In this paper, we discuss various aspects of an image analysis system for images obtained from a laser scanning confocal light microscope with particular emphasis on segmentation techniques. The main areas of interest of the image analysis system are: pre-processing, segmentation, data structures used to represent objects, morphometry, and visualization of three-dimensional microscopic structures. Pre-processing techniques are discussed, both for reduction of spurious intensity variations using digital filters and for intensity correction to account for the loss of signal due to photo bleaching and due to the field curvature of the objective lens. The segmentation techniques discussed in this paper include data driven approaches such as region segmentation based on intensity variations as well as model driven approaches such as boundary refinement based on object models. The segmented image is then used to extract morphometric parameters of microscopic structures such as surface area, volume, center of gravity, eccentricity, and skeleton. Several algorithms are presented to extract this information and methods of presenting the results are also discussed. Finally, various methods and implementation aspects of visualizing both raw data and segmented images are evaluated together with techniques for interactive manipulation of the images.