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

    Inference technique for the synaptic conductances in rhythmically active networks and application to respiratory central pattern generation circuits

    Yaroslav Molkov, Anke Borgmann ... Jeffrey Smith
    A robust method to infer excitatory and inhibitory synaptic conductances from neuronal recordings reveals functional circuit organization in rhythmic networks.
    1. Cell Biology
    2. Neuroscience

    CellSeg3D, Self-supervised 3D cell segmentation for fluorescence microscopy

    Cyril Achard, Timokleia Kousi ... Mackenzie Weygandt Mathis
    Self-supervised deep learning models can accurately perform 3D segmentation of cell nuclei in complex biological tissues, enabling scalable analysis in settings with limited or no ground truth annotations.
    1. Computational and Systems Biology

    Artificial intelligence driven tumor risk stratification from single-cell transcriptomics using phenotype algebra

    Namrata Bhattacharya, Anja Rockstroh ... Debarka Sengupta
    SCellBOW is a language model-based scRNA-seq analysis method that identifies malignant cell subpopulations and infers marker-free survival risks using transfer learning.
    1. Cancer Biology
    2. Cell Biology

    Image-based identification and isolation of micronucleated cells to dissect cellular consequences

    Lucian DiPeso, Sriram Pendyala ... Emily M Hatch
    The development of an automated micronucleus segmentation program enables population-level comparisons between cells with and without micronuclei and defines a highly limited response to micronucleus formation or rupture.
    1. Structural Biology and Molecular Biophysics

    A comprehensive antigen-antibody complex database unlocking insights into interaction interface

    Yuwei Zhou, Wenwen Liu ... Jian Huang
    AACDB provides a comprehensive, manually curated antigen-antibody interface dataset with rich metadata, interaction annotations, and therapeutic target annotations to advance antibody drug development.
    1. Computational and Systems Biology
    2. Neuroscience

    MorphoCellSorter is an Andrews plot-based sorting approach to rank microglia according to their morphological features

    Sarah Benkeder, Son-Michel Dinh ... Jean-Christophe Comte
    MorphoCellSorter is a versatile, user-friendly tool that automates microglial morphology ranking, enabling standardized, reproducible analysis across diverse models, imaging techniques, and conditions using principal component analysis and Andrews plots.
    1. Developmental Biology

    Single nuclei RNA-sequencing of adult brain neurons derived from type 2 neuroblasts reveals transcriptional complexity in the insect central complex

    Derek G Epiney, Gonzalo Morales Chaya ... Chris Q Doe
    The central complex of the adult Drosophila brain, required for sensorimotor integration, is transcriptionally complex as detected by single-cell transcriptome analysis.
    1. Neuroscience

    Dual-color optical activation and suppression of neurons with high temporal precision

    Noëmie Mermet-Joret, Andrea Moreno ... Sadegh Nabavi
    An optogenetic system capable of precise, high-frequency neuronal excitation using red pulsed light and rapid, millisecond inhibition using blue light.
    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.