If several laboratories work in the same field and need to cooperate, it is necessary to exchange and mutually compare their computer results. The quick way to solve this problem is to unite their file formats (if it is practicable) or to install new software systems, which are data or file format compatible. A much better solution is to use only one common system.This article describes the architecture of a new client-server system, which offers possibilities of effective cooperation for laboratories doing the research in the field of the spatial organization of human genome. However, the system design is determined mainly by optical microscopy principles and therefore the system can easily be modified for use in other applications or environments. The most pressing problem during the system design was how to share and process large 3D image data in client-server architecture.