Quick links:: [Publications] [KESM specifications] [Gallery]
3D reconstruction of the hippocampus: A small portion of Nissl-stained hippocampus is visualized in 3D. [More images] [More nuggets]

Our research team has expertise ranging from neuroanatomy, instrumentation, data acquisition, image processing, 3D graphics and visualization, cluster computing, to theoretical and computational neuroscience. The knife-edge scanning microscope (KESM) project involves aspects touched upon by all of the above areas.

Currently, our major focus is on the following tasks:

  1. Tissue staining: En bloc staining methods
    Development of en bloc staining methods for whole mouse brains. Golgi, Nissl, and other stains. (Abbott).
  2. KESM instrumentation: KESM instrumentation and data acquisition
    Sectioning and imaging of whole mouse brains under 100 hours. Knife chatter abatement. Tissue ribbon extraction. (McCormick, Gutierrez-Osuna, and Wiercigroch).
    [KESM specifications]
  3. 3D reconstruction: Neuron morphology
    Reconstruction of neuron cell bodies and processes from sequence of 2D images from KESM (Keyser and McCormick).
  4. Connectivity maps: Mouse brain web (MBW) distributed storage and network connectivity analysis
    XML-based storage of neuron morphology and connectivity data in a web environment for scalable and efficient storage and retrieval. Development of network connectivity analysis algorithms for the study of natural computations in the mouse brain (Choe, Kim, and McCormick).
  5. Multi-scale integration: Reconstruction of mouse brain tissue bridging multi-scale imaging
    From gross neuroanatomy (macro-scale brain atlas) through cellular structure (micro-scale light microscopy) to subcellular structure (nano-scale electron microscopy). Lab-wide effort, in collaboration with Stephen J. Smith at Stanford. (Mouse brain atlas data provided by Arthur Toga at UCLA Laboratory of Neuroimaging.)
Links: Publications; Seminars; Sponsors; Software; Multimedia gallery; *KESM specifications;