Computer Assisted Identification, Segmentation and Quantification of Synapses in the Cerebral Cortex

Synapses are key elements in the organization of nervous circuits. Obtaining serial images from large samples of nervous tissue in an automated manner is now possible through combined focused ion beam milling and scanning electron microscopy. However, the identification, 3D reconstruction and quantification of synapses within these samples are labor intensive procedures that require continuous user intervention. We have developed a software tool to automatically perform the segmentation of synapses in a reconstructed 3D volume of the cerebral cortex, thereby greatly facilitating and accelerating these processes. The tool is interactive, allowing the user to supervise the segmentation process, to modify the appropriate parameters and to validate the results. It is also modular to enable new functions to be implemented as needed. We have also ensured it has a user friendly interface and that it is portable, making it accessible to a wide range of potential users.