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DOE OSTI2025

Design-to-Deployment Continuum Platform for Microscopes and Computing Ecosystems

Science ecosystems with networked computing systems and physical instruments are increasingly being deployed with a goal to achieve the productivity promised by AI-supported remote automation. In support of these efforts, the virtual infrastructure twins (VITs) have been successfully utilized to develop the orchestration codes for these ecosystems without requiring physical access to expensive instruments, such as electron microscopes. Currently, the utility of such a VIT is severely limited by the computing capacity and capability of the computing system used as its host. Furthermore, codes developed on the VIT typically need to be transferred and refactored for production use, particularly, on high-performance systems with accelerators. In response, we develop a design-to-deployment continuum platform wherein a VIT runs natively on the ecosystem's own computing system, and thereby facilitates the continual in-situ testing and transition of codes for production use. Here, we describe the development and testing of software for remote microscope steering and GPU-based image reconstruction using this platform on a multi-GPU computing system networked to Nion microscopes. We demonstrate a continual transition of steering and reconstruction codes developed under VIT platform to production ecosystem deployment.

Al-Najjar, Anees [Oak Ridge National Laboratory (O↗

NASA NTRS2021

The CHIMAERA System for Retrievals of Cloud Top, Optical and Microphysical Properties from Imaging Sensors

Continuity and consistency of geophysical retrieval products obtained from different Earth-observing spaceborne or airborne atmospheric multispectral imagers can be challenging due to inherent differences in the instruments and/or the use of different retrieval algorithms. The Cross-platform HIgh resolution Multi-instrument AtmosphEric Retrieval Algorithms (CHIMAERA) system addresses the latter aspect of the inter-sensor continuity problem for cloud property retrievals by removing retrieval methodology and implementation as a source of inconsistency when applied to instruments that share common measurement capabilities. Transferring an existing retrieval algorithm to a new sensor oftentimes is a nontrivial task, as it is common for an algorithm code to be tightly coupled to the sensor for which it was developed. By creating a clear division between the science algorithm and the instrument I/O codes, CHIMAERA allows easy migration of science algorithms to different sensors. CHIMAERA is built from C and FORTRAN source code, and can operate in a variety of environments ranging from a personal laptop to a high-performance computing environment for near real-time satellite data production. It is highly adaptable, low-maintenance and allows for easy expansion such that adding new instruments into the system requires only instrument-specific I/O and provision of any external lookup tables specific to the instrument's spectral characteristics. CHIMAERA currently supports 14 spaceborne and airborne atmospheric imagers from a single code base, and has been in use since 2007. In this paper we describe the engineering aspects of CHIMAERA and briefly discuss a few examples from its many current applications.

Galina (Gala) Wind↗

DOE OSTI2025

Swap Path Network for Robust Person Search Pre-training

This code corresponds to the WACV25 conference paper, "Swap Path Network for Robust Person Search Pre-training". In that paper, we introduce a new model for the person search task called the Swap Path Net (SPNet). The person search task is a problem in computer vision, where we locate and rank matches to an image of a query person in a set of other images where we want to find them. We also introduce a novel pre-training algorithm specific to the Swap Path Net architecture. The code implements pre-training and fine-tuning of the Swap Path Net (SPNet). This includes ingesting image datasets and updating the weights of the SPNet neural network to train it for the person search task. The repository contains code, configs, and instructions to reproduce all results from the paper.

Jaffe, LucasW [Lawrence Livermore National Laborat↗

NASA NTRS2010

Context Modeler for Wavelet Compression of Spectral Hyperspectral Images

A context-modeling sub-algorithm has been developed as part of an algorithm that effects three-dimensional (3D) wavelet-based compression of hyperspectral image data. The context-modeling subalgorithm, hereafter denoted the context modeler, provides estimates of probability distributions of wavelet-transformed data being encoded. These estimates are utilized by an entropy coding subalgorithm that is another major component of the compression algorithm. The estimates make it possible to compress the image data more effectively than would otherwise be possible. The following background discussion is prerequisite to a meaningful summary of the context modeler. This discussion is presented relative to ICER-3D, which is the name attached to a particular compression algorithm and the software that implements it. The ICER-3D software is summarized briefly in the preceding article, ICER-3D Hyperspectral Image Compression Software (NPO-43238). Some aspects of this algorithm were previously described, in a slightly more general context than the ICER-3D software, in "Improving 3D Wavelet-Based Compression of Hyperspectral Images" (NPO-41381), NASA Tech Briefs, Vol. 33, No. 3 (March 2009), page 7a. In turn, ICER-3D is a product of generalization of ICER, another previously reported algorithm and computer program that can perform both lossless and lossy wavelet-based compression and decompression of gray-scale-image data. In ICER-3D, hyperspectral image data are decomposed using a 3D discrete wavelet transform (DWT). Following wavelet decomposition, mean values are subtracted from spatial planes of spatially low-pass subbands prior to encoding. The resulting data are converted to sign-magnitude form and compressed. In ICER-3D, compression is progressive, in that compressed information is ordered so that as more of the compressed data stream is received, successive reconstructions of the hyperspectral image data are of successively higher overall fidelity.

Kiely, Aaron↗

NASA NTRS2017

Image Navigation and Registration Performance Assessment Evaluation Tools for GOES-R ABI and GLM

The GOES-R Flight Project has developed an Image Navigation and Registration (INR) Performance Assessment Tool Set (IPATS) for measuring Advanced Baseline Imager (ABI) and Geostationary Lightning Mapper (GLM) INR performance metrics in the post-launch period for performance evaluation and long term monitoring. IPATS utilizes a modular algorithmic design to allow user selection of data processing sequences optimized for generation of each INR metric. This novel modular approach minimizes duplication of common processing elements, thereby maximizing code efficiency and speed. Fast processing is essential given the large number of sub-image registrations required to generate INR metrics for the many images produced over a 24 hour evaluation period. This paper describes the software design and implementation of IPATS and provides preliminary test results.

Image registration↗

NASA NTRS2017

Image Navigation and Registration Performance Assessment Evaluation Tools for GOES-R ABI and GLM

image registration↗

NASA NTRS1988

Ray tracing optical analysis of offset solar collector for space station solar dynamic system

OFFSET, a detailed ray tracing computer code, was developed at NASA Lewis Research Center to model the offset solar collector for the Space Station solar dynamic electric power system. This model traces rays from 50 points on the face of the Sun to 10 points on each of the 456 collector facets. The triangular facets are modeled with spherical, parabolic, or toroidal reflective surface contour and surface slope errors. The rays are then traced through the receiver aperture to the walls of the receiver. Images of the collector and of the Sun within the receiver produced by this code provide insight into the collector receiver interface. Flux distribution on the receiver walls, plotted by this code, is improved by a combination of changes to aperture location and receiver tilt angle. Power loss by spillage at the receiver aperture is computed and is considerably reduced by using toroidal facets.

Jefferies, Kent S.↗

NASA NTRS1988

Ray tracing optical analysis of offset solar collector for Space Station solar dynamic system

OFFSET, a detailed ray tracing computer code, was developed at NASA Lewis Research Center to model the offset solar collector for the Space Station solar dynamic electric power system. This model traces rays from 50 points on the face of the sun to 10 points on each of the 456 collector facets. The triangular facets are modeled with spherical, parabolic, or toroidal reflective surface contour and surface slope errors. The rays are then traced through the receiver aperture to the walls of the receiver. Images of the collector and of the sun within the receiver produced by this code provide insight into the collector receiver interface. Flux distribution on the receiver walls, plotted by this code, is improved by a combination of changes to aperture location and receiver tilt angle. Power loss by spillage at the receiver aperture is computed and is considerably reduced by using toroidal facets.

Jefferies, Kent S.↗

NASA NTRS1993

Compensation for the Atmosphere in Radiance Measured by the Airborne Visible/Infrared Imaging Spectrometer and Applications to an Advanced Land Remote Sensing System

The Airborne Visible/Infrared Imaging Spectrometer measures spatial images of the total upwelling spectral radiance from 400 to 2500 nm through 10 nm spectral channels. Quantitative research and application objectives for surface investigations require conversion of the measured radiance to surface reflectance or surface leaving radiance. To calculate apparent surface reflectance an estimation of atmospheric water vapor abundance, cirrus cloud effects, surface pressure elevation and aerosol optical depth is also required. Algorithms for the estimation of these parameters from the AVIRIS data themselves are described. Based upon these determined atmospheric parameters we show an example of the calculation of apparent surface reflectance from the AVIRIS-measured radiance using a radiative transfer code.

Airborne Visible/Infrared Imaging Spectrometer AVI↗

DOE OSTI2026

PlantCV v4: Image analysis software for high‐throughput plant phenotyping

PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data, and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use-case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection.

Schuhl, Haley [Donald Danforth Plant Science Cente↗

DOE OSTI2024

Synergizing human expertise and AI efficiency with language model for microscopy operation and automated experiment design

With the advent of large language models (LLMs), in both the open source and proprietary domains, attention is turning to how to exploit such artificial intelligence (AI) systems in assisting complex scientific tasks, such as material synthesis, characterization, analysis and discovery. Here, we explore the utility of LLMs, particularly ChatGPT4, in combination with application program interfaces (APIs) in tasks of experimental design, programming workflows, and data analysis in scanning probe microscopy, using both in-house developed APIs and APIs given by a commercial vendor for instrument control. We find that the LLM can be especially useful in converting ideations of experimental workflows to executable code on microscope APIs. Beyond code generation, we find that the GPT4 is capable of analyzing microscopy images in a generic sense. At the same time, we find that GPT4 suffers from an inability to extend beyond basic analyses for more in-depth technical experimental design. We argue that an LLM specifically fine-tuned for individual scientific domains can potentially be a better language interface for converting scientific ideations from human experts to executable workflows. Such a synergy between human expertise and LLM efficiency in experimentation can open new doors for accelerating scientific research, enabling effective experimental protocols sharing in the scientific community.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1988

Phenomenological aspects of infrared imaging in aeronautical research

The various factors leading to obtaining a thermography of an aerodynamic body of interest using an infrared imaging camera are scrutinized. Included is a description of how the various heat transfer mechanisms determine the final surface temperature that may be time dependent even for steady state flows. Some constraining factors of the camera are also discussed. Finally, a method is outlined showing how the infrared imaging of aerodynamic configurations may ultimately evolve as a computational fluid dynamics code validation tool.

Gartenberg, Ehud↗

NASA NTRS1990

Space astrophysics with large structures - CASES and P/OF

Space instruments for remote sensing, of the types used for astrophysics and solar-terrestrial physics among many disciplines, will grow to larger physical sizes in the future. The zero-g space environment does not inherently restrict such growth, because relatively lightweight structures can be used. Active servo control of the structures can greatly increase their size for a given mass. The Pinhole/Occulter Facility, a candidate Space Station attached payload, offers an example: it will achieve 0.2 arc s resolution by use of a 50-m baseline for coded-aperture telescopes for hard X-ray and gamma-ray imagers.

Hudson, Hugh S.↗

NASA NTRS1994

A high resolution liquid xenon imaging telescope for 0.3-10 MeV gamma-ray astrophysics: Construction and initial balloon flights

An instrument is described which will provide a direct image of gamma-ray line or continuum sources in the energy range 300 keV to 10 MeV. The use of this instrument to study the celestial distribution of the (exp 26)Al isotope by observing the 1.809 MeV deexcitation gamma-ray line is illustrated. The source location accuracy is 2' or better. The imaging telescope is a liquid xenon time projection chamber coupled with a coded aperture mask (LXe-CAT). This instrument will confirm and extend the COMPTEL observations from the Compton Gamma-Ray Observatory (CGRO) with an improved capability for identifying the actual Galactic source or sources of (exp 26)Al, which are currently not known with certainty. sources currently under consideration include red giants on the asymptotic giant branch (AGB), novae, Type 1b or Type 2 supernovae, Wolf-Rayet stars and cosmic-rays interacting in molecular clouds. The instrument could also identify a local source of the celestial 1.809 MeV gamma-ray line, such as a recent nearby supernova.

Aprile, Elena↗

NASA NTRS2007

A Software Platform for Post-Processing Waveform-Based NDE

Ultrasonic, microwave, and terahertz nondestructive evaluation imaging systems generally require the acquisition of waveforms at each scan point to form an image. For such systems, signal and image processing methods are commonly needed to extract information from the waves and improve resolution of, and highlight, defects in the image. Since some similarity exists for all waveform-based NDE methods, it would seem a common software platform containing multiple signal and image processing techniques to process the waveforms and images makes sense where multiple techniques, scientists, engineers, and organizations are involved. This presentation describes NASA Glenn Research Center's approach in developing a common software platform for processing waveform-based NDE signals and images. This platform is currently in use at NASA Glenn and at Lockheed Martin Michoud Assembly Facility for processing of pulsed terahertz and ultrasonic data. Highlights of the software operation will be given. A case study will be shown for use with terahertz data. The authors also request scientists and engineers who are interested in sharing customized signal and image processing algorithms to contribute to this effort by letting the authors code up and include these algorithms in future releases.

Roth, Donald J.↗

NASA NTRS2005

NASA Tech Briefs, October 2005

Topics covered include: Insect-Inspired Optical-Flow Navigation Sensors; Chemical Sensors Based on Optical Ring Resonators; A Broad-Band Phase-Contrast Wave-Front Sensor; Progress in Insect-Inspired Optical Navigation Sensors; Portable Airborne Laser System Measures Forest-Canopy Height; Deployable Wide-Aperture Array Antennas; Faster Evolution of More Multifunctional Logic Circuits; Video-Camera-Based Position-Measuring System; N-Type delta Doping of High-Purity Silicon Imaging Arrays; Avionics System Architecture Tool; Updated Chemical Kinetics and Sensitivity Analysis Code; Predicting Flutter and Forced Response in Turbomachinery; Upgrades of Two Computer Codes for Analysis of Turbomachinery; Program Facilitates CMMI Appraisals; Grid Visualization Tool; Program Computes Sound Pressures at Rocket Launches; Solar-System Ephemeris Toolbox; Data-Acquisition Software for PSP/TSP Wind-Tunnel Cameras; Corrosion-Prevention Capabilities of a Water-Borne, Silicone-Based, Primerless Coating; Sol-Gel Process for Making Pt-Ru Fuel-Cell Catalysts; Making Activated Carbon for Storing Gas; System Regulates the Water Contents of Fuel-Cell Streams; Five-Axis, Three-Magnetic-Bearing Dynamic Spin Rig; Modifications of Fabrication of Vibratory Microgyroscopes; Chamber for Growing and Observing Fungi; Electroporation System for Sterilizing Water; Thermoelectric Air/Soil Energy-Harvesting Device; Flexible Metal-Fabric Radiators; Actuated Hybrid Mirror Telescope; Optical Design of an Optical Communications Terminal; Algorithm for Identifying Erroneous Rain-Gauge Readings; Condition Assessment and End-of-Life Prediction System for Electric Machines and Their Loads; Lightweight Thermal Insulation for a Liquid-Oxygen Tank; Stellar Gyroscope for Determining Attitude of a Spacecraft; and Lifting Mechanism for the Mars Explorer Rover.

Source record↗

NASA NTRS2013

The WFIRST Galaxy Survey Exposure Time Calculator

This document describes the exposure time calculator for the Wide-Field Infrared Survey Telescope (WFIRST) high-latitude survey. The calculator works in both imaging and spectroscopic modes. In addition to the standard ETC functions (e.g. background and SN determination), the calculator integrates over the galaxy population and forecasts the density and redshift distribution of galaxy shapes usable for weak lensing (in imaging mode) and the detected emission lines (in spectroscopic mode). The source code is made available for public use.

Hirata, Christopher M.↗

NASA NTRS2019

Introduction to Multicasting

This is a presentation for students who will be participating in the App Development Challenge (ADC). This discussion tells the students the data format NASA will be using (which their software must be compatible with). This presentation contains only publicly available images and information, and is provided to help the students with their coding (that they will submit to NASA).

Hirsh, Robert↗