lattice light sheet microscope dataset visualization and analysis
This is a collection of tools for the visualization and analysis of lattice light sheet microscope datasets.
Yi, Xiyu↗
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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.
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A Framework to Support Generator Ramping Uncertainty Analysis and Visualization
Power system operation requires maintaining a continuous balance between system demand and generation within certain constraints. Traditionally, the balancing processes are based on deterministic models, which do not consider possible random deviations of system generation and load from their predicted values. With the increasing penetration of the renewable generation, unexpected balancing problems can happen due to the deviations. This can result in serious risks to system reliability and efficiency. When the available balancing reserve is not enough to cover the predicted net load range with uncertainty, deficiency of balancing needs occurs. In this case, it is necessary to commit or de-commit additional conventional generators to achieve the desired confidence level for the balancing needs. The framework is built for solving this problem. The ramping tool engine is used to predict additional balancing requirements caused by the variability and uncertainty of the renewable energy, under the constraints of the generation ramping capability and interchange schedule. The web browser- based GUI is used to visualize the data in web-environment, which provides flexibility to allow user to see the ramping outputs in any platform. The GOSS structure provides strong support to allow easy communication between ramping engine, and system inputs, as well as the GUI.
Chen, Yousu↗
IViz-OT (Intrusion Detection Visualizer for Operational Technology Network) [SWR-22-63]
The Visualizer dashboard provides grid operator highly-trusted alarming environment for an ongoing or potential cyber-attack based on system anomalies and network-based verification. Once anomalies are detected by the IDS tool (HIDES, NREL SWR-19-65), this platform stores the signatures or alert logs that are generated by the intrusion detector, lays out the detailed summary of the possible alerts, and maps these attacks with high-level scenarios. These scenarios are later combined to define a final event using a decision tree approach and a final report is generated out of this tool for further forensic analysis. It also supports authentication and authorization to support roles-based access control (RBAC) for users and a group of people.
Singh, Vivek Kumar↗
VizStock (Building Stock Visualization Platform) (SWR-21-08)
The Building Stock Visualization Platform uses web-based technologies to display information on the input assumptions and output results of building stock modeling tools for building energy audits.
Merket, Noel↗
VIPER - Method for Visualizing and Interacting with Ionizing Radiation Data Using Augmented Reality
Method for visualizing and interacting with ionizing radiation data using augmented reality. This code provides coupling radiation transport data with immersive augmented reality experiences for users in real-world environments. Moreover, it provides real-time, simulation-based, radiation exposure feedback to user as a function of behavior in the immersive environment.
Smith, MichaelB↗
Novus: An Unmanned Aerial System and Virtual Reality Flight Deck for Data Collection and Visualization
Many emerging technologies offer tremendous new capabilities that will, without question, redefine how we interact with, utilize, understand, and optimize the energy systems around us. Drones offer a new ability to remotely capture data in ways that have previously been impractical. However, their flight control systems remain rudimentary and limit the ability of researchers to fully take advantage of these platforms as remote sensing devices. In this project, we constructed a hexarotor drone and outfitted it with advanced (yet inexpensive) sensors as well as a telemetry data management and control package. We then created a virtual reality flight deck that allows a drone operator to define waypoints "on-the-fly" or take manual control over flight operations. The flight deck provides a live on-board video stream display, a 3-dimensional topographic map with the drone’s position in space overlaid onto it, as well as a data visualization framework that keeps critical information immediately available to the operator. These advances provide a new platform for scientific data collection such as thermography of building envelopes or solar arrays. As the drone is in flight and data are being collected, these data are relayed to the virtual reality environment where they can be inspected for integrity and the flight plan altered if necessary to collect higher quality data. Future work will focus on implementing 3-dimensional mapping using both visible and thermal imagery collected from the drone, and streaming those into the virtual reality flight deck in real time.
Source record↗
GRid Analysis and Visualization Interface (GRAVI) [SWR-24-16]
GRAVI (GRid Analysis and Visualization Interface) is a web application for viewing and analyzing nodal Production Cost Model (PCM) and Capacity Expansion Model (CEM) simulations. The web application provides the ability to animate geospatially coupled timeseries data in an agnostic way regardless of the underlying simulation tool used to generate the data. GRAVI also provides capabilities to animate non-geospatial data relevant to a PCM or CEM model. Furthermore, this web application can be tailored as an real-time operational tool to better understand a live grid.
Webb, Micah↗
Double Visual Defense
This is the official code for the paper "Double Visual Defense: Adversarial Pre-training and Instruction Tuning for Improving Vision-Language Model Robustness". This code can be used to produce vision language models (VLMs), like LLaVA, with enhanced robustness to adversarial attacks (e.g. jailbreaks).
Bartoldson, Brian [Lawrence Livermore National Lab↗
Cyber Awareness Visualization And Event Action Tool
This tool allows the simplified and informed visualization of any data analytics tool with the ability to match the CAVEAT format. CAVEAT is capable of having any kind of control room configured with any arbitrary number of control surfaces.
Lehmer, JacobP.↗
MCP-eGridGPT (MCP-Enabled Chatbot with Electrical Power System Analysis and Interactive Visualization Tool) [SWR-25-126]
This software is an advanced chatbot system that integrates the Model Context Protocol (MCP) to provide intelligent electrical power system analysis and automated visualization generation. The system enables users to interact with complex electrical engineering tools through natural language, automatically analyzes power system data for voltage violations and grid health assessment, and generates professional interactive HTML dashboards and reports. Key features include dynamic tool discovery from MCP servers, multi-LLM provider support, intelligent data interpretation using large language models, automated chart generation, and a web-based interface for real-time analysis. The software bridges sophisticated electrical engineering analysis with user-friendly interfaces, making power system diagnostics accessible through conversational AI.
Choi, Seong [National Laboratory of the Rockies (N↗
SHIVER - Spectroscopy HIstogram Visualizer for Event Reduction
Visualizing data from neutron scattering experiments is the first step in understanding the physics. The program is intended to generate and plot cuts and slices, through the four dimensional single crystal inelastic datasets, measured on direct geometry neutron spectrometers at the Spallation Neutron Source (ARCS, CNCS, HYSPEC, SEQUOIA).
Savici, AndreiT [Oak Ridge National Laboratory (OR↗
Effective Visualization of Radar Data for Users Impacted by Color Vision Deficiency
Color vision deficiency (CVD) is a decreased ability to discern between particular colors. Eight percent of genetic males and half a percent of genetic females have some form of CVD, with many in the radar community falling into this group. When presenting data on a two-dimensional plane, it is common to use colors to represent values via a colormap. Colormap choice in the radar community is influenced by the ability to highlight scientifically interesting features in data, institutional choices, and domain dominance of legacy colormaps. The problem with these current colormaps is that many do not project well for those with CVD (i.e., green next to red). In working with the CVD community to address this problem, multiple colormaps for moments such as equivalent reflectivity factor and Doppler velocity were created for users with forms of CVD such as deuteranomaly, protanomaly, protanopia, and deuteranopia using Python tools such as colorspacious and viscm. We show how these colormaps can improve interpretability for four cases: a mesoscale convective system, a pyrocumulonimbus storm, a wintertime midlatitude cyclone, and widespread storms with a large bird migration. These new radar equivalent reflectivity factor, Doppler velocity, and polarization colormaps are designed to highlight rain, frozen precipitation, nonmeteorological targets, and velocity-based items, are perceptually uniform, and are visually friendly for those with CVD.
54 ENVIRONMENTAL SCIENCES↗
Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling
Mathematical/computational models are needed to understand cell signaling networks, which are complex. Signaling proteins contain multiple functional components and multiple sites of post-translational modification. The multiplicity of components and sites of modification ensures that interactions among signaling proteins have the potential to generate myriad protein complexes and post-translational modification states. As a result, the number of chemical species that can be populated in a cell signaling network, and hence the number of equations in an ordinary differential equation model required to capture the dynamics of these species, is prohibitively large. To overcome this problem, the rule-based modeling approach has been developed for representing interactions within signaling networks efficiently and compactly through coarse-graining of the chemical kinetics of molecular interactions. Here, we provide a demonstration that the rule-based modeling approach can be used to specify and simulate a large model for ERBB receptor signaling that accounts for site-specific details of protein-protein interactions. The model is considered large because it corresponds to a reaction network containing more reactions than can be practically enumerated. The model encompasses activation of ERK and Akt, and it can be simulated using a network-free simulator, such as NFsim, to generate time courses of phosphorylation for 55 individual serine, threonine, and tyrosine residues. The model is annotated and visualized in the form of an extended contact map. With the development of software that implements novel computational methods for calculating the dynamics of large-scale rule-based representations of cellular signaling networks, it is now possible to build and analyze models that include a significant fraction of the protein interactions that comprise a signaling network, with incorporation of the site-specific details of the interactions. Modeling at this level of detail is important for understanding cellular signaling.
59 BASIC BIOLOGICAL SCIENCES↗
Visualization of the impatiens downy mildew pathogen using fluorescence in situ hybridization (FISH)
Background: Plasmopara obducens is the biotrophic oomycete responsible for impatiens downy mildew, a destructive disease of Impatiens that causes high crop loss. Currently, there are no available methods for the microscopic detection of P. obducens from leaves of impatiens, which may be contributing to the spread of the disease. Fluorescence in situ hybridization (FISH) is a sensitive and robust method that uses sequence-specific, fluorescence-labeled oligonucleotide probes to detect target organisms from the environment. To study this important pathogen, we developed and standardized a FISH technique for the visualization of P. obducens from Impatiens walleriana tissues using a species-specific 24-mer oligonucleotide probe designed to target a region of the rRNA internal transcribed spacer 2 (ITS2). Results: Since P. obducens cannot be propagated in vitro, we developed a custom E. coli expression vector that transcribes the P. obducens rRNA-ITS target sequence (clone-FISH) for use as a control and to optimize hybridization conditions. The FISH assay could detect P. obducens sporangiophores, sporangia and oospores, and hyphae from naturally infected I. walleriana leaves and stems. Cross-reactivity was not observed from plant tissue, and the assay did not react when applied to E. coli with self-ligated plasmids and non-target oomycete species. Conclusions: This FISH protocol may provide a valuable tool for the study of this disease and could potentially be used to improve early monitoring of P. obducens , substantially reducing the persistence and spread of this destructive plant pathogen.
59 BASIC BIOLOGICAL SCIENCES↗
Visualizing spatiotemporal pulse propagation: first-order spatiotemporal couplings in laser pulses
Even though a general theory of first-order spatiotemporal couplings exists in the literature, it is often difficult to visualize how these distortions affect laser pulses. In particular, it is difficult to show the spatiotemporal phase of pulses in a meaningful way. We propose a general solution to plotting the electric fields of pulses in three-dimensional space that intuitively shows the effects of spatiotemporal phases. The temporal phase information is color-coded using spectrograms and color response functions, and the beam is propagated to show the spatial phase evolution. In using this plotting technique, we generate two- and three-dimensional images and movies that show the effects of spatiotemporal couplings.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Multidimensional scaling informed by F -statistic: Visualizing grouped microbiome data with inference
Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. Here, in this study, we introduce a new MDS-based ordination method, “F-informed MDS,” which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community’s response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.
Biological and medical sciences↗
GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization
Food safety risk assessments and large-scale epidemiological investigations have the potential to provide better and new types of information when whole genome sequence (WGS) data are effectively integrated. Today, the NCBI Pathogen Detection database WGS collections have grown significantly through improvements in technology, coordination, and collaboration, such as the GenomeTrakr and PulseNet networks. However, high-quality genomic data is not often coupled with high-quality epidemiological or food chain metadata. We have created a set of tools for cleaning, curation, integration, analysis and visualization of microbial genome sequencing data. It has been tested using Salmonella enterica and Listeria monocytogenes data sets provided by NCBI Pathogen Detection (160,000 sequenced isolates in 2018). GenomeGraphR presents foodborne pathogen WGS data and associated curated metadata in a user-friendly interface that allows a user to query a variety of research questions such as, transmission sources and dynamics, global reach, and persistence of genotypes associated with contamination in the food supply and foodborne illness across time or space. The application is freely available (https://fda-riskmodels.foodrisk.org/ genomegraphr/).
60 APPLIED LIFE SCIENCES↗
Direct Visualization of Nano and Microscale Polymer Morphologies in As-Prepared and Dialyzed Polyampholyte Hydrogels by Electron Microscopy Techniques
The structure of polymer networks in hydrogels determines the properties. In this study, we investigated the structure of a charge-balanced polyampholyte, poly(4-vinylbenzenesulfonate-co-[3-(methacryloylamino) propyl] trimethylammonium chloride). From as-prepared samples, nanoscale globules were visualized in polyampholyte hydrogels for the first time. The impact of dialyses processes on polymer structures were also studied. In deionized water, salt ions are leached out, thus polymer chains undergo zipping process to form cellular structure with micrometer-thick polymer walls that allow mechanical toughness to the hydrogel. Samples dialyzed in 6 M potassium hydroxide solution did not show such cellular structure, as in the case of as-prepared samples.
Li, Xinda↗