The Cell Tracking Challenge: 10 years of objective benchmarking

Nature Methods, Год журнала: 2023, Номер 20(7), С. 1010 - 1020

Опубликована: Май 18, 2023

Abstract The Cell Tracking Challenge is an ongoing benchmarking initiative that has become a reference in cell segmentation and tracking algorithm development. Here, we present significant number of improvements introduced the challenge since our 2017 report. These include creation new segmentation-only benchmark, enrichment dataset repository with datasets increase its diversity complexity, silver standard corpus based on most competitive results, which will be particular interest for data-hungry deep learning-based strategies. Furthermore, up-to-date leaderboards, in-depth analysis relationship between performance state-of-the-art methods properties annotations, two novel, insightful studies about generalizability reusability top-performing methods. provide critical practical conclusions both developers users traditional machine algorithms.

Язык: Английский

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DNA double-strand break–capturing nuclear envelope tubules drive DNA repair

Nature Structural & Molecular Biology, Год журнала: 2024, Номер 31(9), С. 1319 - 1330

Опубликована: Апрель 17, 2024

Язык: Английский

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Freeze casting

Nature Reviews Methods Primers, Год журнала: 2024, Номер 4(1)

Опубликована: Апрель 25, 2024

Язык: Английский

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BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Июнь 8, 2022

Abstract Deep learning-based approaches are revolutionizing imaging-driven scientific research. However, the accessibility and reproducibility of deep workflows for imaging scientists remain far from sufficient. Several tools have recently risen to challenge democratizing learning by providing user-friendly interfaces analyze new data with pre-trained or fine-tuned models. Still, few existing models interoperable between these tools, critically restricting a model’s overall utility possibility validating reproducing analyses. Here, we present BioImage Model Zoo ( https://bioimage.io ): community-driven, fully open resource where standardized can be shared, explored, tested, downloaded further adaptation direct deployment in multiple end user-facing (e.g., ilastik, deepImageJ, QuPath, StarDist, ImJoy, ZeroCostDL4Mic, CSBDeep). To enable everyone contribute consume resources, provide model standard cross-compatibility, rich list example practical use-cases, developer documentation, accompanying infrastructure upload, download testing. Our contribution aims lay groundwork make methods microscopy findable, accessible, interoperable, reusable (FAIR) across software platforms.

Язык: Английский

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Segmentation, tracking and cell cycle analysis of live-cell imaging data with Cell-ACDC

BMC Biology, Год журнала: 2022, Номер 20(1)

Опубликована: Авг. 5, 2022

High-throughput live-cell imaging is a powerful tool to study dynamic cellular processes in single cells but creates bottleneck at the stage of data analysis, due large amount generated and limitations analytical pipelines. Recent progress on deep learning dramatically improved cell segmentation tracking. Nevertheless, manual validation correction typically still required tools spanning complete range image analysis are needed.

Язык: Английский

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Community-developed checklists for publishing images and image analyses

Nature Methods, Год журнала: 2023, Номер 21(2), С. 170 - 181

Опубликована: Сен. 14, 2023

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images image-analysis results, there no unified guidelines best practices. Consequently, microscopy image data publications may be unclear or difficult interpret. Here, we present community-developed checklists preparing light describing analyses publications. These offer authors, readers publishers key recommendations formatting annotation, color selection, availability reporting workflows. The goal of our increase the clarity reproducibility figures thereby heighten quality explanatory power data.

Язык: Английский

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Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis

Science Translational Medicine, Год журнала: 2023, Номер 15(725)

Опубликована: Дек. 6, 2023

Pulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing mechanisms and fibrogenesis directly in human tissue has been hampered by the lack organotypic models analytical techniques. In this work, we coupled ex vivo cytokine drug perturbations precision-cut lung slices (hPCLS) with single-cell RNA sequencing induced multilineage circuit fibrogenic cell states hPCLS. We showed that these were highly similar to multicohort atlas from patients pulmonary fibrosis. Using micro-CT-staged patient tissues, characterized appearance interaction myofibroblasts, an ectopic endothelial state, basaloid epithelial cells thickened alveolar septum early-stage Induction hPCLS model provided evidence state was derived type 2 cells, whereas emerged capillary plasticity. Cell-cell communication routes largely conserved hPCLS, antifibrotic treatments type-specific effects. Our work provides experimental framework for perturbational genomics enables analysis homeostasis, regeneration, pathology. further demonstrate offer avenue scalable, high-resolution testing accelerate development translation.

Язык: Английский

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Prefrontal engrams of long-term fear memory perpetuate pain perception

Nature Neuroscience, Год журнала: 2023, Номер 26(5), С. 820 - 829

Опубликована: Апрель 6, 2023

Abstract A painful episode can lead to a life-long increase in an individual’s experience of pain. Fearful anticipation imminent pain could play role this phenomenon, but the neurobiological underpinnings are unclear because fear both suppress and enhance Here, we show mice that long-term associative memory stored neuronal engrams prefrontal cortex determines whether shapes later life. Furthermore, under conditions inflammatory neuropathic pain, expand encompass neurons representing nociception tactile sensation, leading pronounced changes connectivity fear-relevant brain areas. Conversely, silencing reverses chronically established hyperalgesia allodynia. These results reveal discrete subset account for debilitating comorbidity chronic attenuating alleviate itself.

Язык: Английский

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Sparse and stereotyped encoding implicates a core glomerulus for ant alarm behavior

Cell, Год журнала: 2023, Номер 186(14), С. 3079 - 3094.e17

Опубликована: Июнь 15, 2023

Ants communicate via large arrays of pheromones and possess expanded, highly complex olfactory systems, with antennal lobes in the brain comprising up to ∼500 glomeruli. This expansion implies that odors could activate hundreds glomeruli, which would pose challenges for higher-order processing. To study this problem, we generated transgenic ants expressing genetically encoded calcium indicator GCaMP sensory neurons. Using two-photon imaging, mapped complete glomerular responses four ant alarm pheromones. Alarm robustly activated ≤6 activity maps three inducing panic our species converged on a single glomerulus. These results demonstrate that, rather than using broadly tuned combinatorial encoding, employ precise, narrowly tuned, stereotyped representations The identification central hub glomerulus behavior suggests simple neural architecture is sufficient translate pheromone perception into behavioral outputs.

Язык: Английский

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A revised conceptual framework for mouse vomeronasal pumping and stimulus sampling

Current Biology, Год журнала: 2024, Номер 34(6), С. 1206 - 1221.e6

Опубликована: Фев. 5, 2024

The physiological performance of any sensory organ is determined by its anatomy and physical properties. Consequently, complex structures with elaborate features have evolved to optimize stimulus detection. Understanding these their nature forms the basis for mechanistic insights into function. Despite crucial role as a sensor pheromones other behaviorally instructive chemical cues, vomeronasal (VNO) remains poorly characterized mammalian structure. Fundamental principles physico-mechanical function, including basic aspects sampling, remain explored. Here, we revisit classical vasomotor pump hypothesis uptake. Using advanced anatomical, histological, methods, demonstrate that large parts lateral mouse VNO are composed smooth muscle. Vomeronasal muscle tissue comprises two subsets fibers distinct topography, structure, excitation-contraction coupling, and, ultimately, contractile Specifically, contractions population noradrenaline-sensitive cells mediate both transverse longitudinal lumen expansion, whereas cholinergic stimulation targets an adluminal group fibers. latter run parallel VNO's rostro-caudal axis ideally situated antagonistic constriction lumen. This newly discovered arrangement implies novel mode Single-cell transcriptomics pharmacological profiling reveal receptor subtypes involved. Finally, 2D/3D tomography provides non-invasive insight intact mechanics, enables measurement luminal fluid volume, allows assessment relative volume change upon noradrenergic stimulation. Together, propose revised conceptual framework pumping thus, sampling.

Язык: Английский

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