An Image Processing Platform for Neurovasculature Unit Processed by CLARITY

The newly developed CLARITY technique will transfer the whole tissue into hydrogel state by biological and chemical methods to maintain the endogenous fluorescence of tissues. CLARITY has already been used to study the relationship between gray matter atrophy and spinal cord pathology in an experimental autoimmune encephalomyelitis model. It is useful for exploring structure of tissues in brain and therefore, understanding its function. However, studies on reconstruction and quantification of tissues images after CLARITY were limited since CLARITY is a new method in this research area. Here the paper developed an image processing platform using a series of images processing algorithm specially for CLARITY. And an experimental and control group is prepared and imaged mouse brain after CLARITY and customized code for this CLARITY are selected. Finally, it visualized the data using Amira and performed quantitative analysis. The customized platform mainly included the preprocessing part, like cutting, histogram matching, brightness adjustment, filtering and morphological operation. The later part was an algorithm specially for different tissues. Results showed that microglia density along depth remained almost unchanged in two groups, microglia diffuses in 2vo group and vessel length and density were the same as the previous study. The conclusions were CLARTY which provided a new tool for studying tissues of mouse brain at high resolution. The analysis platform could offer a powerful tool for further evaluating structural alteration of brain.