 This paper presents the development of a quantitative polarisation-sensitive reflection mode THZ-solid immersion SI microscope that allows for the study of local polarisation-dependent THZ response of mesoscale tissue elements with high resolution, and its application to retrieve refractive index distributions over freshly excised rat brain for two orthogonal linear polarisations of the THZ beam. The results show pronounced bifringents in the corpus callosum, formed by well-oriented and densely packed axons bridging the cerebral hemispheres, which is verified by THZ pulse spectroscopy of poor sign brain. The findings highlight the potential of quantitative polarisation THZ microscopy in biophotonics and medical imaging. This article was authored by N. V. Chernamurdin, D. R. Illinois-Inkova, V. A. Gelnoff and others.