A decision on how to choose the appropriate data quantification procedure lies behind the most serious methodological challenges in microbeam X-ray fluorescence imaging of tissue slices. This problem becomes particularly cumbersome whenever intermediate thickness samples must be utilized in order to increase the signal to noise ratio. Noteworthy, it is always the case when laboratory-based X-ray sources are used, which arises from their relatively limited beam flux. In our study, we put particular attention to the quantitative elemental microanalysis of dried brain tissue samples taken from the obese rats treated by the transcranial direct current stimulation. For doing so, we took advantage of tissue probing by an X-ray microscope system for accessing P, S, Cl, K, Ca, Fe, Cu, and Zn in the brain structures triggering food intake and appetite regulation. Proper data quantification schemes are presented by showing the elements whereby the radiation loss by self-absorption of fluorescence radiation is negligible. The impact of sample self-absorption correction on quantitative data is studied for the brain structures with various water fraction spanning from 75-83%. It is demonstrated that K, Ca, Fe, Cu, and Zn can effectively be quantified by the thin-sample approach, regardless sample matrix. Quantitative results demonstrate that the clinical efficacy of transcranial direct current stimulation is linked to significant changes in surface masses of elements triggering brain membrane currents: K, Cl, and also, those defining the redox state: Fe in the hunger center.