This paper describes the research and development of the two compact vision systems for real-time cell detection and manipulation in the capillary in order to apply on the "desktop bioplant" project which will achieve sort of cell manipulation tasks such as positioning, cutting, sizing, and so on, automatically between different interconnected modules. The first prototype vision system with sufficient magnification and image resolution has been designed to be boarded onto the PDMS chip. Design schema and preliminary experimental results of first proposed system have been also given. A second system with a commercially available small size and light-weight microscope unit has also been prototyped to be integrated under microfluidic channel. The integration of two models with desktop bioplant could bring a good solution to automation of the cell manipulation including nuclear transportation. While the size and weight of the total systems are decreased to provide portability and compatibility, determining the position and management of an egg-cell in a capillary has vital importance for the automation of nuclear transportation in a capillary with using micro robotics