AIMC Topic: Zebrafish

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A deep learning framework for quantitative analysis of actin microridges.

NPJ systems biology and applications
Microridges are evolutionarily conserved actin-rich protrusions present on the apical surface of squamous epithelial cells. In zebrafish epidermal cells, microridges form self-evolving patterns due to the underlying actomyosin network dynamics. Howev...

EmbryoNet: using deep learning to link embryonic phenotypes to signaling pathways.

Nature methods
Evolutionarily conserved signaling pathways are essential for early embryogenesis, and reducing or abolishing their activity leads to characteristic developmental defects. Classification of phenotypic defects can identify the underlying signaling mec...

Structure and function in artificial, zebrafish and human neural networks.

Physics of life reviews
Network science provides a set of tools for the characterization of the structure and functional behavior of complex systems. Yet a major problem is to quantify how the structural domain is related to the dynamical one. In other words, how the divers...

An end-to-end pipeline based on open source deep learning tools for reliable analysis of complex 3D images of ovaries.

Development (Cambridge, England)
Computational analysis of bio-images by deep learning (DL) algorithms has made exceptional progress in recent years and has become much more accessible to non-specialists with the development of ready-to-use tools. The study of oogenesis mechanisms a...

Deep Learning-Enabled Morphometric Analysis for Toxicity Screening Using Zebrafish Larvae.

Environmental science & technology
Toxicology studies heavily rely on morphometric analysis to detect abnormalities and diagnose disease processes. The emergence of ever-increasing varieties of environmental pollutants makes it difficult to perform timely assessments, especially using...

Emergence of time persistence in a data-driven neural network model.

eLife
Establishing accurate as well as interpretable models of network activity is an open challenge in systems neuroscience. Here, we infer an energy-based model of the anterior rhombencephalic turning region (ARTR), a circuit that controls zebrafish swim...

A study of transfer of information in animal collectives using deep learning tools.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences
We studied how the interactions among animals in a collective allow for the transfer of information. We performed laboratory experiments to study how zebrafish in a collective follow a subset of trained animals that move towards a light when it turns...

Quantifying stiffness and forces of tumor colonies and embryos using a magnetic microrobot.

Science robotics
Stiffness and forces are two fundamental quantities essential to living cells and tissues. However, it has been a challenge to quantify both 3D traction forces and stiffness (or modulus) using the same probe in vivo. Here, we describe an approach tha...

Social behavioral profiling by unsupervised deep learning reveals a stimulative effect of dopamine D3 agonists on zebrafish sociality.

Cell reports methods
It has been a major challenge to systematically evaluate and compare how pharmacological perturbations influence social behavioral outcomes. Although some pharmacological agents are known to alter social behavior, precise description and quantificati...