SEARCH · Engineering Papers

Results for “species classification”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4

All sources NASA NTRS DOE OSTI

NASA NTRS2018

NASA NeMO-Net

We present preliminary results from NASA NeMO-Net, the first neural multi-modal observation and training network for global coral reef assessment. NeMO-Net is an open-source deep convolutional neural network (CNN) and interactive active learning training software in development which will assess the present and past dynamics of coral reef ecosystems. NeMO-Net exploits active learning and data fusion of mm-scale remotely sensed 3D images of coral reefs captured using fluid lensing with the NASA FluidCam instrument, presently the highest-resolution remote sensing benthic imaging technology capable of removing ocean wave distortion, as well as hyperspectral airborne remote sensing data from the ongoing NASA CORAL mission and lower-resolution satellite data to determine coral reef ecosystem makeup globally at unprecedented spatial and temporal scales. Aquatic ecosystems, particularly coral reefs, remain quantitatively misrepresented by low- resolution remote sensing as a result of refractive distortion from ocean waves, optical attenuation, and remoteness. Machine learning classification of coral reefs using FluidCam mm-scale 3D data show that present satellite and airborne remote sensing techniques poorly characterize coral reef percent living cover, morphology type, and species breakdown at the mm, cm, and meter scales. Indeed, current global assessments of coral reef cover and morphology classification based on km-scale satellite data alone can suffer from segmentation errors greater than 40%, capable of change detection only on yearly temporal scales and decameter spatial scales, significantly hindering our understanding of patterns and processes in marine biodiversity at a time when these ecosystems are experiencing unprecedented anthropogenic pressures, ocean acidification, and sea surface temperature rise. NeMO-Net leverages our augmented machine learning algorithm that demonstrates data fusion of regional FluidCam (mm, cm-scale) airborne remote sensing with global low-resolution (m, km-scale) airborne and spaceborne imagery to reduce classification errors up to 80% over regional scales. Such technologies can substantially enhance our ability to assess coral reef ecosystems dynamics.

NASA↗

NASA NTRS1981

Spectral reflectance of hydrophytes

Identification of hydrophytes will improve the delineation and classification of wetlands on remotely sensed imagery. Spectral reflectance measurements of 10 species of hydrophytes were made with an Exotech radiometer during three phenological stages, flowering and early seed, senescent, and early emergent. Reflectance data were analyzed to determine significant (P not greater than 0.5) differences between species in each of four spectral regions during each phenological stage. Eight species had significantly (P not greater than 0.05) different reflectances during the flower and early seed stage. Among the ten species only one could not be spectrally isolated during at least 1 phenological stage. The results indicate that films sensitive to both visible and infrared spectra (e.g., Ektachrome infrared) should enable recognition of different species of hydrophytes.

Best, R. G.↗

NASA NTRS2012

Observing Changing Ecological Diversity in the Anthropocene

As the world enters the Anthropocene, the planet's environment is changing rapidly, putting critical ecosystem services at risk. Understanding and forecasting how ecosystems will change over the coming decades requires understanding the sensitivity of species to environmental change. The extant distribution of species and functional groups contains valuable information about the performance of different species in different environments. However, with high rates of environmental change, information inherent in ranges of many species will disappear, since that information exists only under quasi-equilibrium conditions. The information content of distributional data obtained now is greater than data obtained in the future. New remote sensing technologies can map chemical and structural traits of plant canopies and allow inference of trait and in many cases, species ranges. Current satellite remote sensing data can only produce relatively simple classifications, but new techniques have dramatically higher biological information content.

environmental changes↗

DOE OSTI2025

Identification and Classification of Fungal GPCR Gene Families

G protein-coupled receptors (GPCRs) are transmembrane proteins crucial for signal transduction in eukaryotes, responding to diverse extracellular signals. Researchers have found and systematically summarized 14 distinct types of GPCRs in fungi but their distribution among numerous fungal species remained largely unexamined. Additionally, three families of mammalian homologs (Rhodopsin, Glutamate, and Frizzled) have been found in previous studies, but they are not included in the systematic classification of fungal GPCRs. Our study establishes a unified classification of 17 GPCR classes in fungi, combining 14 fungal and 3 mammalian previously recognized groups, and classifies 28,294 GPCRs across 1357 fungal species, significantly expanding the scale of GPCRs in fungi and demonstrating their broader distribution. We found that mammalian homologs are notably more prevalent in Early Diverging Fungi (EDF), whereas the previous 14 classes are predominantly found in Ascomycota and Basidiomycota. The most abundant class detected in fungi was Pth11-like GPCRs, exclusively found in Pezizomycotina and involved in fungal pathogenicity. Our analysis suggested that Pezizomycotina ancestor possessed an extensive array of Pth11-like GPCRs, but over time, some species underwent considerable reductions in these GPCRs in conjunction with genome contractions. Utilizing a custom-built convolutional neural network (CNN) for the identification of fungal GPCRs, we identified several putative novel fungal GPCRs. Predicted interactions between these prospective new GPCRs and G-alpha proteins, as simulated by AlphaFold Multimer, provided additional support for their functional relevance. In conclusion, our work defines the first large-scale, unified classification of fungal GPCRs, reveals lineage-specific expansions and contractions, and uncovers previously unrecognized GPCR candidates with potential functional roles in fungal signaling.

G protein-coupled receptors↗

NASA NTRS1999

Remote Thermal IR Spectroscopy of our Solar System

Indirect methods to detect extrasolar planets have been successful in identifying a number of stars with companion planets. No direct detection of an extrasolar planet has yet been reported. Spectroscopy in the thermal infrared region provides a potentially powerful approach to detection and characterization of planets and planetary systems. We can use knowledge of our own solar system, its planets and their atmospheres to model spectral characteristics of planets around other stars. Spectra derived from modeling our own solar system seen from an extrasolar perspective can be used to constrain detection strategies, identification of planetary class (terrestrial vs. gaseous) and retrieval of chemical, thermal and dynamical information. Emission from planets in our solar system peaks in the thermal infrared region, approximately 10 - 30 microns, substantially displaced from the maximum of the much brighter solar emission in the visible near 0.5 microns. This fact provides a relatively good contrast ratio to discriminate between stellar (solar) and planetary emission and optimize the delectability of planetary spectra. Important molecular constituents in planetary atmospheres have rotational-vibrational spectra in the thermal infrared region. Spectra from these molecules have been well characterized in the laboratory and studied in the atmospheres of solar system planets from ground-based and space platforms. The best example of such measurements are the studies with Fourier transform spectrometers, the Infrared Interferometer Spectrometers (IRIS), from spacecraft: Earth observed from NIMBUS 8, Mars observed from Mariner 9, and the outer planets observed from Voyager spacecraft. An Earth-like planet is characterized by atmospheric spectra of ozone, carbon dioxide, and water. Terrestrial planets have oxidizing atmospheres which are easily distinguished from reducing atmospheres of gaseous giant planets which lack oxygen-bearing species and are characterized by spectra containing hydrocarbons such as methane and ethane. Spectroscopic information on extrasolar planets thus can permit their classification. Spectra and spectral lines contain information on the temperature structure of the atmosphere. Line and band spectra can be used to identify the molecular constituents and retrieve species abundances, thereby classifying and characterizing the planet. At high enough spectral resolution characteristic planetary atmospheric dynamics and unique phenomena such as failure of local thermodynamic equilibrium can be identified. Dynamically induced effects such as planetary rotation and orbital velocity shift and change the shape of spectral features and must be modeled in detailed spectral studies. We will use our knowledge of the compositional, thermal and dynamical characteristics of planetary atmospheres in our own solar system to model spectra observed remotely on similar planets in extrasolar planetary systems. We will use a detailed radiative transfer and beam integration program developed for the modeling and interpretation of thermal infrared spectra measured from nearby planet planets to generate models of an extra-solar "Earth" and "Jupiter". From these models we will show how key spectral features distinguish between terrestrial and gaseous planets, what information can be obtained with different spectral resolution, what spectral features can be used to search for conditions for biogenic activity, and how dynamics and distance modify the observed spectra. We also will look at unique planetary phenomena such as atmospheric lasing and discuss their utility as probes for detection and identification of planets. Results of such studies will provide information to constrain design for instrumentation needed to directly detect extrasolar planets.

Kostiuk, Theodor↗

NASA NTRS1979

Forest Classification and Inventory System using Landsat, digital terrain, and ground sample data

Accurate timber inventory data for cost-effective forest management is the primary goal of a Forest Classification and Inventory System (FOCIS) designed to provide estimates of timber volume by species aggregated by compartments, townships, or other spatial management units. FOCIS uses Landsat spectral data, including a synthesized texture channel, and Forest Service ground sample data to produce timber volume-homogeneous classes through a two-step unsupervised clustering process. Registered digital terrain data, including derived slope angle and slope aspect channels, are used to predict species proportions through a trend surface model, again using ground sample data for model calibration. In the final stage of FOCIS, volume estimates and predicted species proportions are merged and aggregated to yield timber volumes by species within management areas.

Strahler, A. H.↗

NASA NTRS1978

Automatic classification of reforested Pinus SPP and Eucalyptus SPP in Mogi-Guacu, SP, Brazil, using LANDSAT data

The author has identified the following significant results. Single date LANDSAT CCTs were processed, by Image-100 to classify Pinus and Eucalyptus species and their age groups. The study area Mogi-Guagu was located in the humid subtropical climate zone of Sao Paulo. The study was divided into ten preliminary classes and featured selection algorithms were used to calculate Bhattacharyya distance between all possible pairs of these classes in the four available channels. Classes having B-distance values less than 1.30 were grouped in four classes: (1) class PE - P. elliottii, (2) class P0 - Pinus species other than P. elliotii, (3) class EY - Eucalyptus spp. under two years, and (4) class E0 - Eucalyptus spp. more than two years old. The percentages of correct classification ranged from 70.9% to 94.12%. Comparisons of acreage estimated from the Image-100 with ground truth data showed agreement. The Image-100 percent recognition values for the above four classes were 91.62%, 87.80%, 89.89%, and 103.30%, respectively.

Dejesusparada, N.↗

DOE OSTI2024

Evaluation of an autonomous acoustic surveying technique for grassland bird communities in Nebraska

Monitoring trends in wildlife communities is integral to making informed land management decisions and applying conservation strategies. Birds inhabit most niches in every environment and because of this they are widely accepted as an indicator species for environmental health. Traditionally, point counts are the common method to survey bird populations, however, passive acoustic monitoring approaches using autonomous recording units have been shown to be cost-effective alternatives to point count surveys. Advancements in automatic acoustic classification technologies, such as BirdNET, can aid in these efforts by quickly processing large volumes of acoustic recordings to identify bird species. While the utility of BirdNET has been demonstrated in several applications, there is little understanding of its effectiveness in surveying declining grassland birds. We conducted a study to evaluate the performance of BirdNET to survey grassland bird communities in Nebraska by comparing this automated approach to point count surveys. We deployed ten autonomous recording units from March through September 2022: five recorders in row-crop fields and five recorders in perennial grassland fields. During this study period, we visited each site three times to conduct point count surveys. We compared focal grassland bird species richness between point count surveys and the autonomous recording units at two different temporal scales and at six different confidence thresholds. Total species richness (focal and non-focal) for both methods was also compared at five different confidence thresholds using species accumulation curves. The results from this study demonstrate the usefulness of BirdNET at estimating long-term grassland bird species richness at default confidence scores, however, obtaining accurate abundance estimates for uncommon bird species may require validation with traditional methods.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1998

Characterization and detection of Anopheles vestitipennis and Anopheles punctimacula (Diptera: Culicidae) larval habitats in Belize with field survey and SPOT satellite imagery

Surveys of larval habitats of Anopheles vestitipennis and Anopheles punctimacula were conducted in Belize, Central America. Habitat analysis and classification resulted in delineation of eight habitat types defined by dominant life forms and hydrology. Percent cover of tall dense macrophytes, shrubs, open water, and pH were significantly different between sites with and without An. vestitipennis. For An. punctimacula, percent cover of tall dense macrophytes, trees, detritus, open water, and water depth were significantly different between larvae positive and negative sites. The discriminant function for An. vestitipennis correctly predicted the presence of larvae in 65% of sites and correctly predicted the absence of larvae in 88% of sites. The discriminant function for An. punctimacula correctly predicted 81% of sites for the presence of larvae and 45% for the absence of larvae. Canonical discriminant analysis of the three groups of habitats (An. vestitipennis positive; An. punctimacula positive; all negative) confirmed that while larval habitats of An. punctimacula are clustered in the tree dominated area, larval habitats of An. vestitipennis were found in both tree dominated and tall dense macrophyte dominated environments. The forest larval habitats of An. vestitipennis and An. punctimacula seem to be randomly distributed among different forest types. Both species tend to occur in denser forests with more detritus, shallower water, and slightly higher pH. Classification of dry season (February) SPOT multispectral satellite imagery produced 10 land cover types with the swamp forest and tall dense marsh classes being of particular interest. The accuracy assessment showed that commission errors for the tall, dense marsh and swamp forest appeared to be minor; but omission errors were significant, especially for the swamp forest (perhaps because no swamp forests are flooded in February). This means that where the classification indicates there are An. vestitipennis breeding sites, they probably do exist; but breeding sites in many locations are not identified and could be more abundant than indicated.

NASA Discipline General Space Life Sciences↗

NASA NTRS2004

Functional Groups Based on Leaf Physiology: Are they Spatially and Temporally Robust?

The functional grouping hypothesis, which suggests that complexity in ecosystem function can be simplified by grouping species with similar responses, was tested in the Florida scrub habitat. Functional groups were identified based on how species in fire maintained Florida scrub regulate exchange of carbon and water with the atmosphere as indicated by both instantaneous gas exchange measurements and integrated measures of function (%N, delta C-13, delta N-15, C-N ratio). Using cluster analysis, five distinct physiologically-based functional groups were identified in the fire maintained scrub. These functional groups were tested to determine if they were robust spatially, temporally, and with management regime. Analysis of Similarities (ANOSIM), a non-parametric multivariate analysis, indicated that these five physiologically-based groupings were not altered by plot differences (R = -0.115, p = 0.893) or by the three different management regimes; prescribed burn, mechanically treated and burn, and fire-suppressed (R = 0.018, p = 0.349). The physiological groupings also remained robust between the two climatically different years 1999 and 2000 (R = -0.027, p = 0.725). Easy-to-measure morphological characteristics indicating functional groups would be more practical for scaling and modeling ecosystem processes than detailed gas-exchange measurements, therefore we tested a variety of morphological characteristics as functional indicators. A combination of non-parametric multivariate techniques (Hierarchical cluster analysis, non-metric Multi-Dimensional Scaling, and ANOSIM) were used to compare the ability of life form, leaf thickness, and specific leaf area classifications to identify the physiologically-based functional groups. Life form classifications (ANOSIM; R = 0.629, p 0.001) were able to depict the physiological groupings more adequately than either specific leaf area (ANOSIM; R = 0.426, p = 0.001) or leaf thickness (ANOSIM; R 0.344, p 0.001). The ability of life forms to depict the physiological groupings was improved by separating the parasitic Ximenia americana from the shrub category (ANOSIM; R = 0.794, p = 0.001). Therefore, a life form classification including parasites was determined to be a good indicator of the physiological processes of scrub species, and would be a useful method of grouping for scaling physiological processes to the ecosystem level.

Foster, Tammy E.↗

NASA NTRS2006

Automated Classification of Thermal Infrared Spectra Using Self-organizing Maps

Existing and planned space missions to a variety of planetary and satellite surfaces produce an ever increasing volume of spectral data. Understanding the scientific informational content in this large data volume is a daunting task. Fortunately various statistical approaches are available to assess such data sets. Here we discuss an automated classification scheme based on Kohonen Self-organizing maps (SOM) we have developed. The SUM process produces an output layer were spectra having similar properties lie in close proximity to each other. One major effort is partitioning this output layer into appropriate regions. This is prefonned by defining dosed regions based upon the strength of the boundaries between adjacent cells in the SOM output layer. We use the Davies-Bouldin index as a measure of the inter-class similarities and intra-class dissimilarities that determines the optimum partition of the output layer, and hence number of SOM clusters. This allows us to identify the natural number of clusters formed from the spectral data. Mineral spectral libraries prepared at Arizona State University (ASU) and John Hopkins University (JHU) are used to test and evaluate the classification scheme. We label the library sample spectra in a hierarchical scheme with class, subclass, and mineral group names. We use a portion of the spectra to train the SOM, i.e. produce the output layer, while the remaining spectra are used to test the SOM. The test spectra are presented to the SOM output layer and assigned membership to the appropriate cluster. We then evaluate these assignments to assess the scientific meaning and accuracy of the derived SOM classes as they relate to the labels. We demonstrate that unsupervised classification by SOMs can be a useful component in autonomous systems designed to identify mineral species from reflectance and emissivity spectra in the therrnal IR.

Roush, Ted L.↗

NASA NTRS2015

Excited Vibrational Level Rotational Constants for SiC2: A Sensitive Molecular Diagnostic for Astrophysical Conditions

Silacyclopropynylidene, SiC2, is a known and highly abundant circumstellar molecule. Its spectrum has been established as a major component of lines observed toward the carbon-rich star IRC +10216 (CW Leonis). It has been detected in its low-lying v(sub 3) = 1 and 2 vibrational states as well as in various isotopic compositions. Increasing sensitivity and spatial resolution will enable many more emission or absorption lines to be detected. In order to detect new molecular species, unassigned lines of known species must be identified. This work uses established ab initio quartic force fields to produce data necessary for this classification of lines related to SiC2. Agreement between the theoretical vibrational frequencies and known rotational and spectroscopic constants is quite good, as good as 5 cm(exp -1) and 3 MHz, respectively in some cases. Additionally, experimentally unknown vibrational frequencies and rotational constants are provided for the first overtones and combination bands in addition to 3(sub v3), the second overtone of the low-lying antisymmetric stretch/carbide rotation mode. Frequencies of v(sub 3) = 3 low-J rotational transitions of the main isotopic species are also estimated from published data for v(sub 3) ≤ 2. Further, we determine rotational and centrifugal distortion parameters for which in most cases vibrational effects due to the v(sub 3) mode were reduced to first, and in several cases also to second order. These values may approximate equilibrium values better than the ground state values. The data produced herein will aid in the experimental and observational characterization of this known astromolecule in order to identify some of the unassigned lines for a known entity.

Astrochemistry↗

NASA NTRS2023

Coronado Ecological Conservation: Assessing Vegetation Change Due to Border Wall Construction and Shifting Social Trails

Species monitoring is essential for mitigating the impacts of plant invasion, such as radical changes in an area’s ecosystem, degraded soil health, increased wildfire severity, landslides, and increased flooding. For this project, NASA DEVELOP partnered with the National Park Service (NPS) to investigate invasive species in disturbed lands: specifically, areas affected by off-trail travel and U.S.-Mexico border construction activities. The team assessed how construction has impacted the distribution of Lehmann’s lovegrass and Russian thistle invasives throughout Coronado National Memorial, AZ from 1986-2022. Using data from Landsat 5 and 8, Sentinel-2, NAIP, and PlanetScope, the team computed NDVI, NDMI, MSAVI2, EVI, and Tasseled Cap Wetness, Brightness, and Greenness transformations as vegetation health indicators to input into various machine learning algorithms. To minimize noise, the team conducted Principal Component Analysis on vegetation indices and spectral bands before running k-means clustering and random forest classification algorithms. Between all datasets, the team found that the median area fully overtaken by invasive plants was 5.37% of the park’s total area in 2022. The NPS will use end products to help increase restoration efforts in disturbed areas with high concentrations of invasive plants, and this project can serve as a jumping off point for future invasive species monitoring. The NPS’s collection of ground data for 2022-2023, in conjunction with future data collection, will notably improve the accuracy of classification models, leading to more precise monitoring of invasive species spread over time.

Coronado National Memorial↗

NASA NTRS1996

Chemical Characteristics of Continental Outflow Over the Tropical South Atlantic Ocean from Brazil and Africa

The chemical characteristics of air parcels over the tropical South Atlantic during September - October 1992 are summarized by analysis of aged marine and continental outflow classifications. Positive correlations between CO and CH3CL and minimal enhancements of C2CL40, and various ChloroFluoroCarbon (CFC) species in air parcels recently advected over the South Atlantic basin strongly suggest an impact on tropospheric chemistry from biomass burning on adjacent continental areas of Brazil and Africa. Comparison of the composition of aged Pacific air with aged marine air over the South Atlantic basin from 0.3 to 12.5 km altitude indicates potential accumulation of long-lived species during the local dry season. This may amount to enhancements of up to two-fold for C2H6, 30% for CO, and 10% for CH3Cl. Nitric oxide and NO(x) were significantly enhanced (up to approx. 1 part per billion by volume (ppbv)) above 10 km altitude and poorly correlated with CO and CH3Cl. In addition, median mixing ratios of NO and NO(x) were essentially identical in aged marine and continental outflow air masses. It appears that in addition to biomass burning, lightning or recycled reactive nitrogen may be an important source of NO(x) to the upper troposphere. Methane exhibited a monotonic increase with altitude from approx. 1690 to 1720 ppbv in both aged marine and continental outflow air masses. The largest mixing ratios in the upper troposphere were often anticorrelated with CO, CH3Cl, and CO2, suggesting CH, contributions from natural sources. We also argue, based on CH4/CO ratios and relationships with various hydrocarbon and CFC species, that inputs from biomass burning and the northern hemisphere are unlikely to be the dominant sources of CO, CH4 and C2H6 in aged marine air. Emissions from urban areas would seem to be necessary to account for the distribution of at least CH4 and C2H6. Over the African and South American continents an efficient mechanism of convective vertical transport coupled with large-scale circulations conveys biomass burning, urban, and natural emissions to the upper troposphere over the South Atlantic basin. Slow subsidence over the eastern South Atlantic basin may play an important role in establishing and maintaining the rather uniform vertical distribution of long-lived species over this region. The common occurrence of values greater than 1 for the ratio CH3OOH/H2O2 in the upper troposphere suggests that precipitation scavenging effectively removed highly water soluble gases (H2O2, HNO3, HCOOH, and CH3COOH) and aerosols during vertical convective transport over the continents. However, horizontal injection of biomass burning products over the South Atlantic, particularly water soluble species and aerosol particles, was frequent below 6 km altitude.

Talbot, R. W.↗

NASA NTRS2024

Rhode Island Ecological Conservation: Methods for Monitoring Rhode Island Habitats: Contributing to a Framework for Targeted Conservation and Management

Global avian population decline since the 1970s is largely attributable to habitat loss and degradation from anthropogenic disturbances. NASA DEVELOP’s Rhode Island Ecological Conservation team partnered with the Audubon Society of Rhode Island to compute land use land cover (LULC) maps of Rhode Island to aid in the conservation of the state’s 140 bird species. This project aimed to support the partner’s land acquisition strategies with updated and specific LULC classifications showing potential bird-habitat locations across the state. We incorporated remotely sensed data from Landsat 8 and 9 Operational Land Imager (OLI) into LULC maps using unsupervised classification techniques in ArcGIS Pro and supervised classification in Google Earth Engine. We generated six land classifications for 2023, which showed land cover dominated by upland habitats (forests, scrub/shrub, and grasslands), followed by development. We used TerrSet’s Land Change Modeler to forecast LULC change through 2043, using 2011 and 2021 National Land Cover Database (NLCD) land cover maps derived from Landsat 8 and 9 imagery. Project results suggest that non-urban upland and wetland habitats will decrease over time, while development will continue to encroach on non-urban avian habitats. Our maps and associated data will allow for more efficient land acquisition and management efforts to support avian habitat conservation across Rhode Island. Our study shows that data acquisition and processing from open data sources is feasible and further analysis can be done through GIS classification tools. More analysis is needed beyond this study to obtain more detailed land cover maps, though Audubon can aid its targeted conservation efforts with our current, historic, and forecasted LULC maps.

Remote sensing↗

NASA NTRS2011

Canopy Spectral Invariants: Application to Classification of Forest Types from Hyperspectral Data - Part 2

Many studies have been conducted to demonstrate the ability of hyperspectral data to discriminate plant dominant species. Most of them have employed the use of empirically based techniques, which are site specific, requires some initial training based on characteristics of known leaf and/or canopy spectra and therefore may not be extendable to operational use or adapted to changing or unknown land cover. In this paper we propose a physically based approach for separation of dominant forest type using hyperspectral data. The radiative transfer theory of canopy spectral invariants underlies the approach, which facilitates parameterization of the canopy reflectance in terms of the leaf spectral scattering and two spectrally invariant and structurally varying variables - recollision and directional escape probabilities. The methodology is based on the idea of retrieving spectrally invariant parameters from hyperspectral data first, and then relating their values to structural characteristics of three-dimensional canopy structure. Theoretical and empirical analyses of ground and airborne data acquired by Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) over two sites in New England, USA, suggest that the canopy spectral invariants convey information about canopy structure at both the macro- and micro-scales. The total escape probability (one minus recollision probability) varies as a power function with the exponent related to the number of nested hierarchical levels present in the pixel. Its base is a geometrical mean of the local total escape probabilities and accounts for the cumulative effect of canopy structure over a wide range of scales. The ratio of the directional to the total escape probability becomes independent of the number of hierarchical levels and is a function of the canopy structure at the macro-scale such as tree spatial distribution, crown shape and size, within-crown foliage density and ground cover. These properties allow for the natural separation of dominant forest classes based on the location of points on the total escape probability vs the ratio log-log plane.

Schull, M. A.↗

NASA NTRSDate not supplied

Congruence of Clusters Defined By Whole Genome Sequencing and MALDI-TOF for Bacteria Isolated From Cleanrooms

Introduction: Oligotrophic conditions can render cleanrooms inhospitable to microbes. Despite these constraints, fungi and bacteria are frequently isolated from surfaces in astromaterials cleanrooms at the Johnson Space Center. Bacillus species are of particular concern because endospores belonging to this genus are resilient and can affect astromaterials. Current monitoring programs rely on 16S rRNA sequencing and the VITEK2 Compact system. These methods have limited power to resolve Bacillus species. Matrix-assisted laser desorption - time of flight mass spectrometry (MALDI-TOF MS), provides a rapid, low cost, method of identifying bacterial isolates and has a higher resolution than 16S rRNA sequencing, particularly for Bacillus species; however, few studies have compared this method to the industry gold standard, whole genome sequencing (WGS). Methods: Based on 16S rRNA classification, we selected 14 isolates for analysis with MALDI-TOF and WGS. Mass spectra were generated with MALDI-TOF MS and processed with custom scripts to identify clusters of closely related isolates and calculate a matrix of pairwise cosine similarity scores. Hybrid Illumina and Nanopore sequencing were used to generate draft genomes. Pairwise similarity scores were calculated from these genomes based on the average amino acid identity (AAI) predicted from single copy core genes. Congruence of clustering between these methods, was assessed by calculating adjusted Rand and Wallace coefficients. Results: Clusters of species generated from MALDI-TOF MS showed good agreement of phylotypes generated with WGS. Pairs of strains that were > 94% similar to each other in terms of predicted amino acid sequences consistently showed cosine similarities of mass spectra > 0.65 and, of the 9 clusters identified with WGS, 8 were identical with MALDI-TOF. This corresponds to an adjusted Rand index of 0.95 and a 95% confidence interval of 0.80 – 1.00 for adjusted Wallace coefficients. The only discordance was for a pair of isolates that were classified as Paenibacillus species. This pair showed relatively high similarity (0.84) in terms of MALDI-TOF MS but only 85% similarity in terms of AAI. Conclusion: This study shows that MALDI-TOF and WGS exhibit a similar ability to delineate Bacillus species isolated from cleanrooms and taxonomic units described by these two methods are consistent with one another. Since MALDI-TOF MS is low in cost and high in throughput, this approach appears to be an ideal option for routine microbial monitoring and identifying Bacillus species.

Farnaz Mazhari↗

DOE OSTI2024

Avian Activity Classification Using Recurrent Networks to Fuse Videos with Metadata on Imbalanced Datasets

Activity classification plays a crucial role in various real-life scenarios involving both humans and animals. There is an increasing need for precise activity classification focused on avian-solar interactions, as the usage of solar energy facilities, such as photovoltaic array power stations, has been observed to impact bird species richness, behavior, and activity. However, there has been no work to develop an automated system to monitor and classify these avian-solar interactions. All current methods rely on human observers, which is time and human resources costly and subject to errors related to searcher efficiency. With the recent success of Deep Learning models in activity classification problems, this paper develops a recurrent neural network-based model to automatically classify six avian activities around solar energy facilities. Our proposed model integrates critical feature engineering metadata with video frame data, enabling improved learning and more accurate activity classification. Furthermore, we address the challenge of data imbalance during training and demonstrate the efficacy of our model in detecting and classifying different activities within video tracks. Additionally, we analyze the saliency/backpropagation map of the trained proposed model and validate its decision-making rationale.

Avian activity classification; bidirectional LSTM;↗