YOLO‐Behaviour: A simple, flexible framework to automatically quantify animal behaviours from videos

Methods in Ecology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 12, 2025

Abstract Manually coding behaviours from videos is essential to study animal behaviour but it labour‐intensive and susceptible inter‐rater bias reliability issues. Recent developments of computer vision tools enable the automatic quantification behaviours, supplementing or even replacing manual annotation. However, widespread adoption these methods still limited, due lack annotated training datasets domain‐specific knowledge required optimize models for research. Here, we present YOLO‐Behaviour, a flexible framework identifying visually distinct video recordings. The robust, easy implement, requires minimal annotations as data. We demonstrate flexibility with case studies event‐wise detection in house sparrow nestling provisioning, Siberian jay feeding, human eating frame‐wise detections various pigeons, zebras giraffes. Our results show that reliably detects accurately retrieve comparable accuracy metrics extracted were less correlated annotation, potential reasons discrepancy between annotation are discussed. To mitigate this problem, can be used hybrid approach first detecting events using pipeline then manually confirming detections, saving time. provide detailed documentation guidelines on how implement YOLO‐Behaviour framework, researchers readily train deploy new their own systems. anticipate another step towards lowering barrier entry applying behaviour.

Language: Английский

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An improved FLARE system for recording and manipulating neuronal activity

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 18, 2025

Summary Recording and manipulating neuronal ensembles that underlie cognition behavior in vivo is challenging. FLARE a light– calcium-gated transcriptional reporting system for labeling activated neurons on the order of minutes. However, limited by its sensitivity to prolonged activities. Here, we present an improved version FLARE, termed cytoFLARE. cytoFLARE incorporates cytosolic expression transcription factor more sensitive pair calcium sensing domains. We showed provides calcium– light-dependent signals HEK293T cells higher signal-to-background ratios cultures. further established transgenic Drosophila models applied label upon sensory or optogenetic stimulation within defined time window. Notably, through cytoFLARE-driven actuator, successfully reactivated involved larval nociceptive system. Our findings demonstrate first characterization application time-gated integrators .

Language: Английский

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An improved FLARE system for recording and manipulating neuronal activity

Cell Reports Methods, Journal Year: 2025, Volume and Issue: unknown, P. 101012 - 101012

Published: March 1, 2025

To address the need for methods tagging and manipulating neuronal ensembles underlying specific behaviors, we present an improved version of FLARE, termed cytoFLARE (cytosol-expressed FLARE). incorporates cytosolic tethering a transcription factor expression more sensitive pair calcium-sensing domains. We show that captures calcium- light-dependent signals in HEK293T cells higher signal-to-background ratios cultures. further establish transgenic Drosophila models apply to label activated neurons upon sensory or optogenetic stimulation within defined time window. Notably, through cytoFLARE-driven actuators, successfully reactivated inhibited involved larval nociceptive system. Our findings demonstrate characterization application time-gated calcium integrators both recording activity larvae.

Language: Английский

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YOLO-Behaviour: A simple, flexible framework to automatically quantify animal behaviours from videos

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 27, 2024

Abstract Manually coding behaviours from videos is essential to study animal behaviour but it labour-intensive and susceptible inter-rater bias reliability issues. Recent developments of computer vision tools enable the automatic quantification behaviours, supplementing or even replacing manual annotations. However, widespread adoption these methods still limited, due lack annotated training datasets domain-specific knowledge required optimize models for research. Here, we present YOLO-Behaviour, a flexible framework identifying visually distinct video recordings. The robust, easy implement, requires minimal annotations as data. We demonstrate flexibility with case studies event-wise detection in house sparrow nestling provisioning, Siberian jay feeding, human eating frame-wise detections various pigeons, zebras, giraffes. Our results show that reliably detects accurately, retrieve comparable accuracy metrics annotation. extracted were less correlated annotation, potential reasons discrepancy between annotation are discussed. To mitigate this problem, can be used hybrid approach first detecting events using pipeline then manually confirming detections, saving time. provide detailed documentation guidelines on how implement YOLO-Behaviour framework, researchers readily train deploy new their own systems. anticipate another step towards lowering barrier entry applying behaviour.

Language: Английский

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Intestinal stem cells enhance local mucosal immunity through apoptotic body phagocytosis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 3, 2024

ABSTRACT Modulation of immune tone at mucosal surfaces is critical to maintain homeostasis while facilitating the handling emerging threats. One dynamic component modulation phagocytosis and clearance apoptotic bodies known as efferocytosis that inhibits inflammation by promoting its resolution. Here, we evaluated effects body intestinal epithelial stem progenitor cells (ISCs). Unexpectedly, instead immunomodulation through efferocytosis, this process elevated local system activity. To achieve result, ISCs actively engaged in a unique fashion, leading their engulfment ultimate delivery lysosomes for processing. We found were capable recruiting inert material such using actin-based intrinsic biomechanical processes. Uptake was facilitated complement factor C3 produced themselves. turn generated signals heightening T cell activity driven part ISC-generated TNF. Taken together, uptake inflammatory alert specific cells. This altered paradigm response phagocytosed fits needs active demonstrates currently defined not universal all types.

Language: Английский

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