Links to the Scientific Research Community

Table of Contents

Movies of Lathe Microtome cutting and tape collection in action!

SBPSL Full PowerPoint Presentation (Warning large file! *.ppt file is 29Mbytes)

Movie: Piloting down a virtual neuron's dendritic tree using "Dendritic Explorer" test program (49 Second *.avi file, 22 Mbytes)

Dendritic Explorer test program overview slide

Contacts

Links to the Scientific Research Community

"Nothing tends so much to the advancement of knowledge as the application of a new instrument. The native intellectual powers of men in different times are not so much the causes of the different success of their labours, as the peculiar nature of the means and artificial resources in their possession."

- Sir Humphrey Davy

The links on this page are all to top notch researchers diligently working toward creating neuroscience's next generation of brain imaging instruments and protocols. Please email ken@extremeneuroanatomy.com to let me know of any links that you think should be on this page but are not.

Proposals for Full Human Brain Circuitry Mapping

Large Scale Analysis of Neural Structures - A paper by Ralph Merkle that provides a compelling, well-documented argument for the feasibility of creating a synapse-resolution atlas of an entire human brain.

Human Brain Project - A large-scale NIH initiative (providing research funding to dozens of universities) aimed at developing the internet-based “neuroinformatics” infrastructure needed to integrate today’s vast amount of neuroscientific facts into a coherent whole. This project grew out of the National Academy of Sciences committee on the creation of a National Neural Circuitry Database.

Synapse-Resolution Imaging Research Groups

Worm Atlas – Full Synapse-Resolution Connectivity Atlas from TEM serial sections, as well as derived neural circuitry diagrams, for the nematode worm C. Elegans.

Synapse Web – (Synapse Web, Medical College of Georgia, http://synapses.mcg.edu/) Serial section TEM reconstructions of rat hippocampus dendritic processes and spines. Site provides three online brain volumes (approximately one hundred cubic microns in volume each) of raw (but registered) TEM images and a web-based viewer. From the Laboratory of Synapse Structure and Function.

synapses.bu.edu – Website for Boston University’s TEM serial section 3D reconstruction group. See the paper on the synapse.bu.edu site: “Three-dimensional structure of synapses in the brain and on the web” in the Proceedings of the 2002 International Joint Conference on Neural Networks, May 12-17, Honolulu, Hawaii, pp. 1-4. by John Fiala for a discussion of applying the serial section TEM reconstruction technique to mammalian brain structures as large as individual cortical columns.

Laboratory of Retinal Microcircuitry – Complete 3D reconstructions (from TEM images of serial sections) of the complex neural circuitry of the mammalian retina.

Serial-Sectioning Scanning Electron Microscopy – Also known as "Serial-Block Face Scanning Electron Microscopy" (SBFSEM). A block-face imaging technique that uses microtome-sectioning inside the vacuum chamber of a scanning electron microscope. The neural tissue is stained with heavy metals, and backscattering contrast is used to visualize neuronal processes. Winfried Denk at the Max-Planck Institute for Medicine in Heidelberg, Germany, and Stephen J Smith at Stanford University School of Medicine have been funded through the McKnight foundation to work on this research. (Link to recent PLOS Biology journal article on this research)

National Center for Microscopy and Imaging Research - Has partially automated the process of electron tomographic imaging and has made remote, internet-based TEM imaging sessions possible.

3-Dimensional Electron Microscopy – Contains a large array of links to the 3D-EM research community.

Proposed Axonal Connectivity Resolution Full Brain Imaging Groups

High Resolution Mouse Brain Atlas – Harvard University project that has sliced and imaged a mouse brain at sufficient resolution to locate most individual neuronal cell bodies. What is more exciting is their stated future research goal, “The map we propose to develop at 1 micron resolution will meet the objective we and others have contemplated, of plotting for the first time the detailed trajectories of white matter tracts throughout the brain even, for the larger caliber axons, down to the level of individual myelinated fibers. Such a refined anatomy in the mouse brain, especially cortico-cortical white matter anatomy, will likely prove to be extrapolatable to other mammals, and should delineate the fundamental white matter organization in even the human cerebrum.”

Brain Tissue Scanner – Ingenious knife-edge scanning instrument combines the functions of a microtome and a microscope imager. Project aims to build a system that will allow an entire mouse brain (~1cm³) to be scanned in one month.

Remote, Web-Based Microscopic Imaging of a Stored Library of Brain Slices

iScope Project – Internet enabled digital light microscope and robotic slide loader that will be able to provide a remote user the ability to image any part of the Mouse Brain Library. This project’s automated imaging of stored brain slices is a direct analog to the Single Brain Physical Slice Library describe here.

Commercial Automatic Slide Loader – Automatically loads and images up to 50 microscope slides for use in high-throughput histology labs.

National Center for Microscopy and Imaging Research - Has partially automated the process of electron tomographic imaging and has made remote, internet-based TEM imaging sessions possible.