The Connectome Project

Colorful dotsWe are interested in the segmentation, visualization and analysis of brain scans in electron and optical microscopy in the multi-terabyte range.

Sponsored by NSF, NIH and private foundations.

Team Members: Ray Jones, Seymour Knowles-Barley, Verena Kaynig, Steffen Kirchhoff, Johanna Beyer, Ali Al-Awami, Adi Peleg, Daniel Haehn, Hanspeter Pfister

The wiring of brains is staggeringly complex. Our own brains have tens of billions of neurons connected through perhaps one hundred trillion synapses. This circuitry is the result of our development and experience; the neural activity that courses through and alters it, somehow accounts for our thoughts, our behavior, our memories. To echo Wheeler's synopsis of Einstein's theory of gravity: neural circuits tell activity how to propagate and neural activity tells circuits how to change. One hundred years from now, this brain circuitry will be known; today, for the first time, we can contemplate mapping it in detail. New forms of laser-scanning light microscopy and semi-automated electron microscopy allow high resolution imaging of “connectomes”—that is, complete neural wiring diagrams.

Our group collaborates with the Center for Brain Science on the segmentation and visualization and analysis of such images. Some of the challenges our group deals with involve the processing of multi-terabyte and multi-spectral image datasets.

Software tools for connectome research including RhoANA, our segmentation pipeline, and Mojo, our connectome annotation tool, are available at