Browse our Tools and Resources

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    1. Developmental Biology
    2. Neuroscience

    Volumetric trans-scale imaging of massive quantity of heterogeneous cell populations in centimeter-wide tissue and embryo

    Taro Ichimura, Taishi Kakizuka ... Takeharu Nagai
    Volumetric trans-scale imaging with a subcellular resolution across a wide field-of-view of 1.5 × 1.0 cm2 has been realized, facilitating the analysis of cellular dynamics during embryogenesis and brain function.
    1. Neuroscience

    Predicting individual traits from models of brain dynamics accurately and reliably using the Fisher kernel

    Christine Ahrends, Mark W Woolrich, Diego Vidaurre
    The HMM-Fisher kernel approach leverages individual signatures of brain dynamics for prediction, which can be used, for example, to search for brain dynamics-informed biomarkers of neuropsychiatric disease or predict treatment response.
    1. Neuroscience

    Driver lines for studying associative learning in Drosophila

    Yichun Shuai, Megan Sammons ... Yoshinori Aso
    A new collection of driver lines enables experimental manipulation of over 300 cell types centered around the mushroom body in Drosophila.
    1. Computational and Systems Biology

    CausalXtract, a flexible pipeline to extract causal effects from live-cell time-lapse imaging data

    Franck Simon, Maria Colomba Comes ... Herve Isambert
    CausalXtract is a computational tool to discover causal effects, beyond classical Granger and Schreiber causality approaches, from live-cell imaging data for a range of fundamental and translational research applications.
    1. Cell Biology
    2. Genetics and Genomics

    Robust single-nucleus RNA sequencing reveals depot-specific cell population dynamics in adipose tissue remodeling during obesity

    Jisun So, Olivia Strobel ... Hyun Cheol Roh
    Significant technical improvement in single-nucleus RNA-seq reveals distinct adipocyte subpopulations that respond differently to obesity, including those undergoing adaptive healthy expansion and others displaying severe dysfunction.
    1. Neuroscience

    The NeuroML ecosystem for standardized multi-scale modeling in neuroscience

    Ankur Sinha, Padraig Gleeson ... Robin Angus Silver
    The NeuroML model description language, with its extensive software ecosystem, supports researchers in the development of FAIR, data-driven, biologically detailed models of neural systems.
    1. Cell Biology

    Atlas of Fshr expression from novel reporter mice

    Hongqian Chen, Hui-Qing Fang ... Peng Liu
    Exploiting the power of the Fshr reporter, the first comprehensive genetic record of the spatial distribution of FSHR expression offers prospects for extensive exploration of FSH-FSHR biology.
    1. Neuroscience

    Three-dimensional single-cell transcriptome imaging of thick tissues

    Rongxin Fang, Aaron Halpern ... Xiaowei Zhuang
    By integrating multiplexed error-robust fluorescence in situ hybridization (MERFISH), deep learning, optical sectioning, and protocol optimization, thick-tissue 3D MERFISH allows volumetric single-cell transcriptome imaging of thick-tissue samples, broadening the scope of applications of spatial genomics.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    A novel human pluripotent stem cell gene activation system identifies IGFBP2 as a mediator in the production of haematopoietic progenitors in vitro

    Paolo Petazzi, Telma Ventura ... Antonella Fidanza
    A novel tool is used to assess gene function in vitro by targeted endogenous transcriptional activation to unveil novel players in development and disease.
    1. Structural Biology and Molecular Biophysics

    Streamlining segmentation of cryo-electron tomography datasets with Ais

    Mart GF Last, Leoni Abendstein ... Thomas H Sharp
    The software package Ais simplifies automated segmentation in cryo-electron tomography, enabling users to segment, detect particles, and visualize data in a streamlined and accessible workflow.