Alexis N. Williams

From Acquisition to Answers: Developing Open-Source Automation and Quantitative Analysis Workflows with Built-In Statistics for Electron Microscopy

Alexis N. Williams, Lynnicia N Massenburg, Sita Sirisha Madugula, Amber N. Bible et autres

Automated electron microscopes are making it routine to collect large volumes of data at a pace that outstrips manual interpretation. This gap is especially evident when experiments span heterogeneous samples, variable contrast, noisy data, and subtle or sparse nanoscale features. Here we …

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Error-Guaranteed Compression with Preservation of Downstream Quantities for Electron Microscopy

Jaemoon Lee, Eric R. Hoglund, Qian Gong, Andrew R. Lupini et autres

Recent electron microscopy workflows, particularly 4D Scanning Transmission Electron Microscopy (4D STEM), generate massive data volumes, sometimes exceeding tens of terabytes per dataset. This growth is outpacing improvements in storage, network, and I/O bandwidths. Although lossless compression offers a viable solution, it …

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TileBac: A Benchmark CryoEM Dataset of Bacteria in Ultralow-Dose Montage Tiles

Lynnicia N. Massenburg, Sita Sirisha Madugula, Spenser R. Brown, Amber B. Webb et autres

Abstract Current segmentation models are capable of routine identification of biological features in noisy cryogenic electron microscopy (cryoEM) images. However, there are still challenges with complete segmentation of high boundary, thin objects such as bacterial cell envelopes and flagella. Moreover, ultralow-dose cryoEM …

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Top Model Decision Tree: Selecting Segmentation Models for Reliable Quantitative Analysis in Low- and Ultralow-Dose CryoEM

Lynnicia N. Massenburg, Sita S. Madugula, Spenser R. Brown, Amber N. Bible et autres

Abstract Deep learning neural networks provide a powerful approach for segmenting low-contrast cryogenic electron microscopy (cryoEM) images. However, model performance can vary significantly across imaging conditions and may hinder downstream quantitative analyses. Here, we present a structured evaluation workflow to systematically screen …

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Facility-Scale Workflows for Data Acquisition, Standardization, Machine Learning Analysis, and Reproducible Science

Sita Sirisha Madugula, Spenser R. Brown, Amber N. Bible, Ruben Millan Solsona et autres

Abstract Scientific user facilities routinely generate large-scale microscopy datasets across diverse instruments and vendors, differing substantially in file formats, dimensionality, and resolution. Beyond these inconsistencies, datasets are frequently fragmented living across isolated instruments and constrained by security policies and uneven metadata practices. …

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Automated Bacterial Identification and Morphological Feature Analysis in Low‐Dose Cryo‐EM Using YOLOv11

Sita Sirisha Madugula, Lynnicia N. Massenburg, Spenser R. Brown, Amber N. Bible et autres

Bacteria rapidly adapt to environmental cues through morphological and ultrastructural changes that correlate with physiology and behavior. Cryogenic transmission electron microscopy (cryo‐TEM) can capture these phenotypic changes in near‐native, vitrified states, but manual analysis of low‐dose micrographs is labor intensive and limits …

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CryoBlob – A Feature Detection Tool for Low Dose CryoEM

Debangshu Mukherjee, Spenser R. Brown, Anna L. Jones, ChristiAnna L. Brantley et autres

Facility-scale workflows for data acquisition, standardization, machine learning analysis, and reproducible science

Sita Sirisha Madugula, Spenser R. Brown, Amber N. Bible, Ruben Millan-Solsona et autres

Scientific user facilities routinely generate large-scale microscopy datasets across diverse instruments and vendors, differing substantially in file formats, dimensionality, and resolution.

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The redefined role of PhaG and CoA ligases in medium-chain-length 3-hydroxy acid and polyhydroxyalkanoate production in Pseudomonas putida

A. R. Ola Pasternak, Walter T. Woodside, Eugene Kuatsjah, Sekgetho Charles Mokwatlo et autres

Abstract Under nutrient starvation conditions, many microorganisms such as Pseudomonas putida store excess carbon in medium-chain-length polyhydroxyalkanoate ( mcl -PHA) granules. Biosynthesis of PHAs from the fatty acid biosynthetic pathway requires PhaG, which has long been thought to encode a 3-hydroxyacyl-ACP:CoA transferase, …

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Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures

Sita Sirisha Madugula, Lynnicia N. Massenburg, Spenser R. Brown, Amber N. Bible et autres

Bacteria adapt by undergoing dynamic structural changes in response to environmental cues, which are often indicative of deeper phenotypic shifts in physiology and behavior. Understanding these changes across length scales is crucial for elucidating bacterial lifecycles, informing antifouling surface design, enhancing pathogen …

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Frameshifting Stimulatory Sequence Induces Large Structural Change of Ribosomal Proteins When Bound to E. coli Ribosomes

Emily Armbruster, Kevin L. Weiss, Loukas Petridis, Jose M. Borreguero et autres

Biological macromolecular machines occupy a continuum of structural conformations to perform cellular tasks. Mapping this conformational space provides an insight into its functionality. While the cryo-electron microscopy resolution revolution has expanded our ability to characterize the conformational continuums, there are obstacles in …

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Strategies to Prepare Frozen-Hydrated Duckweed for Cryogenic Electron Tomography of Thylakoid Membranes

Lynnicia N Massenburg, Kimberly Shawn Reeves, Gergely Nagy, Hugh O’Neill et autres

Plant chloroplasts have dynamic thylakoid membrane organization to orchestrate photosynthesis. High resolution inelastic neutron scattering spectroscopy has recently been shown to measure bulk thylakoid membrane dynamics in living plant leaves [1]. Changes in membrane thickness, bilayer-bilayer interactions and embedded protein decoration and …

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