In this thesis, an extensive exploration of the low surface brightness Universe has been undertaken. A special emphasis has been placed on reducing the limitations arising from the use of integrated photometry, such as the residuals due to the observation and reduction of astronomical data, the effects of the point spread function and the presence of Galactic cirri. With this goal, numerous techniques have been developed and successfully applied to a large number of different data sets. In particular, an improvement in the image quality of the IAC Stripe82 Legacy Survey has been carried out, a data set that has been widely used in this thesis. Some complementary limitations such as big data analysis and the estimation of astronomical distances are also addressed. A comprehensive study has also been carried out of the so-called ultra-diffuse galaxies with significant results about its currently debated nature. Through the direct use of several astronomical facilities it has been possible to obtain a wealth experience in data processing, achieving great efficiency in the production of high quality images at low surface brightness. Some of the images produced are the deepest and highest quality in selected objects, such as intracluster light in galaxy clusters or galactic stellar halos, results that are currently under analysis. In general, this thesis has achieved a thorough study of the low surface brightness Universe and its observational limitations.