosis in both longnose gar resulted from fused trunk vertebrae in the affected areas. Results of morphological examinations and computerized tomography (CT) scans showed no evidence of injury-induced responses and suggested a congenital or possibly environmentally induced aetiology for disruption of the normal vertebral segmentation process.

Texas↗
USGS2014

A new clarification method to visualize biliary degeneration during liver metamorphosis in sea lamprey ( Petromyzon marinus )

Biliary atresia is a rare disease of infancy, with an estimated 1 in 15,000 frequency in the southeast United States, but more common in East Asian countries, with a reported frequency of 1 in 5,000 in Taiwan. Although much is known about the management of biliary atresia, its pathogenesis is still elusive. The sea lamprey ( Petromyzon marinus ) provides a unique opportunity to examine the mechanism and progression of biliary degeneration. Sea lamprey develop through three distinct life stages: larval, parasitic, and adult. During the transition from larvae to parasitic juvenile, sea lamprey undergo metamorphosis with dramatic reorganization and remodeling in external morphology and internal organs. In the liver, the entire biliary system is lost, including the gall bladder and the biliary tree. A newly-developed method called &ldquo;CLARITY&rdquo; was modified to clarify the entire liver and the junction with the intestine in metamorphic sea lamprey. The process of biliary degeneration was visualized and discerned during sea lamprey metamorphosis by using laser scanning confocal microscopy. This method provides a powerful tool to study biliary atresia in a unique animal model.

Journal of Visualized Experiments↗