In recent years, the combination of whole-brain immunolabelling, light sheet fluorescence microscopy (LSFM) and subsequent registration of data with a common reference atlas, has enabled 3D visualization and quantification of fluorescent markers or tracers in the adult mouse brain. Today, the common coordinate framework version 3 developed by the Allen’s Institute of Brain Science (AIBS CCFv3), is widely used as the standard brain atlas for registration of LSFM data. However, the AIBS CCFv3 is based on histological processing and imaging modalities different from those used for LSFM imaging and consequently, the data differ in both tissue contrast and morphology. To improve the accuracy and speed by which LSFM-imaged whole-brain data can be registered and quantified, we have created an optimized digital mouse brain atlas based on immunolabelled and solvent-cleared brains. Compared to the AIBS CCFv3 atlas, our atlas resulted in faster and more accurate mapping of neuronal activity as measured by c-Fos expression, especially in the hindbrain. We further demonstrated utility of the LSFM atlas by comparing whole-brain quantitative changes in c-Fos expression following acute administration of semaglutide in lean and diet-induced obese mice. In combination with an improved algorithm for c-Fos detection, the LSFM atlas enables unbiased and computationally efficient characterization of drug effects on whole-brain neuronal activity patterns. In conclusion, we established an optimized reference atlas for more precise mapping of fluorescent markers, including c-Fos, in mouse brains processed for LSFM.

近年来，全脑免疫标记、光片荧光显微镜 (LSFM) 以及随后将数据与通用参考图谱注册相结合，使成年小鼠大脑中的荧光标记或示踪剂的 3D 可视化和量化成为可能。今天，由艾伦脑科学研究所（AIBS CCFv3）开发的通用坐标框架版本3，被广泛用作LSFM数据注册的标准脑图谱。然而，AIBS CCFv3 基于与 LSFM 成像不同的组织学处理和成像模式，因此，数据在组织对比度和形态方面都不同。为了提高 LSFM 成像全脑数据的登记和量化的准确性和速度，我们基于免疫标记和溶剂清除的大脑创建了一个优化的数字小鼠大脑图谱。与 AIBS CCFv3 图谱相比，我们的图谱可以更快、更准确地绘制神经元活动的映射，如通过 c-Fos 表达测量的，尤其是在后脑中。我们通过比较瘦和饮食诱导的肥胖小鼠急性施用司美鲁肽后 c-Fos 表达的全脑定量变化，进一步证明了 LSFM 图谱的效用。结合用于 c-Fos 检测的改进算法，LSFM 图谱能够对药物对全脑神经元活动模式的影响进行无偏和计算高效的表征。总之，我们建立了一个优化的参考图谱，以便在为 LSFM 处理的小鼠大脑中更精确地绘制荧光标记物，包括 c-Fos。