Tissue-clearing in combination with light-sheet microscopy enabled scientists to observe entire organs and animals without the necessity of histological sectioning. However, the variety of different tissue-clearing methods often ponders the question of which protocol to use. Here we provide the chemical fundamentals for dehydration-based tissue-clearing approaches and show important, yet neglected parameters, for preserving morphology and drastically improving tissue transparency and light transmission. These parameters are the polarity of the dehydration agent, color of the tissue-cleared sample and temperature of the refractive index (RI) matching medium. Further, we use a hyperhydration and delipidation step to shorten the subsequent dehydration time and thus improving endogenous fluorescent signal.We use kidneys to show and quantify the pathology of polycystic kidney disease (PKD) in mice with different genetic background and compare our result with MRI imaging performed in the same mice. Additionally, we show the unobstructed motor neuron connectome in Chx10 positive mice, originating in the brainstem and projecting to the end of the spinal cord.Further, we introduce an updated version of the mesoSPIM light-sheet macroscope termed macro2mesoSPIM. With this updated version we use a heating chamber to optimize tissue transparency and use a set of modified long-working distance objectives, providing a field of view from 2cm-1.9mm and a resolution from 6.5um up to 600nm.Taken together, we provide scientists we the basics for understanding the important parameters for their tissue of interest and we introduce an upgrade to the mesoSPIM light-sheet system enabling for meso to macroscale imaging whit high resolution