Computer-assisted registration, segmentation, and 3D reconstruction from images of neuronal tissue sections

Neuroscientists have studied the relationship between nerve cell morphology and function for over a century. To pursue these studies, they need accurate three-dimensional models of nerve cells that facilitate detailed anatomical measurement and the identification of internal structures. Although serial transmission electron microscopy has been a source of such models since the mid 1960s, model reconstruction and analysis remain very time consuming. The authors have developed a new approach to reconstructing and visualizing 3D nerve cell models from serial microscopy. An interactive system exploits recent computer graphics and computer vision techniques to significantly reduce the time required to build such models. The key ingredients of the system are a digital "blink comparator" for section registration, "snakes," or active deformable contours, for semiautomated cell segmentation, and voxel-based techniques for 3D reconstruction and visualization of complex cell volumes with internal structures.