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    1. Neuroscience

    Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping

    Kathryn M Tabor et al.
    A new resource of transgenic zebrafish lines facilitates precise targeting of neuronal cell-types within the brain, supported by online software for visualizing transgene expression patterns.
    1. Neuroscience

    An arbitrary-spectrum spatial visual stimulator for vision research

    Katrin Franke et al.
    Towards a community effort, we here present a flexible yet standardised visual stimulator design based on open hardware and software.
    1. Human Biology and Medicine
    2. Neuroscience

    A consensus guide to capturing the ability to inhibit actions and impulsive behaviors in the stop-signal task

    Frederick Verbruggen et al.
    Clear guidelines and open-source software resources are provided for the stop-signal task, in order to streamline the use of this important tool, and to thereby increase its validity and reliability.
    1. Computational and Systems Biology
    2. Developmental Biology

    A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

    Hernán Morales-Navarrete et al.
    MotionTracking is freely available software that can generate multi-scale geometrical models of mammalian tissue and perform quantitative analysis of tissue architecture.
    1. Neuroscience

    DeepFly3D, a deep learning-based approach for 3D limb and appendage tracking in tethered, adult Drosophila

    Semih Günel et al.
    DeepFly3D, a deep learning-based software, measures limb and appendage movements in tethered, behaving Drosophila and enables precise behavioral measurements during neural recordings, stimulation, and other biological experiments.
    1. Computational and Systems Biology
    2. Human Biology and Medicine

    The MR-Base platform supports systematic causal inference across the human phenome

    Gibran Hemani et al.
    Compiling public datasets into a single, centralised repository and linking directly to analytical software completely transforms the scale and scope of causal inference across the phenome.
    1. Cell Biology
    2. Developmental Biology

    CytoCensus, mapping cell identity and division in tissues and organs using machine learning

    Martin Hailstone et al.
    Easy-to-use image analysis software enables single cell quantitation of cell types and division rates in complex 3D tissues including living Drosophila brains, mouse embryos and Zebrafish organoids.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications

    Sebastià Franch-Expósito et al.
    CNApp is a novel and unique web-based software that enables the performance of comprehensive and integrative analysis of genomic copy number alterations to uncover new associations with patient-oriented relevance.
    1. Computational and Systems Biology
    2. Developmental Biology

    Untwisting the Caenorhabditis elegans embryo

    Ryan Patrick Christensen et al.
    Open-source software can untwist images of live Caenorhabditis elegans embryos, allowing epidermal and neuronal cell position and morphology to be examined in previously inaccessible developmental time periods.
    1. Structural Biology and Molecular Biophysics

    Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

    Michael A Cianfrocco, Andres E Leschziner
    A freely available software environment on Amazon's cloud computing network makes processing of cryo-EM data accessible and affordable.