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

    Anti-drift pose tracker (ADPT), a transformer-based network for robust animal pose estimation cross-species

    Guoling Tang, Yaning Han ... Pengfei Wei
    ADPT enhances the robustness of animal pose estimation by minimizing keypoint tracking drift, enabling more accurate multi-animal tracking and facilitating refined behavioral analysis across species.
    1. Neuroscience

    A toolbox for ablating excitatory and inhibitory synapses

    Aida Bareghamyan, Changfeng Deng ... Don B Arnold
    Novel genetically encoded tools PFE3, paGFE3, and chGFE3 can be used to reversibly ablate excitatory synapses constitutively, and inhibitory synapses in a light- or chemically dependent manner.
    1. Computational and Systems Biology

    Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing

    Masaaki Uematsu, Jeremy M Baskin
    SAVEMONEY is a computational tool that guides users to mix plasmids prior to nanopore sequencing, reducing the effective cost of whole-plasmid sequencing to below that of Sanger sequencing.
    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.