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    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens

    Stephan Kamrad et al.
    An open-source python package for phenotype analyses provides a versatile, modular and user-friendly solution to determine complementary fitness-related traits from large-scale assays of microbial colonies.
    1. Structural Biology and Molecular Biophysics

    Fully automated, sequential focused ion beam milling for cryo-electron tomography

    Tobias Zachs et al.
    The automation of cryo-focused ion beam milling enables previously unfeasible cryo-electron tomography projects.
    1. Computational and Systems Biology
    2. Neuroscience

    3DeeCellTracker, a deep learning-based pipeline for segmenting and tracking cells in 3D time lapse images

    Chentao Wen et al.
    A deep learning-based pipeline was developed for extracting cellular signals flexibly from moving cells in 3D time lapse images, and it outperformed previous methods under different imaging conditions.
    1. Neuroscience

    CaImAn an open source tool for scalable calcium imaging data analysis

    Andrea Giovannucci et al.
    CaImAn is an open-software package that equips the neuroscience community with a set of turnkey, fast and scalable solutions to pre-processing problems arising in single cell calcium imaging data analysis.
    1. Developmental Biology
    2. Plant Biology

    Live tracking of moving samples in confocal microscopy for vertically grown roots

    Daniel von Wangenheim et al.
    A set of tools to image and track growing plant roots in optimized growing conditions within a vertical stage confocal microscope will open up new possibilities in research of root development.
    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. Cell Biology
    2. Structural Biology and Molecular Biophysics

    3D in situ imaging of the female reproductive tract reveals molecular signatures of fertilizing spermatozoa in mice

    Lukas Ded et al.
    Fertilizing mouse spermatozoa, characterized by intact CatSper channels, lack of protein tyrosine phosphorylation, and reacted acrosomes, in the female reproductive tract provide molecular insight into sperm selection for successful fertilization.
    1. Cell Biology
    2. Physics of Living Systems

    KymoButler, a deep learning software for automated kymograph analysis

    Maximilian AH Jakobs et al.
    KymoButler is a machine learning approach towards the reliable, quick, and fully automated analysis of the dynamics of fluorescently labelled particles in living cells.
    1. Cell Biology
    2. Computational and Systems Biology

    A quantitative approach for analyzing the spatio-temporal distribution of 3D intracellular events in fluorescence microscopy

    Thierry Pécot et al.
    QuantEv is a fully automatic and semi-parametric method that allows quantitative analysis of the spatio-temporal distribution of complex molecular trafficking objects at the scale of the whole cell.
    1. Developmental Biology

    The Drosophila Individual Activity Monitoring and Detection System (DIAMonDS)

    Ki-Hyeon Seong et al.
    The DIAMonDS can automatically and sequentially identify time points of multiple life cycle events such as pupariation, eclosion, and death in individual flies at high temporal resolution and large scale.