Within this study, we successfully applied a dual-color, single-molecule, 2-D super-resolution method to determine the protein distribution of serotonin receptor in brain tissue. In particular, we were able to visualize serotonin receptor clusters at nanometer resolution level (down to 22.5 nm) in native and fixed dense light-scattering brain tissues. Our results were obtained from samples that are typically used in immunohistochemistry, which simplifies the implementation of our approach and shows a promising potential for more accurate analysis applications. The fast-imaging process further allows the recording of large sets of high-resolution images, which renders the comparative analysis between different tissue samples possible. The 2-D image of nanoscopically mapped serotonin receptors was used for a novel cluster-based analysis with respect to their sizes, densities, elongations, and relationship to bulk fluorescent structures (glia tissue). Herein, we would like to stress that the presented clustering method is the only technique which enables the combined analysis of localization microscopy and bulk fluorescence imaging. The proposed spatial analysis method allowed us to characterize the effects of long-term paraffin conservation and epitope retrieval on brain tissue. Also, the analysis method reveals differences between pathological (MDD) and healthy brain samples and indicates its potential application in tissue classification. In the case of receptors, which are expressed on glial as well as neural cells, the distribution of clusters is certainly influenced by several factors like, e.g., the cell type and cell-cell interactions or changes in pathological tissue morphology. Therefore, we applied correlative analysis between images of the glia tissue and single-molecule cluster distribution, which should include only the clusters associated with the labeled glial cells in the analysis.