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. This innovative design-based stereology has almost entirely supplanted the application of the older geometric model-based stereology in most biological analysis purposes.Quantifying the distribution of specific neurons throughout the whole brain is crucial for understanding physiological actions, pathological alterations and pharmacological treatments. It can often be used in vitro studies to increase sampling validity for quantitative parameters. As changes of physiologically related ranges within the tissue are usually far below a fold variation, stereology gives a strong analytical tool for in vivo histological studies. When correctly applied, stereology can allow for constant detection of differences only slightly bigger than inter animal variation. By utilising proper sampling procedures and using counting or mapping protocols (known as probes), stereology makes it feasible to avoid potential artefacts and errors that could significantly skew outcomes. Getting accurate measures is a significant component of producing a study result with statistical validity. Stereology is the method of sampling and counting material utilising particular protocols to get an estimate of a quantitative parameter, such as number, length, volume, etc.
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