arXiv subjects

Luis Rangel DaCosta

Publications and source records attributed to Luis Rangel DaCosta.

7 recordsLinked to original sources

arXiv2025

Contrast transfer functions help quantify neural network out-of-distribution generalization in HRTEM

Neural networks, while effective for tackling many challenging scientific tasks, are not known to perform well out-of-distribution (OOD), i.e., within domains which differ from their training data. Understanding neural network OOD generalization is paramount to their successful deployment in experimental workflows, especially when ground-truth knowledge about the experiment is hard to establish or experimental conditions significantly vary. With inherent access to ground-truth information and fine-grained control of underlying distributions, simulation-based data curation facilitates precise investigation of OOD generalization behavior. Here, we probe generalization with respect to imaging conditions of neural network segmentation models for high-resolution transmission electron microscopy (HRTEM) imaging of nanoparticles, training and measuring the OOD generalization of over 12,000 neural networks using synthetic data generated via random structure sampling and multislice simulation. Using the HRTEM contrast transfer function, we further develop a framework to compare information content of HRTEM datasets and quantify OOD domain shifts. We demonstrate that neural network segmentation models enjoy significant performance stability, but will smoothly and predictably worsen as imaging conditions shift from the training distribution. Lastly, we consider limitations of our approach in explaining other OOD shifts, such as of the atomic structures, and discuss complementary techniques for understanding generalization in such settings.

cs.LG↗

arXiv2023

pynucastro 2.1: an update on the development of a python library for nuclear astrophysics

pynucastro is a python library that provides visualization and analyze techniques to classify, construct, and evaluate nuclear reaction rates and networks. It provides tools that allow users to determine the importance of each rate in the network, based on a specified list of thermodynamic properties. Additionally, pynucastro can output a network in C++ or python for use in simulation codes, include the AMReX-Astrophysics simulation suite. We describe the changes in pynucastro since the last major release, including new capabilities that allow users to generate reduced networks and thermodynamic tables for conditions in nuclear statistical equilibrium.

nucl-th↗

arXiv2023

A robust synthetic data generation framework for machine learning in High-Resolution Transmission Electron Microscopy (HRTEM)

Machine learning techniques are attractive options for developing highly-accurate automated analysis tools for nanomaterials characterization, including high-resolution transmission electron microscopy (HRTEM). However, successfully implementing such machine learning tools can be difficult due to the challenges in procuring sufficiently large, high-quality training datasets from experiments. In this work, we introduce Construction Zone, a Python package for rapidly generating complex nanoscale atomic structures, and develop an end-to-end workflow for creating large simulated databases for training neural networks. Construction Zone enables fast, systematic sampling of realistic nanomaterial structures, and can be used as a random structure generator for simulated databases, which is important for generating large, diverse synthetic datasets. Using HRTEM imaging as an example, we train a series of neural networks on various subsets of our simulated databases to segment nanoparticles and holistically study the data curation process to understand how various aspects of the curated simulated data -- including simulation fidelity, the distribution of atomic structures, and the distribution of imaging conditions -- affect model performance across several experimental benchmarks. Using our results, we are able to achieve state-of-the-art segmentation performance on experimental HRTEM images of nanoparticles from several experimental benchmarks and, further, we discuss robust strategies for consistently achieving high performance with machine learning in experimental settings using purely synthetic data.

cond-mat.mtrl-sci↗

arXiv2023

Generalization Across Experimental Parameters in Machine Learning Analysis of High Resolution Transmission Electron Microscopy Datasets

Neural networks are promising tools for high-throughput and accurate transmission electron microscopy (TEM) analysis of nanomaterials, but are known to generalize poorly on data that is "out-of-distribution" from their training data. Given the limited set of image features typically seen in high-resolution TEM imaging, it is unclear which images are considered out-of-distribution from others. Here, we investigate how the choice of metadata features in the training dataset influences neural network performance, focusing on the example task of nanoparticle segmentation. We train and validate neural networks across curated, experimentally-collected high-resolution TEM image datasets of nanoparticles under controlled imaging and material parameters, including magnification, dosage, nanoparticle diameter, and nanoparticle material. Overall, we find that our neural networks are not robust across microscope parameters, but do generalize across certain sample parameters. Additionally, data preprocessing heavily influences the generalizability of neural networks trained on nominally similar datasets. Our results highlight the need to understand how dataset features affect deployment of data-driven algorithms.

cond-mat.mtrl-sci↗

arXiv2021

A Fast Algorithm for Scanning Transmission Electron Microscopy (STEM) Imaging and 4D-STEM Diffraction Simulations

Scanning transmission electron microscopy (STEM) is an extremely versatile method for studying materials on the atomic scale. Many STEM experiments are supported or validated with electron scattering simulations. However, using the conventional multislice algorithm to perform these simulations can require extremely large calculation times, particularly for experiments with millions of probe positions as each probe position must be simulated independently. Recently, the PRISM algorithm was developed to reduce calculation times for large STEM simulations. Here, we introduce a new method for STEM simulation: partitioning of the STEM probe into "beamlets," given by a natural neighbor interpolation of the parent beams. This idea is compatible with PRISM simulations and can lead to even larger improvements in simulation time, as well requiring significantly less computer RAM. We have performed various simulations to demonstrate the advantages and disadvantages of partitioned PRISM STEM simulations. We find that this new algorithm is particularly useful for 4D-STEM simulations of large fields of view. We also provide a reference implementation of the multislice, PRISM and partitioned PRISM algorithms.

cond-mat.mtrl-sci↗

arXiv2020

Multibeam Electron Diffraction

One of the primary uses for transmission electron microscopy (TEM) is to measure diffraction pattern images in order to determine a crystal structure and orientation. In nanobeam electron diffraction (NBED) we scan a moderately converged electron probe over the sample to acquire thousands or even millions of sequential diffraction images, a technique that is especially appropriate for polycrystalline samples. However, due to the large Ewald sphere of TEM, excitation of Bragg peaks can be extremely sensitive to sample tilt, varying strongly for even a few degrees of sample tilt for crystalline samples. In this paper, we present multibeam electron diffraction (MBED), where multiple probe forming apertures are used to create mutiple STEM probes, all of which interact with the sample simultaneously. We detail designs for MBED experiments, and a method for using a focused ion beam (FIB) to produce MBED apertures. We show the efficacy of the MBED technique for crystalline orientation mapping using both simulations and proof-of-principle experiments. We also show how the angular information in MBED can be used to perform 3D tomographic reconstruction of samples without needing to tilt or scan the sample multiple times. Finally, we also discuss future opportunities for the MBED method.

cond-mat.mtrl-sci↗

arXiv2020

py4DSTEM: a software package for multimodal analysis of four-dimensional scanning transmission electron microscopy datasets

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full 2D image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields and other sample-dependent properties. However, extracting this information requires complex analysis pipelines, from data wrangling to calibration to analysis to visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail, and present results from several experimental datasets. We have also implemented a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open source HDF5 standard. We hope this tool will benefit the research community, helps to move the developing standards for data and computational methods in electron microscopy, and invite the community to contribute to this ongoing, fully open-source project.

cond-mat.mtrl-sci↗