The brain is an important and extremely complex organ. ![]() The results indicated that this whole-brain cell counting pipeline has the potential to become a routine tool for cell type neuroscience studies. To apply this pipeline, we acquired and quantified the brain-wide distributions and somatic morphology of somatostatin-expressing neurons in transgenic mouse brains. We evaluated the data continuity of the 3D dataset and the accuracy of stereological cell counting in 3D. We employed a Brain-wide Positioning System to collect high-throughput anatomical information with the co-localized cytoarchitecture of the whole brain at subcellular resolution and utilized the NeuroGPS algorithm to locate and count cells in the whole brain. Here, we propose a pipeline to automatically acquire and analyse the brain-wide distribution of type-specific neurons in a mouse brain. However, the precise cell number and density of specific neurons in the entire brain remain unknown because of a lack of suitable research tools. Quantifying the distribution of specific neurons throughout the whole brain is crucial for understanding physiological actions, pathological alterations and pharmacological treatments.
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