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. Cell Biology
    2. Immunology and Inflammation

    UFMTrack, an Under-Flow Migration Tracker enabling analysis of the entire multi-step immune cell extravasation cascade across the blood-brain barrier in microfluidic devices

    Mykhailo Vladymyrov, Luca Marchetti ... Britta Engelhardt
    The established under-flow migration tracker (UFMTrack) framework allows for automated and scalable studies of immune cell interactions with and extravasation across endothelial monolayer under flow in vitro.
    1. Developmental Biology

    A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate

    Eric R Brooks, Andrew R Moorman ... Jennifer A Zallen
    Single-cell RNA sequencing and computational analysis define a spatial and temporal map of gene expression during early patterning and morphogenesis of the mouse cranial neural plate, providing a resource for elucidating the transcriptional basis of mammalian brain development.
    1. Biochemistry and Chemical Biology

    Decoding m6Am by simultaneous transcription-start mapping and methylation quantification

    Jianheng Fox Liu, Ben R Hawley ... Samie R Jaffrey
    CROWN-seq provides the first precise and quantitative map of N6,2’-O-dimethyladenosine (m6Am) in mRNA and snRNA, revealing the link between m6Am modification and efficient transcription, rather than translation and RNA stability.
    1. Developmental Biology

    3D reconstruction of neuronal allometry and neuromuscular projections in asexual planarians using expansion tiling light sheet microscopy

    Jing Lu, Hao Xu ... Kai Lei
    A high-resolution, high-speed tissue imaging analysis reveals how neural and muscular tissues coordinate during planarian growth and regeneration.
    1. Developmental Biology

    Spatial transcriptomics in the adult Drosophila brain and body

    Jasper Janssens, Pierre Mangeol ... Frank Schnorrer
    Spatial transcriptomics of adult Drosophila brain and body sections determined the spatial expression for 150 genes, which identified the locations of unknown neuronal cell types and transcriptional diversity within muscle.
    1. Computational and Systems Biology
    2. Neuroscience

    A statistical framework for analysis of trial-level temporal dynamics in fiber photometry experiments

    Gabriel Loewinger, Erjia Cui ... Francisco Pereira
    A fiber photometry analysis framework based on functional mixed models enhances the detection of effects by testing signal-variable associations at each trial timepoint and accounting for between-animal heterogeneity.
    1. Neuroscience

    Using normative models pre-trained on cross-sectional data to evaluate intra-individual longitudinal changes in neuroimaging data

    Barbora Rehak Buckova, Charlotte Fraza ... Jaroslav Hlinka
    Normative modelling adapted for longitudinal neuroimaging enables precise evaluation of individual brain changes over time, revealing subtle disease dynamics and temporal patterns missed by traditional analytical approaches.
    1. Neuroscience

    ThermoMaze behavioral paradigm for assessing immobility-related brain events in rodents

    Mihály Vöröslakos, Yunchang Zhang ... György Buzsáki
    The ThermoMaze behavioral paradigm enables the collection of extensive physiological data while animals remain at distinct experimenter-controlled locations during rest.
    1. Neuroscience

    A deep learning framework for automated and generalized synaptic event analysis

    Philipp S O'Neill, Martín Baccino-Calace ... Igor Delvendahl
    miniML, a deep learning-based method, facilitates synaptic event analysis with high accuracy and versatility across diverse synaptic preparations, enabling high-throughput investigations of neural function and dysfunction.
    1. Neuroscience

    An Intranet of Things approach for adaptable control of behavioral and navigation-based experiments

    John C Bowler, George Zakka ... Attila Losonczy
    behaviorMate provides a flexible, open-source platform for in vivo investigations that relies on a network of devices to enable observation of neural activity during navigation using physical treadmill and VR setups.