This course begins with a description of the image degradations inherent to three-dimensional microscopy by optical sectioning –as opposed to physical sectioning. The course continues with a description of the advantages and disadvantages of different computational methods to undo the degradations introduced by the process of image formation and recording and the availability of the different methods in commercially and freely distributed packages. The last part of the course gives guidelines on 3D data collection for deconvolution or, more precisely, how not to collect 3D stacks to be used for deconvolution with different methods.