Reconstruction, Electron Microscopy
Reconstruction of neural circuits using large volumes of electron microscopy (EM) data is essential for understanding the function and dysfunction of the nervous system. The reconstruction task involves the geometric tracing of each neurite and the identification of the interconnections between neurons in order to obtain a complete wiring diagram of the nervous system, known as the connectome.
To reconstruct the connectome that reveals synaptic connections, the tissue has to be imaged at a sufficiently high resolution. EM can provide image data at nanometer scale and has been a key source of 3D imaging data for the study of neuroanatomy for years (Macagno et al. 1979; Stevens et al. 1980). For example, the entire nervous system (302 neurons and over 7,000 synaptic connections) of the nematode Caenorhabditis elegans was reconstructed (White et al. 1986) using serial section transmission electron microscopy (ssTEM).
KeywordsConvolutional Neural Network Electron Microscopy Data Topological Error Provide User Interface Membrane Detection
- Andres B, Köthe U, Helmstaedter M, Denk W, Hamprecht FA (2008) Segmentation of SBFSEM volume data of neural tissue by hierarchical classification. In: Proceedings of the DAGM symposium, Munich, Germany, pp 142–152Google Scholar
- Cardona A (2010) Segmented ssTEM stack of neural tissue. http://www.ini.uzh.ch/~acardona/data.html
- Edwards J, Daniel E, Kinney J, Bartol T, Sejnowski T, Johnston D, Harris K, Bajaj C (2013) VolRoverN: enhancing surface and volumetric reconstruction for realistic dynamical simulation of cellular and subcellular function. Neuroinformatics, volume 12(2):277–289Google Scholar
- Jain V, Bollmann B, Richardson M, Berger DR, Helmstaedter MN, Briggman KL, Denk W, Bowden JB, Mendenhall JM, Abraham WC, Harris KM, Kasthuri N, Hayworth KJ, Schalek R, Tapia JC, Lichtman JW, Seung HS (2010) Boundary learning by optimization with topological constraints. In: Proceedings of the IEEE conference on computer vision and pattern recognition, San Francisco, CA, USA, pp 2488–2495Google Scholar
- Knowles-Barley S, Roberts M, Kasthuri N, Lee D, Pfister H, Lichtman JW (2013) Mojo 2.0: connectome annotation tool. Front NeuroinformatGoogle Scholar
- Lucchi A, Smith K, Achanta R, Lepetit V, Fua P (2010) A fully automated approach to segmentation of irregularly shaped cellular structures in EM images. In: Medical image computing and computer-assisted intervention, vol 6362 of lecture notes in computer science, Beijing, China, pp 463–471Google Scholar
- Yang H-Y (2011) Reconstruction of 3D neuronal structures from densely packed electron microscopy data stacks. Ph.D. thesis, Texas A&M UniversityGoogle Scholar
- Yang H.-F, Choe Y (2009) Cell tracking and segmentation in electron microscopy images using graph cuts. In: Proceedings of the IEEE international symposium on biomedical imaging, Boston, MA, USA, pp 306–309Google Scholar