Tools and Resources

A Tools and Resources article allows authors to publish the details of new experimental techniques, datasets, software tools, and other resources.

Latest articles

    1. Neuroscience

    Establishment of transgenic fluorescent mice for labeling synapses and screening synaptogenic adhesion molecules

    Lei Yang, Jingtao Zhang ... Chen Zhang
    A Syt1-tdTomato transgenic mice with normal synaptic transmission is established to label synapse in situ and screen synaptogenic adhesion molecules.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Transformer-based spatial–temporal detection of apoptotic cell death in live-cell imaging

    Alain Pulfer, Diego Ulisse Pizzagalli ... Santiago Fernandez Gonzalez
    ADeS, a novel deep learning approach for apoptosis detection, achieves 98% accuracy in vitro and in vivo while providing unprecedented insights into the spatial–temporal foundation of cell death.
    1. Cell Biology

    A novel imaging method (FIM-ID) reveals that myofibrillogenesis plays a major role in the mechanically induced growth of skeletal muscle

    Kent W Jorgenson, Jamie E Hibbert ... Troy A Hornberger
    A novel imaging method for measuring myofibril size/number reveals that the radial growth of muscle fibers that occurs in response to increased mechanical loading is largely mediated by myofibrillogenesis.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration

    Mathias Fynbo Jensen, Morten Nielsen
    NetTCR 2.2 demonstrates advances in predicting MHC-peptide-TCR interactions through integration of pan- and peptide-specific training strategies, loss-scaling and sequence similarity scoring.
    1. Cell Biology

    An open-source, high-resolution, automated fluorescence microscope

    Ando Christian Zehrer, Ana Martin-Villalba ... Helge Ewers
    High-quality fluorescence live-cell and single molecule imaging via computer-controlled, user-assembled microscope that fits in incubator, can in large parts be 3D printed and employs open source software and electronics.
    1. Computational and Systems Biology
    2. Neuroscience

    Dissecting muscle synergies in the task space

    David O'Reilly, Ioannis Delis
    A novel network information framework quantifies muscle interactions, characterises their task-relevance, and identifies networks of muscles with similar and complementary functional roles.
    1. Neuroscience

    Towards biologically plausible phosphene simulation for the differentiable optimization of visual cortical prostheses

    Maureen van der Grinten, Jaap de Ruyter van Steveninck ... Yağmur Güçlütürk
    The provided framework based on biological models and clinical literature can aid in the optimization of visual cortical prostheses through computational or behavioral simulation experiments, serving as a flexible tool for computational, clinical, and behavioral neuroscientists working on visual neuroprosthetics.
    1. Neuroscience

    RatInABox, a toolkit for modelling locomotion and neuronal activity in continuous environments

    Tom M George, Mehul Rastogi ... Caswell Barry
    A new python package standardises and simplifies how spatial behaviour and neural representations are modelled in continuous environments.
    1. Neuroscience

    Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing

    Aixin Zhang, Lei Jin ... Xiaoyin Chen
    Barcoded rabies virus tracing combined with single-cell RNAseq and in situ sequencing achieves high-throughput retrograde projection mapping and synaptic connectivity mapping at cellular resolution.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    A kinase to cytokine explorer to identify molecular regulators and potential therapeutic opportunities

    Marina Chan, Yuqi Kang ... Taranjit S Gujral
    KinCytE is a web-based platform that explores kinase-cytokine-driven signaling and its relevance to understanding and treating diseases linked to disruptions in these pathways.