fluorescence / live-cell microscopy

Microenvironmental Fingerprint of Maturing Tau Condensates from Spectral and Lifetime Phasor Analysis of a Solvatochromic Dye

This paper develops a multimodal framework using spectral and lifetime phasor analysis to characterize microenvironmental changes in Tau condensates during maturation.

Linking Covariates to State Durations in Dynamic Brain Networks via Hidden Semi-Markov Models

This paper introduces a covariate-dependent hidden semi-Markov model to analyze brain network state durations, finding that age and sex influence dwell times in specific brain states.

BEHAV3D-Explorer enables natural language-assisted profiling of 3D cellular dynamics

BEHAV3D-Explorer provides a user-friendly platform for analyzing 3D live-cell imaging data using natural language guidance to select analysis strategies and configure workflows.

FACT frees Ubp10 from nucleosome sequestration after rapid H2B deubiquitination

The paper shows that FACT facilitates Ubp10 release from nucleosomes after H2B deubiquitination, revealing release as the rate-limiting step for Ubp10 turnover.

Multimodal cellular context enables molecular phenotyping from single-molecule trajectories

The paper introduces MIST, a framework that integrates single-molecule trajectory data with cellular context to improve molecular phenotyping in E. coli.

MitoDecode: quantitative phenotypic decoding of mitochondrial stress states from fluorescence images

MitoDecode assesses mitochondrial stress types and severity from fluorescence images without segmentation, showing adaptability across cell types and stress conditions.

Breaking the bottleneck: semi-automated quantification of actin filament dynamics

The paper introduces SMAUG, a semi-automated tool for analyzing actin filament dynamics from TIRF microscopy images, reducing analysis time while maintaining accuracy.

siRNA/mRNA payload of lipid nanoparticles quantified using fluorescence microscopy and correlation spectroscopy

The paper quantifies mRNA and siRNA payload in lipid nanoparticles using fluorescence microscopy and FCS, showing size-dependent payload and coencapsulation dynamics.

SNAzzy: an image processing pipeline for investigating global Synchronous Network Activity

SNAzzy processes and analyzes high-throughput microscopy data from Drosophila embryos to study synchronous network activity.

Automahout: an autonomous image analysis system for cell tracking

Automahout autonomously tracks cells in time-lapse images using a self-tuning system that annotates, trains, and refines models without human input, achieving high TRA scores on public datasets.

Dopamine synthesis capacity and tau pathology differentially modulate rest-to-task functional network dynamics

This study examines how dopamine synthesis and tau pathology affect functional brain network dynamics during rest and task performance in young and older adults.

Evaluating State-Transition Models in Short Resting-State fMRI with Continuous-Dynamics Controls

This study compares hidden Markov models (HMMs) and vector autoregressive (VAR) models in resting-state fMRI to determine if apparent state transitions reflect discrete dynamics or continuous activity, finding that VAR often outperforms HMMs in continuous cases.

Diversification of budding yeast polarization dynamics after compensatory experimental evolution

This study shows that evolution can restore cellular function without conserving microscopic organization, leading to novel molecular phenotypes in budding yeast.

Systematic comparison of genetically encoded F-actin probes for visualizing actomyosin dynamics in vivo using C. elegans

The paper compares three F-actin probes in C. elegans, finding mStayGold offers best brightness and photostability, while mNeonGreen is suitable for photobleaching applications.

A red fluorescent sensor for intensity-and lifetime imaging of cAMP in living cells

The paper develops a red fluorescent sensor, chILI, for detecting cAMP in living cells through intensity and lifetime imaging, demonstrating its use in mouse brain neurons.

2D U-NET Deep Learning Architecture for Atherosclerotic Lesion Segmentation and Quantification

This paper develops a 2D U-NET model to segment and quantify atherosclerotic lesions in mouse aortic sections, achieving high accuracy and significantly reducing measurement time.

Evolution of Vesicle Shape Parameters Based on A Deep-Learning Based Image Analysis Framework Over Extended Time Periods

The paper uses a deep-learning framework to analyze shape dynamics of GUVs over time, measuring morphometric changes and budding behavior.

Influence of antibody-antigen interaction on fluorescence of Rhodamine 6G conjugated to the antibodies measured in human serum

This study measures how antibody-antigen interactions affect the fluorescence of Rhodamine 6G-conjugated antibodies in human serum, showing non-linear spectral changes.

KaryoTap-based scDNA seq assessment of aneuploidy induction by hydroquinone in hematopoietic stem cells

This study assesses whether hydroquinone induces aneuploidy in hematopoietic stem cells using KaryoTap and FISH, finding no reproducible increase in whole-chromosome aneuploidy.

PhenoMe: An interactive AI framework for interpretable, microscopy-driven phenotyping

PhenoMe provides an open-source framework for analyzing microscopy images using foundation model-derived embeddings and experimental metadata to enable phenotyping and data exploration.

Open filament tracks drive Bacteroidota gliding motility

The paper uses 3D super-resolution tracking to show that Bacteroidota gliding involves multiple open filament tracks, challenging the single closed loop model.

Single-molecule bouncing at a liquid interface governs presynaptic enrichment

The paper shows that single-molecule bouncing at a presynaptic interface enables protein enrichment without slowing diffusion.

Molecular crowding differentially regulates magnetic field-dependent fluorescence, recovery kinetics, and photostability of the magnetosensitive protein MagLOV2

This study investigates how different molecular crowders affect the magnetic field-dependent fluorescence and recovery kinetics of MagLOV2 in E. coli lysate.

Machine learning-assisted Repli-Histo labeling reveals distinct transcription-dependent constraints on chromatin motion in living cells

The paper uses machine learning to classify chromatin classes and shows how different transcription systems affect nucleosome motion in distinct chromatin regions.

Quantitative imaging of calcium dynamics with a green fluorescent biosensor and fluorescence lifetime imaging

The paper describes protocols for calcium imaging using a genetically encoded biosensor and fluorescence lifetime imaging to improve measurement robustness.

Time- Space Resolved Fluorescence Spectroscopy in Live Chlamydomonas Cells under Light-Harvesting Regulation

The paper develops a time-space resolved fluorescence spectroscopy technique to study light-harvesting dynamics in Chlamydomonas cells under state transitions.

Experimental Methods for CRISPR Enzyme Assays with Fluorescence Readout

The paper presents a standardized experimental protocol and analysis framework for fluorescence-based CRISPR enzyme assays to improve reproducibility and consistency in kinetic measurements.

Label-free identification of bacterial species using adapted vision transformers

This paper develops a vision transformer model for rapid bacterial species identification from time-lapse images without fluorescent labels, achieving high accuracy on clinical isolates.

VesiScope: A stand-alone tool for the automatic detection, quantification and size analysis of GUVs from phase contrast microscopy images

VesiScope detects and analyzes GUVs from phase contrast images using a YOLOv11 model, enabling accurate and efficient label-free quantification.

Streamlined Production of Recombinant Adeno-Associated Viruses Using Gateway Cloning Technology for Neural Circuit All-Optical Interrogation

The paper introduces a Gateway-based cloning platform for efficient construction of rAAV vectors optimized for neuroscience applications, enabling precise optical interrogation of neural circuits with tools like ULoVE.