The absence of common image storage, processing and visualisation approaches is a very serious problem of the collaboration between optical microscopy laboratories. The results produced by individual groups are therefore often not comparable. Even a simple visualisation of image data acquired in a different laboratory is often time-consuming because of the non-existence of a common 3D image file format. In this paper we present a solution to these problems for the specific task of acquisition, storage, processing and visualisation of 3D image data of fluorescently stained genetic material used in the research of the spatial organisation of human genome. We have developed a special software system based on the client/server architecture that enables the collaboration of laboratories active in this field. Each laboratory acquires the 3D image data using its own microscopes but stores them together with a detailed description of the samples on a central high-performance multi-processor UNIX server that acts as a file server, database server and image analysis server that accepts orders from individual clients. The requested parts of image data as well as image analysis results are sent back to the clients via Internet. In order to provide high computational power the server was equipped with the fastest processors available and the whole network architecture has been optimised for speed.