The new CRISP filter at the Swedish 1-m Solar Telescope provides opportunities for observing the solar atmosphere with unprecedented spatial resolution and cadence. In order to benefit from the high quality of observational data from this instrument, we have developed methods for calibrating and restoring polarized Stokes images, obtained at optical and near infrared wavelengths, taking into account field-of-view variations of the filter properties. In order to facilitate velocity measurements, a time series from a 3D hydrodynamical granulation simulation is used to compute quiet Sun spectral line profiles at different heliocentric angles. The synthetic line profiles, with their convective blueshifts, can be used as absolute references for line-of-sight velocities. Observations of the Ca II 8542 Å line are used to study magnetic fields in chromospheric fibrils. The line wings show the granulation pattern at mid-photospheric heights whereas the overlying chromosphere is seen in the core of the line. Using full Stokes data, we have attempted to observationally verify the alignment of chromospheric fibrils with the magnetic field. Our results suggest that in most cases fibrils are aligned along the magnetic field direction, but we also find examples where this is not the case. Detailed interpretation of Stokes data from spectral lines formed in the chromospheric data can be made using non-LTE inversion codes. For the first time, we use a realistic 3D MHD chromospheric simulation of the quiet Sun to assess how well NLTE inversions recover physical quantities from spectropolarimetric observations of Ca II 8542 Å. We demonstrate that inversions provide realistic estimates of depth-averaged quantities in the chromosphere, although high spectral resolution and high sensitivity are needed to measure quiet Sun chromospheric magnetic fields. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Submitted. Paper 2: Manuscript. Paper 3: Submitted. Paper 4: Submitted.