How to create a Connectome Observatory of the mouse brain and beyond, by Ken Hayworth

Dr. Kenneth Hayworth spoke in teleXLR8 on Sunday, November 13, at 10am PST.

How to create a Connectome Observatory of the mouse brain and beyond

Several laboratories are now using Focused Ion Beam Scanning Electron Microscopes (FIB-SEM) to image small volumes of plastic embedded brain tissue at resolutions approaching 5x5x5nm voxel size. The fact that FIBSEM can obtain such resolution is of fundamental importance since at this resolution all neuronal processes should be traceable with 100% accuracy using fully automatic algorithms. A fundamental physical limitation of the FIB ablation process is that this resolution can only be obtained for very small samples on the order of 20 microns across. To overcome this limitation I have developed a technique using a heated, oil-lubricated, ultrasonically vibrating diamond knife which can section large blocks of plastic-embedded brain tissue into 20 micron thick strips optimally sized for high-resolution FIB-SEM imaging. Crucially, this thick sectioning procedure results in such high-quality surfaces that the finest neuronal processes can be traced from strip to strip.

In this talk I will present these results as well as a detailed design for a machine automating this thick sectioning procedure on the scale of a whole mouse brain. An entire plastic-embedded mouse brain would first be sectioned on this machine into a tape containing 500 tissue slabs (each 20 microns thick). The same machine is then used to section each of these slabs into 300 tissue pillars each 15mm long and 20x20microns in cross section. These “pillar tapes” have been carefully designed to allow random access FIB-SEM imaging of any 20x20x20micron sub-volume within the mouse brain quickly and with 100% reliability.

Spreading these pillar tapes among 20 specially designed FIB-SEM machines would create a “Connectome Observatory” of the mouse brain. Similar to an astronomical observatory, individual neuroscience researchers could request time on this Connectome Observatory, and over a ten year period could use it to map out 50 separate brain regions each with a dense reconstruction of 300x300x300microns in volume and trace over 8 meters of the finest projecting axons between these 50 regions.

Ken Hayworth is of course our long time contributor to SIM, friend and colleague at carboncopies.org, and the inventor of the Automatic Tape Collecting Lathe Ultramicrotome (ATLUM) and the Tape-to-SEM process.

See the write-up at teleXLR8: Ken Hayworth on How to create a Connectome Observatory of the mouse brain and beyond, OpenQwaq, November 13 2011, 10am PST

Report / write-up / photos coming soon!!