This thesis covers three experiments with cold and ultracold (Bose-Einstein condensate based) alkali Rb-87 gases for quantum simulation. In the first experiment, we quantum simulate Abelian and non-Abelian gauge fields in the parameter space of a four-level quantum system. Then, we describe the experimental framework to perform optimal in-situ microscopy of elongated quantum gases. We then study the thermodynamics of individual one-dimensional Bose gases using in-situ resonant absorption imaging. Finally, we combine holographic microscopy and impulse correlations to digitally enhance our absorption images.