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. Medicine
    2. Stem Cells and Regenerative Medicine

    Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19

    Courtney Tindle et al.
    An integrated stem cell-based disease modeling and computational approach demonstrates how proximal airway epithelium is critical for SARS-CoV-2 infectivity and distal alveolar cells are critical for simulating the host responses.
    1. Neuroscience

    A unified platform to manage, share, and archive morphological and functional data in insect neuroscience

    Stanley Heinze et al.
    The InsectBrain Database is a novel, freely available software tool designed to accelerate research in the field of insect neuroscience and to improve implementation of open data concepts.
    1. Neuroscience

    DeepEthogram, a machine learning pipeline for supervised behavior classification from raw pixels

    James P Bohnslav et al.
    DeepEthogram automatically classifies animal behavior videos into researcher-defined behaviors of interest, saving researcher time and enabling more detailed downstream analysis of behavior.
    1. Biochemistry and Chemical Biology
    2. Neuroscience

    Precise optical control of gene expression in C elegans using improved genetic code expansion and Cre recombinase

    Lloyd Davis et al.
    A method combining optimised genetic code expansion and optogenetics allows dissection of neural circuits with single-cell precision in freely moving animals.
    1. Computational and Systems Biology

    PARROT is a flexible recurrent neural network framework for analysis of large protein datasets

    Daniel Griffith, Alex S Holehouse
    PARROT makes it easy for anyone to train and use system- or data-specific deep learning models that map between protein sequence and arbitrary sequence annotations.
    1. Immunology and Inflammation

    Ascorbic acid supports ex vivo generation of plasmacytoid dendritic cells from circulating hematopoietic stem cells

    Anders Laustsen et al.
    Probing of various culture conditions leads to fundamental advances in ex vivo production of plasmacytoid dendritic cells for use in immunotherapy.
    1. Neuroscience

    The BigBrainWarp toolbox for integration of BigBrain 3D histology with multimodal neuroimaging

    Casey Paquola et al.
    The BigBrainWarp toolbox facilitates integration of 3D human brain histology with neuroimaging, helping neuroscientists to utilise cytoarchitectural information in conjunction with in vivo imaging.
    1. Neuroscience

    Classification and genetic targeting of cell types in the primary taste and premotor center of the adult Drosophila brain

    Gabriella R Sterne et al.
    A split-GAL4 collection provides precise genetic targeting of 138 neuronal cell types in the subesophageal zone of adult Drosophila melanogaster.
    1. Genetics and Genomics
    2. Neuroscience

    Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization

    Brian R Lee et al.
    High-quality, multimodal, electrophysiological, morphological, and transcriptomic data collection from a single cell using a refined Patch-seq protocol.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    MiSiC, a general deep learning-based method for the high-throughput cell segmentation of complex bacterial communities

    Swapnesh Panigrahi et al.
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