• perineuronal nets
• parvalbumin
• brain-wide analysis
• Allen Brain Mouse Atlas
• U-Net

First described by Camillo Golgi, perineuronal nets (PNNs) are extracellular matrix (ECM) aggregates that surround the cell body and the proximal dendrites of various cell types, particularly fast-spiking parvalbumin-expressing interneurons. Originally thought to merely provide mechanical support, it is now widely acknowledged that PNNs represent the substrate for several physiological processes and pathological conditions. Despite the growing body of literature dissecting PNN function in various systems, a comprehensive characterization of their distribution in the entire adult mouse brain is still not available. Thus, our knowledge is restricted to a few areas of interest and more general principles of PNN biology are not accessible. In the present work, we face the issue by developing a computational tool for the brain-wide analysis of PNNs, both in terms of diffuse per area fluorescence and PNN density. This is achieved by aligning histological samples to an unbiased template represented by the Allen Brain Common Coordinate Framework. Additionally, to increase the number of specimens that the pipeline can process, we trained the deep neural network U-Net for automated PNN detection. This approach will allow unraveling the differences in PNN expression under different experimental conditions, potentially shedding new light on the effects of the ECM in brain physiology, pathology, and development.