Optical microscopy in all its variants has been traditionally limited by diffraction. Objects that are smaller than about half the wavelength of light are beyond the resolution achievable by optical microscopy techniques. To answer most relevant questions in scientific labor the need to obtain information on space scales smaller than this fundamental limit naturally arises. During the last decade a set of techniques improving the resolving power of optical microscopy has emerged. One of these techniques is known as STochastic Optical Reconstruction Microscopy (STORM). While this imaging technique has been extensively used to image systems with biological relevance, most of the studies focus on nearly ideal specimens, in which fluorescence background and sample thickness is generally not an obstacle for achieving beyond-diffraction resolution. This thesis summarizes the advances in photophysics and optical physics that, in combination with image analysis tools, allow for the experimental realization of image reconstruction by a pointillistic approach. The methodology for sample preparation proper to the fruit fly brain and the labelling of regions of interest in it are also discussed. Given the nature of the imaging technique, a quantification scheme applied to the imaging of fruit fly tissue sections is discussed in detail for the case of single-color STORM. Multi-color images are also shown, providing evidence of the compatibility of the method with adapted immunohistochemistry protocols that extend the reach of the technique. The results are then proof that the technique can be used to image thick samples where background fluorescence and scattering from tissue are present. An example of how this approach is compatible with systems relevant to soft matter physics is also given, opening a window of possibilities for colloidal studies where the diffraction limit of microscopy must be overcome to obtain important information in the nanoscale.