New microscopy imaging techniques have enabled the acquisition of cellular and sub-cellular information with unprecedented accuracy and specificity. Fluorescence techniques have enabled labeling of numerous, previously inaccessible, molecules and organelles, while Raman spectrographic techniques, for example, have enabled label free acquisition. Together with the development of high throughput techniques, these technologies now allow for the acquisition of a significant amount of information about cellular processes and have enabled high throughput and high content screening. Beyond image formation and acquisition, computational techniques comprise an important part of the process of obtaining biological understanding from such experiments. Here we review the pros and cons of the main approaches that have been used to extract information from digital images of cells. In addition, we also offer an overview of modern computational techniques that beyond allowing for discrimination between two hypothesis, also allow for modeling, visualization, and understanding of biological phenomena.