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Whole-brain pipelines are essential tools to study brain activity on a brain-wide scale. Currently, these pipelines, which combine different cutting-edge techniques—ranging from the use of transgenic animals to machine learning software—remain a niche area, limited to experts in the field. This chapter introduces BRANT (BRAin-wide Neuron quantification Toolkit), a scalable and user-friendly pipeline for three-dimensional (3D) analysis of whole-brain neuronal activation pattern that combines FosTRAP transgenic strategy, CLARITY tissue clearing protocol, high-resolution RAPID-enabled light-sheet fluorescent microscopy (LSFM), and 3D automated data analysis. By providing a detailed overview of its methodology and applications, this resource seeks to enhance accessibility and encourage the broader use of BRANT in whole-brain analysis.

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BRANT Pipeline to Map Neuronal Activations Across the Entire Brain: An Implementation Guide

  • 实验方案

  • 发表日期：

    2026年

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  • Alessandra Franceschini

摘要

Whole-brain pipelines are essential tools to study brain activity on a brain-wide scale. Currently, these pipelines, which combine different cutting-edge techniques—ranging from the use of transgenic animals to machine learning software—remain a niche area, limited to experts in the field. This chapter introduces BRANT (BRAin-wide Neuron quantification Toolkit), a scalable and user-friendly pipeline for three-dimensional (3D) analysis of whole-brain neuronal activation pattern that combines FosTRAP transgenic strategy, CLARITY tissue clearing protocol, high-resolution RAPID-enabled light-sheet fluorescent microscopy (LSFM), and 3D automated data analysis. By providing a detailed overview of its methodology and applications, this resource seeks to enhance accessibility and encourage the broader use of BRANT in whole-brain analysis.