The analysis of processes on a cellular and sub-cellular level plays a crucial role in life sciences. Commonly microscopic assays make use of stains and cellular markers in order to enhance image contrast, but in many cases, cell imaging requires the sample to be undisturbed during the imaging process, making staining, dying and fixing impractical. Non-destructive techniques are especially useful in long term imaging or in the study of sensitive cell types, such as stem cells, embryos or nerve cells. Novel advances in computation, imaging and incubator technology have recently made it possible to prolong the imaging time, reduced the cost of storing data and opened a door to the development of new computer aided analytical tools based on microscopic image data. Here we illustrate how Hoffman Modulation Contrast imaging and Confocal Microscopy can be combined with visual computing and present results from determination of cell number, volume, spatial location and blastomere connectivity, using examples from embryos grown for in vitro fertilisation. We give examples of how knowledge of the imaging technique can be used to further improve the computer analysis and also how visually guided tools may aid in the diagnostic interpretation of image data and improve the result. Finally we discuss how the use of microscopic data as a basis for embryo modelling may help in both research and educational purposes. The aim of this chapter is to give an example of how microscopic imaging can be combined with standard computer vision techniques to aid in the interpretation of microscopic data, and demonstrate how visual computing techniques can make an essential difference in terms of scientific output and understanding.