In many applications in biology, images are typically scanned at the micro or nano scale (cells, DNA). We are developing new methodologies for analyzing biological images that are obtained from scanning electron microscopy. We have applied our methods to track axons from serial images, which facilitates the study of neuroanatomical structures and function of an organism.
Semi-Automated Reconstruction of the Neuromuscular Junctions in the C. elegans
For a nervous system to function, it must be wired properly. Specifically, neurons need to find their targets and form synapses. The neuron maintains such connections for years, accommodating growth of the organism and making allowance for other neurons that synapse to access the same target. Fulfilling these functions make topological demands on neurons and their targets. To study this process we are reconstructing the neuromuscular junctions in the nematode C. elegans.
To determine the topology of this complex synaptic region we have reconstructed a segment of the ventral nerve cord from serial electron micrographs. The data are registered and assembled automatically and then reconstruction of individual neurons is performed using a modified path finding approach.
Axon Tracking in Serial Block-Face Scanning Electron Microscopy
We address the problem of building three-dimensional connectivity maps for neurons from sectional electron microscopy. Sectional data consists of a stack of very high-resolution, two-dimensional images that are oriented to capture cross sections of elongated neuronal processes. High magnification serial microscopy images have the potential to expand the field of neurophysiological modeling by providing ground-truth neuroanatomical data. However, their complexity and vast size make them impractical for human interpretation. This project aims at building automatic and semi-automatic tools to assist researchers in analyzing such data.
For a nervous system to function, it must be wired properly. Specifically, neurons need to find their targets and form synapses. The neuron maintains such connections for years, accommodating growth of the organism and making allowance for other neurons that synapse to access the same target. Fulfilling these functions make topological demands on neurons and their targets. To study this process we are reconstructing the neuromuscular junctions in the nematode C. elegans. 
We address the problem of building three-dimensional connectivity maps for neurons from sectional electron microscopy. Sectional data consists of a stack of very high-resolution, two-dimensional images that are oriented to capture cross sections of elongated neuronal processes. High magnification serial microscopy images have the potential to expand the field of neurophysiological modeling by providing ground-truth neuroanatomical data. However, their complexity and vast size make them impractical for human interpretation. This project aims at building automatic and semi-automatic tools to assist researchers in analyzing such data.