fluorescence / live-cell microscopy

CoReg is a motion correction tool for in vivo calcium imaging that outperforms existing methods by using tracking-based registration.

SubCellSeg is a 3D segmentation model that outperforms structure-specific models by jointly training on diverse subcellular structures and achieving zero-shot generalization.

The paper develops biosensors to track conformational changes of GTPases in live cells, revealing dynamics of Cdc42 activity and microclusters involved in cell motility.

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

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

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

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

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

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.

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.

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.

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

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

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

This paper uses deep learning to analyze fossil grass pollen morphology and reconstruct 25,000 years of ecological change in East African grasslands, showing reduced diversity and shifts in C3:C4 ratios during the last ice age.

msaGUI is a no-code tool for analyzing and visualizing multispectral images through customizable workflows and exportable outputs.

SAP provides a transferable, training-free framework for automated segmentation of plant time-series imagery across species and conditions.

mAIcrobe provides an open-source framework for bacterial image analysis using deep learning models, enabling analysis of diverse bacterial species and microscopy modalities.

The paper uses dynamic mode decomposition to analyze live-cell imaging data and investigates KIF13B's role in ciliary transport, finding it does not affect IFT velocity or frequency in a deletion mutant.

This paper introduces a method to mitigate spatio-temporal blending in FLIM by using MSSR-based masking, improving spatial resolution while preserving lifetime accuracy.

One Python script, configured through LLM-assisted command-line calls, segments and quantifies 2D/3D multi-channel fluorescence images with provenance records; in a yeast temperature series it exposed a non-responding subpopulation.

The paper examines how preserved cortical hierarchy in blindsight-positive patients explains their ability to detect stimuli without awareness after V1 damage.

PhenoStream automates crop trait extraction from aerial imagery, enabling high-throughput phenotyping with reduced latency and manual effort.

This paper improves sickle cell disease morphology analysis by combining a YOLO detector with a DenseNet classifier for accurate detection and classification of red blood cell morphologies in full-scope microscopy images.

The paper develops an automated image processing pipeline for analyzing yeast cell cycle dynamics using deep learning and dual segmentation, achieving faster analysis with minimal deviation from manual methods.

BLISS reveals dynamic HP1α clusters in chromocenters of undifferentiated ESCs, showing they are hyperdynamic and have lower fluorescence lifetimes than FLIM-averaged values.

The paper develops a multicolor fluorescent labelling toolkit for Gram-negative bacteria, enabling reliable imaging and analysis across scales in host-pathogen contexts.

This study identifies 129 proteins recruited to cell wounds during repair using a genetic screen in Drosophila, revealing Rab GTPases' roles in actin dynamics and repair steps.

CALIPERS enables cell cycle-aware live imaging by integrating a modified FUCCI variant, analysis software, and reporter lines for phenotyping and regeneration studies.