Search USGSSearch

USGS · 70204334

Full-range, solar-reflected hyperspectral microscopy to support earth remote sensing research

Abstract

Over the past 20 years, hyperspectral microscopy has grown into a robust field of analysis for a number of applications. The visible to near-infrared (VNIR; 400 to 1000 nm) region of the spectrum has demonstrated utility for the characterization of healthy and diseased tissue and of biomolecular indicators at the cellular level. Here, we describe the development of a hyperspectral imaging (HSI) microscope that is aimed at material characterization to complement traditional stand-off, earth remote sensing with hyperspectral sensors. We combine commercial off the shelf technology to build an HSI microscope to collect spectral data with illumination provided by a tunable laser. Hyperspectral imaging microscopy (HIM) facilitates detailed examination of target materials at the subcentimeter spatial scale. The custom-built, laser illumination HSI microscope covers the NIR to shortwave infrared (NIR/SWIR; 900 to 2500 nm) solar-reflected spectral range. It is combined with a separate VNIR sensor (400 to 900 nm) that utilizes quartz–tungsten–halogen lamps for illumination. The combined sensors provide a means to collect <10,000 s of spectra in the full VNIR/SWIR spectral range from both pure substances and precisely engineered linear and nonlinear mixtures. The large abundance of spectra allows for a more detailed understanding of the variability and multivariate probability distributions of spectral signatures. This additional information aids in understanding the variability observed in ground truth spectra collected from portable spectrometers, and it greatly enhances sample description and metadata content. In addition, HIM data cubes can serve as proxies, as “microscenes,” for systems engineering applications such as trade studies for HSI acquired by air- and space-borne sensors.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

E. Terrence Slonecker, David W. Allen, Ronald G. Resmini, Robert S. Rand, Emily Paine. 2018. Full-range, solar-reflected hyperspectral microscopy to support earth remote sensing research. https://doi.org/10.1117/1.jrs.12.026024

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related USGS reports

Satellite remote sensing of river discharge: A framework for assessing the accuracy of discharge estimates made from satellite remote sensing observations

This research presents an evaluation of the accuracy and uncertainty of estimates of river discharge made using satellite observed data sources as input to a modified form of Manning’s equation. Conventional U.S. Geological Survey (USGS) streamflow gaging station data and in-situ measurements of width, depth, height, slope, discharge, and velocity from 30 USGS gage sites were used as ground-truth to assess accuracy. This study explores accuracy in relation to the amount of ground truth information available, the number of calibration points available, and the accuracy of the input data. This research indicates that remotely sensed discharge estimates associated with the modified Manning equation may be expected to have an uncertainty in range of 10% overall given a sufficient number of calibration points. The uncertainty associated with the modified Manning algorithm increased markedly for depths <3 meters (m) and for discharges <1000 cubic meters per second (m 3 / s) for many rivers after calibration. Rivers that exhibit (1) a wide range of flow conditions, (2) a significant number of dams in the watershed and along the channel, and (3) a high baseflow index are more likely to have relatively large errors overall and particularly at the low end of the streamflow range. Uncertainty in remotely sensed measurements of water-surface elevation (WSE) and width in the expected range (WSE, + / − 10 cm; Width, + / − 15 m) introduces uncertainty in the discharge estimates on the order of 10% and is greatest at the low end of discharge as rivers get shallower and narrower. As WSE and width measurement uncertainty increases, discharge uncertainty increases accordingly. In general, the observation errors are greater than the errors associated with the algorithm for a well-calibrated model (e.g., 20 calibration points).

Journal of Applied Remote Sensing

Mapping the probability of freshwater algal blooms with various spectral indices and sources of training data

Algal blooms are pervasive in many freshwater environments and can pose risks to the health and safety of humans and other organisms. However, monitoring and tracking of potentially harmful blooms often relies on in-person observations by the public. Remote sensing has proven useful in augmenting in situ observations of algal concentration, but many hurdles hinder efficient application by end users. First, numerous approaches to estimate aquatic chlorophyll-a are available and can produce inconsistent results. Second, lack of quantitative in situ observations limits opportunities to train models for specific waterbodies, such that models developed for other systems must be used instead. We (1) implement univariate and multivariate logistic regression models to estimate the probability that aquatic chlorophyll-a concentrations exceed an accepted threshold beyond which harmful effects become likely and (2) evaluate the use of visually classified bloom/no-bloom satellite imagery to augment in situ training data. Using a binary classification of aquatic chlorophyll-a exceeding 10 μg / L, we found that (1) logistic regression models were ∼80 % accurate, (2) univariate models trained with visually classified data produce nearly the same accuracy (79%) as models trained with in situ observations (80%), and (3) augmenting in situ chlorophyll-a observations with visual classifications outperformed (82% accuracy) models trained on in situ observations alone (80% accuracy). These results provide a framework for evaluating multiple spectral indices in retrieving algal bloom presence or absence and illustrate that training data derived directly from satellite imagery can be useful in augmenting in situ observations.

Idaho, Oregon

Optical characterization of two cyanobacteria genera, Aphanizomenon and Microcystis, with hyperspectral microscopy.

Cyanobacterial blooms are a nuisance and a potential hazard in freshwater systems worldwide. Remote sensing has been used to detect cyanobacterial blooms, but few studies have distinguished between genera of cyanobacteria. Because some genera are more likely to be toxic than others, this is a useful distinction.In this study, hyperspectral imaging reflectance microscopy was used to examine cyanobacteria from Upper Klamath Lake, Oregon, USA, at high spatial and spectral resolution to determine if two species found commonly in the lake, Aphanizomenon flos-aquae and Microcystis aeruginosa, can be separated spectrally. Of the analytical methods applied, a spectral shape algorithm applied to the derivative was found to be most successful in classifying these species in microscope scenes. Further work is required to determine if the spectral characterization of cyanobacterial genera can be scaled up to other remote sensing applications.

Oregon