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NASA NTRS2008

Cell-Detection Technique for Automated Patch Clamping

A unique and customizable machinevision and image-data-processing technique has been developed for use in automated identification of cells that are optimal for patch clamping. [Patch clamping (in which patch electrodes are pressed against cell membranes) is an electrophysiological technique widely applied for the study of ion channels, and of membrane proteins that regulate the flow of ions across the membranes. Patch clamping is used in many biological research fields such as neurobiology, pharmacology, and molecular biology.] While there exist several hardware techniques for automated patch clamping of cells, very few of those techniques incorporate machine vision for locating cells that are ideal subjects for patch clamping. In contrast, the present technique is embodied in a machine-vision algorithm that, in practical application, enables the user to identify good and bad cells for patch clamping in an image captured by a charge-coupled-device (CCD) camera attached to a microscope, within a processing time of one second. Hence, the present technique can save time, thereby increasing efficiency and reducing cost. The present technique involves the utilization of cell-feature metrics to accurately make decisions on the degree to which individual cells are "good" or "bad" candidates for patch clamping. These metrics include position coordinates (x,y) in the image plane, major-axis length, minor-axis length, area, elongation, roundness, smoothness, angle of orientation, and degree of inclusion in the field of view. The present technique does not require any special hardware beyond commercially available, off-the-shelf patch-clamping hardware: A standard patchclamping microscope system with an attached CCD camera, a personal computer with an imagedata- processing board, and some experience in utilizing imagedata- processing software are all that are needed. A cell image is first captured by the microscope CCD camera and image-data-processing board, then the image data are analyzed by software that implements the present machine-vision technique. This analysis results in the identification of cells that are "good" candidates for patch clamping (see figure). Once a "good" cell is identified, a patch clamp can be effected by an automated patchclamping apparatus or by a human operator. This technique has been shown to enable reliable identification of "good" and "bad" candidate cells for patch clamping. The ultimate goal in further development of this technique is to combine artificial-intelligence processing with instrumentation and controls in order to produce a complete "turnkey" automated patch-clamping system capable of accurately and reliably patch clamping cells with a minimum intervention by a human operator. Moreover, this technique can be adapted to virtually any cellular-analysis procedure that includes repetitive operation of microscope hardware by a human.

McDowell, Mark↗

DOE OSTI2023

POWTEX visits POWGEN

The high-intensity time-of-flight (TOF) neutron diffractometer POWTEX for powder and texture analysis is currently being built prior to operation in the eastern guide hall of the research reactor FRM II at Garching close to Munich, Germany. Because of the world-wide 3 He crisis in 2009, the authors promptly initiated the development of 3 He-free detector alternatives that are tailor-made for the requirements of large-area diffractometers. Herein is reported the 2017 enterprise to operate one mounting unit of the final POWTEX detector on the neutron powder diffractometer POWGEN at the Spallation Neutron Source located at Oak Ridge National Laboratory, USA. As a result, presented here are the first angular- and wavelength-dependent data from the POWTEX detector, unfortunately damaged by a 50 g shock but still operating, as well as the efforts made both to characterize the transport damage and to successfully recalibrate the voxel positions in order to yield nonetheless reliable measurements. Also described is the current data reduction process using the PowderReduceP2D algorithm implemented in Mantid [Arnold et al. (2014). Nucl. Instrum. Methods Phys. Res. A , 764 , 156–166]. The final part of the data treatment chain, namely a novel multi-dimensional refinement using a modified version of the GSAS-II software suite [Toby & Von Dreele (2013). J. Appl. Cryst. 46 , 544–549], is compared with a standard data treatment of the same event data conventionally reduced as TOF diffraction patterns and refined with the unmodified version of GSAS-II . This involves both determining the instrumental resolution parameters using POWGEN's powdered diamond standard sample and the refinement of a friendly-user sample, BaZn(NCN) 2 . Although each structural parameter on its own looks similar upon comparing the conventional (1D) and multi-dimensional (2D) treatments, also in terms of precision, a closer view shows small but possibly significant differences. For example, the somewhat suspicious proximity of the a and b lattice parameters of BaZn(NCN) 2 crystallizing in Pbca as resulting from the 1D refinement (0.008 Å) is five times less pronounced in the 2D refinement (0.038 Å). Similar features are found when comparing bond lengths and bond angles, e.g. the two N—C—N units are less differently bent in the 1D results (173 and 175°) than in the 2D results (167 and 173°). The results are of importance not only for POWTEX but also for other neutron TOF diffractometers with large-area detectors, like POWGEN at the SNS or the future DREAM beamline at the European Spallation Source.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Digital Twin for Chemical Science (DTCS) v0.01

Directly visualizing the trajectories of chemistry can unravel novel insights into the behavior of catalysts, gas phase reactions, photo-induced dynamics, and building blocks for quantum information processing. The ability of explicitly identifying, tracking, and tagging the exchange of matter, hence the annihilation and creation of new chemical species, can be best realized through a close coupling of theory and experiment. While the synchrotron-based characterization facilities propelled rapidly in its hardware, providing higher brightness, better resolution, and more precision, the software infrastructure is lagging. We developed DTCS (Digital Twin for Chemical Science) v.01, a central platform that faithfully mimics advanced instrumentations in Scientific User Facilities, by solving a variety of technical challenges in data acquisition, analysis, and model-driven interpretation. Rooted in physics and accelerated by AI, we validated this concept by direct comparison with precise experimental X-ray Photoelectron Spectroscopy (XPS) observations using a ubiquitous metal-water interfacial scenario, i.e., Ag/H2O as our main narrative. The DTCS v.01 input mirrors how the bench chemists work, with the output directly linked to the end station computer, thereby providing a user-friendly, knowledge-driven, and accessible user experience with mechanistic insights standardized in a way that are ready to be published, versioned, and transferred flexibly.

Qian, Jin↗

DOE OSTI2023

IRIS-HEP Strategic Plan for the Next Phase of Software Upgrades for HL-LHC Physics

The quest to understand the fundamental building blocks of nature and their interactions is one of the oldest and most ambitious of human scientific endeavors. CERN's Large Hadron Collider (LHC) represents a huge step forward in this quest. The discovery of the Higgs boson, the observation of exceedingly rare decays of $B$ mesons, and stringent constraints on many viable theories of physics beyond the Standard Model (SM) demonstrate the great scientific value of the LHC physics program. The next phase of this global scientific project will be the High-Luminosity LHC (HL-LHC) which will collect data starting circa 2029 and continue through the 2030s. The primary science goal is to search for physics beyond the SM and, should it be discovered, to study its implications. In the HL-LHC era, the ATLAS and CMS experiments will record around 100 times as many collisions as were used to discover the Higgs boson (and at twice the energy). Both NSF and DOE are making large detector upgrade investments so the HL-LHC can operate in this high-rate environment. Similar investment in software R&D for acquiring, managing, processing and analyzing HL-LHC data is critical to maximize the return-on-investment in the upgraded accelerator and detectors. This report presents a strategic plan for a possible second 5-year funded phase (2023 through 2028) for the Institute for Research and Innovation in Software for High Energy Physics (IRIS-HEP) which will close remaining software and computing gaps to deliver HL-LHC science.

43 PARTICLE ACCELERATORS↗

NASA NTRS1987

Wetlands Survey

Ducks Unlimited, Inc. is dedicated to preservation of the world's waterfowl. Current inventories of wetland resources are crucial to effective waterfowl management. They contracted with NASA to use data from the LANDSAT satellites Thematic Mapper (TM), an advanced Earth scanning instrument that collects data in seven bands of the spectrum utilizing the Earth Resources Laboratory Applications Software (ELAS). The TM measures and records six values of light energy reflected from Earth and one value of heat energy as it scans the Earth below. On each orbital sweep, sensors produce a series of digital scenes representing features of Earth segments measuring about 100 by 110 miles, each scene covering about eight million acres, and each containing some 40 million bits of information called picture elements or pixels. They are computer processed and the resulting mosaic is projected on a digital display device.

Source record↗

DOE OSTI2023

Multispectral and thermal surface imagery and surface elevation mosaics - SGP July 2022

This data set contains high-resolution image products (orthomosaics) acquired from midsized uncrewed aerial systems that have been processed for value-added quality. The instrument itself, a multispectral imager, the Altum by Micasense, captures six spectral bands (red, green blue, NIR, red edge, and LWIR/thermal1) as radiance, which is converted to reflectance via custom code. The code used to develop these images first uses tools from the Micasense Python library2 to apply dark level corrections, row gradient corrections, and radiometric corrections. Next, it uses the processing API from Agisoft Metashape software to align and mosaic the processed imagery, following the processes developed by the USGS' structure from motion workflow documentation.3 Captures at different altitudes (recorded in MSL) produce an orthomosaic, a tif image containing information related to the six spectral bands, and a digital elevation model (DEM), a tif image containing information related to the elevation of the surveyed terraine. Metadata included in every image can be used to extract lat, lon, and reflectance values. 1 https://www.arm.gov/publications/tech_reports/handbooks/doe-sc-arm-tr-281.pdf 2 https://micasense.github.io/imageprocessing/MicaSense%20Image%20Processing%20Setup.html 3 https://pubs.usgs.gov/of/2021/1039/ofr20211039.pdf

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1987

The development of an air motion measurement system for NASA's Electra aircraft

The development of the Turbulent Air Motion Measurement System (TAMMS), which is to measure dynamical and photochemical processes over a wide range of spatial and temporal scales, is examined. The composition and operation of the TAMMS subsystems, which include (1) fast-response meteorological sensors; (2) a boom/inertial navigation system; (3) baseline meteorological sensors; (4) an analog/digital interface; (5) control and data acquisition; and (6) data/reduction and spectral analysis software, are described. The planned flight testing and calibration of the TAMMS are discussed. The TAMMS platform wil be able to estimate the turbulent fluxes of heat, moisture, momentum, and any chemical species for which fast-response instrumentation is available.

Ritter, J.↗

NASA NTRS2003

NASA Tech Briefs, January 2003

Topics covered include: Optoelectronic Tool Adds Scale Marks to Photographic Images; Compact Interconnection Networks Based on Quantum Dots; Laterally Coupled Quantum-Dot Distributed-Feedback Lasers; Bit-Serial Adder Based on Quantum Dots; Stabilized Fiber-Optic Distribution of Reference Frequency; Delay/Doppler-Mapping GPS-Reflection Remote-Sensing System; Ladar System Identifies Obstacles Partly Hidden by Grass; Survivable Failure Data Recorders for Spacecraft; Fiber-Optic Ammonia Sensors; Silicon Membrane Mirrors with Electrostatic Shape Actuators; Nanoscale Hot-Wire Probes for Boundary-Layer Flows; Theodolite with CCD Camera for Safe Measurement of Laser-Beam Pointing; Efficient Coupling of Lasers to Telescopes with Obscuration; Aligning Three Off-Axis Mirrors with Help of a DOE; Calibrating Laser Gas Measurements by Use of Natural CO2; Laser Ranging Simulation Program; Micro-Ball-Lens Optical Switch Driven by SMA Actuator; Evaluation of Charge Storage and Decay in Spacecraft Insulators; Alkaline Capacitors Based on Nitride Nanoparticles; Low-EC-Content Electrolytes for Low-Temperature Li-Ion Cells; Software for a GPS-Reflection Remote-Sensing System; Software for Building Models of 3D Objects via the Internet; "Virtual Cockpit Window" for a Windowless Aerospacecraft; CLARAty Functional-Layer Software; Java Library for Input and Output of Image Data and Metadata; Software for Estimating Costs of Testing Rocket Engines; Energy-Absorbing, Lightweight Wheels; Viscoelastic Vibration Dampers for Turbomachine Blades; Soft Landing of Spacecraft on Energy-Absorbing Self-Deployable Cushions; Pneumatically Actuated Miniature Peristaltic Vacuum Pumps; Miniature Gas-Turbine Power Generator; Pressure-Sensor Assembly Technique; Wafer-Level Membrane-Transfer Process for Fabricating MEMS; A Reactive-Ion Etch for Patterning Piezoelectric Thin Film; Wavelet-Based Real-Time Diagnosis of Complex Systems; Quantum Search in Hilbert Space; Analytic Method for Computing Instrument Pointing Jitter; and Semiselective Optoelectronic Sensors for Monitoring Microbes.

Source record↗

DOE OSTI2023

Status of DUNE Offline Computing

We summarize the status of Deep Underground Neutrino Experiment (DUNE) Offline Software and Computing program. We describe plans for the computing infrastructure needed to acquire, catalog, reconstruct, simulate and analyze the data from the DUNE experiment and its prototypes in pursuit of the experiment's physics goals of precision measurements of neutrino oscillation parameters, detection of astrophysical neutrinos, measurement of neutrino interaction properties and searches for physics beyond the Standard Model. In contrast to traditional HEP computational problems, DUNE's Liquid Argon Time Projection Chamber data consist of simple but very large (many GB) data objects which share many characteristics with astrophysical images. We have successfully reconstructed and simulated data from 4% prototype detector runs at CERN. The data volume from the full DUNE detector, when it starts commissioning late in this decade will present memory management challenges in conventional processing but significant opportunities to use advances in machine learning and pattern recognition as a frontier user of High Performance Computing facilities capable of massively parallel processing. Our goal is to develop infrastructure resources that are flexible and accessible enough to support creative software solutions as HEP computing evolves.

43 PARTICLE ACCELERATORS↗

NASA NTRS2007

Pointing History Engine for the Spitzer Space Telescope

The Pointing History Engine (PHE) is a computer program that provides mathematical transformations needed to reconstruct, from downlinked telemetry data, the attitude of the Spitzer Space Telescope (formerly known as the Space Infrared Telescope Facility) as a function of time. The PHE also serves as an example for development of similar pointing reconstruction software for future space telescopes. The transformations implemented in the PHE take account of the unique geometry of the Spitzer telescope-pointing chain, including all data on relative alignments of components, and all information available from attitude-determination instruments. The PHE makes it possible to coordinate attitude data with observational data acquired at the same time, so that any observed astronomical object can be located for future reference and re-observation. The PHE is implemented as a subroutine used in conjunction with telemetry-formatting services of the Mission Image Processing Laboratory of NASA s Jet Propulsion Laboratory to generate the Boresight Pointing History File (BPHF). The BPHF is an archival database designed to serve as Spitzer s primary astronomical reference documenting where the telescope was pointed at any time during its mission.

Bayard, David↗

NASA NTRS2000

Description of the AILS Alerting Algorithm

This document provides a complete description of the Airborne Information for Lateral Spacing (AILS) alerting algorithms. The purpose of AILS is to provide separation assurance between aircraft during simultaneous approaches to closely spaced parallel runways. AILS will allow independent approaches to be flown in such situations where dependent approaches were previously required (typically under Instrument Meteorological Conditions (IMC)). This is achieved by providing multiple levels of alerting for pairs of aircraft that are in parallel approach situations. This document#s scope is comprehensive and covers everything from general overviews, definitions, and concepts down to algorithmic elements and equations. The entire algorithm is presented in complete and detailed pseudo-code format. This can be used by software programmers to program AILS into a software language. Additional supporting information is provided in the form of coordinate frame definitions, data requirements, calling requirements as well as all necessary pre-processing and post-processing requirements. This is important and required information for the implementation of AILS into an analysis, a simulation, or a real-time system.

Samanant, Paul↗

NASA NTRS2011

Jitter Controller Software

Sinusoidal jitter is produced by simply modulating a clock frequency sinusoidally with a given frequency and amplitude. But this can be expressed as phase jitter, frequency jitter, or cycle-to-cycle jitter, rms or peak, absolute units, or normalized to the base clock frequency. Jitter using other waveforms requires calculating and downloading these waveforms to an arbitrary waveform generator, and helping the user manage relationships among phase jitter crest factor, frequency jitter crest factor, and cycle-to-cycle jitter (CCJ) crest factor. Software was developed for managing these relationships, automatically configuring the generator, and saving test results documentation. Tighter management of clock jitter and jitter sensitivity is required by new codes that further extend the already high performance of space communication links, completely correcting symbol error rates higher than 10 percent, and therefore typically requiring demodulation and symbol synchronization hardware to operating at signal-to-noise ratios of less than one. To accomplish this, greater demands are also made on transmitter performance, and measurement techniques are needed to confirm performance. It was discovered early that sinusoidal jitter can be stepped on a grid such that one can connect points by constant phase jitter, constant frequency jitter, or constant cycle-cycle jitter. The tool automates adherence to a grid while also allowing adjustments off-grid. Also, the jitter can be set by the user on any dimension and the others are calculated. The calculations are all recorded, allowing the data to be rapidly plotted or re-plotted against different interpretations just by changing pointers to columns. A key advantage is taking data on a carefully controlled grid, which allowed a single data set to be post-analyzed many different ways. Another innovation was building a software tool to provide very tight coupling between the generator and the recorded data product, and the operator's worksheet. Together, these allowed the operator to sweep the jitter stimulus quickly along any of three dimensions and focus on the response of the system under test (response was jitter transfer ratio, or performance degradation to the symbol or codeword error rate). Additionally, managing multi-tone and noise waveforms automated a tedious manual process, and provided almost instantaneous decision- making control over test flow. The code was written in LabVIEW, and calls Agilent instrument drivers to write to the generator hardware.

Lansdowne, Chatwin↗

NASA NTRS2017

Archive Management of NASA Earth Observation Data to Support Cloud Analysis

NASA collects, processes and distributes petabytes of Earth Observation (EO) data from satellites, aircraft, in situ instruments and model output, with an order of magnitude increase expected by 2024. Cloud-based web object storage (WOS) of these data can simplify the execution of such an increase. More importantly, it can also facilitate user analysis of those volumes by making the data available to the massively parallel computing power in the cloud. However, storing EO data in cloud WOS has a ripple effect throughout the NASA archive system with unexpected challenges and opportunities. One challenge is modifying data servicing software (such as Web Coverage Service servers) to access and subset data that are no longer on a directly accessible file system, but rather in cloud WOS. Opportunities include refactoring of the archive software to a cloud-native architecture; virtualizing data products by computing on demand; and reorganizing data to be more analysis-friendly.

Lynnes, Christopher↗

NASA NTRS2017

Archive Management of NASA Earth Observation Data to Support Cloud Analysis

Lynnes, Christopher↗

DOE OSTI2021

Cylinder Occupancy and Measurement Suite

This software automatically records data from the Unattended Cylinder Verification Station, determines the state of the instrument, captures images of uranium hexafluoride shipment cylinders, and determines their weight. The code has been developed primarily for the International Atomic Energy Agency, but this type of instrument could be of interest to any facility operator in the uranium supply chain that handles uranium hexafluoride shipment cylinders (e.g. the 30B and 48Y cylinder). Operators may be interested in having this instrument confirm shipper declared measurement values upon receipt of a cylinder. They may also use it to aid in process monitoring if the quantity of material in the cylinder changes due to a processing activity.

Stewart, Scott L↗

NASA NTRS1999

Contamination Effects on EUV Optics

During ground-based assembly and upon exposure to the space environment, optical surfaces accumulate both particles and molecular condensibles, inevitably resulting in degradation of optical instrument performance. Currently, this performance degradation (and the resulting end-of-life instrument performance) cannot be predicted with sufficient accuracy using existing software tools. Optical design codes exist to calculate instrument performance, but these codes generally assume uncontaminated optical surfaces. Contamination models exist which predict approximate end-of-life contamination levels, but the optical effects of these contamination levels can not be quantified without detailed information about the optical constants and scattering properties of the contaminant. The problem is particularly pronounced in the extreme ultraviolet (EUV, 300-1,200 A) and far (FUV, 1,200-2,000 A) regimes due to a lack of data and a lack of knowledge of the detailed physical and chemical processes involved. Yet it is in precisely these wavelength regimes that accurate predictions are most important, because EUV/FUV instruments are extremely sensitive to contamination.

Tveekrem, J.↗

NASA NTRS2017

Atmospheric Correction for Hyperspectral Ocean Color Retrieval with Application to the Hyperspectral Imager for the Coastal Ocean (HICO)

The classical multi-spectral Atmospheric Correction (AC) algorithm is inadequate for the new generation of spaceborne hyperspectral sensors such as NASA's first hyperspectral Ocean Color Instrument (OCI) onboard the anticipated Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) satellite mission. The AC process must estimate and remove the atmospheric path radiance contribution due to the Rayleigh scattering by air molecules and scattering by aerosols from the measured top-of-atmosphere (TOA) radiance, compensate for the absorption by atmospheric gases, and correct for reflection and refraction of the air-sea interface. In this work, we present and evaluate an improved AC for hyperspectral sensors developed within NASA's Sea-viewing Wide Field-of-view Sensor (SeaWiFS) Data Analysis System software package (SeaDAS). The improvement is based on combining the classical AC approach of multi-spectral capabilities to correct for the atmospheric path radiance, extended to hyperspectral, with a gas correction algorithm to compensate for absorbing gases in the atmosphere, including water vapor. The SeaDAS-hyperspectral version is capable of operationally processing the AC of any hyperspectral airborne or spaceborne sensor. The new algorithm development was evaluated and assessed using the Hyperspectral Imager for Coastal Ocean (HICO) scenes collected at the Marine Optical BuoY (MOBY) site, and other SeaWiFS Bio-optical Archive and Storage System (SeaBASS) and AERosol Robotic NETwork - Ocean Color (AERONET-OC) coastal sites. A hyperspectral vicarious calibration was applied to HICO, showing the validity and consistency of HICO's ocean color products. The hyperspectral AC capability is currently available in SeaDAS to the scientific community at https://oceancolor.gsfc.nasa.gov/.

Ocean Color↗

NASA NTRS1994

Galileo mission planning for Low Gain Antenna based operations

The Galileo mission operations concept is undergoing substantial redesign, necessitated by the deployment failure of the High Gain Antenna, while the spacecraft is on its way to Jupiter. The new design applies state-of-the-art technology and processes to increase the telemetry rate available through the Low Gain Antenna and to increase the information density of the telemetry. This paper describes the mission planning process being developed as part of this redesign. Principal topics include a brief description of the new mission concept and anticipated science return (these have been covered more extensively in earlier papers), identification of key drivers on the mission planning process, a description of the process and its implementation schedule, a discussion of the application of automated mission planning tool to the process, and a status report on mission planning work to date. Galileo enhancements include extensive reprogramming of on-board computers and substantial hard ware and software upgrades for the Deep Space Network (DSN). The principal mode of operation will be onboard recording of science data followed by extended playback periods. A variety of techniques will be used to compress and edit the data both before recording and during playback. A highly-compressed real-time science data stream will also be important. The telemetry rate will be increased using advanced coding techniques and advanced receivers. Galileo mission planning for orbital operations now involves partitioning of several scarce resources. Particularly difficult are division of the telemetry among the many users (eleven instruments, radio science, engineering monitoring, and navigation) and allocation of space on the tape recorder at each of the ten satellite encounters. The planning process is complicated by uncertainty in forecast performance of the DSN modifications and the non-deterministic nature of the new data compression schemes. Key mission planning steps include quantifying resource or capabilities to be allocated, prioritizing science observations and estimating resource needs for each, working inter-and intra-orbit trades of these resources among the Project elements, and planning real-time science activity. The first major mission planning activity, a high level, orbit-by-orbit allocation of resources among science objectives, has already been completed; and results are illustrated in the paper. To make efficient use of limited resources, Galileo mission planning will rely on automated mission planning tools capable of dealing with interactions among time-varying downlink capability, real-time science and engineering data transmission, and playback of recorded data. A new generic mission planning tool is being adapted for this purpose.

Gershman, R.↗