This tool is supported wholly or in part by
The Human Brain Project.
- Uel J. McMahan Laboratory, Stanford University, Dept. of Neurobiology, Dept. of Structural Biology
EM3D is a software application designed to facilitate the analysis and visualization of electron microscope (EM) tomography data by cellular and molecular biologists. Such data are collected as a tilt series, a sequence of 2D electron micrographs taken at many tilt angles with respect to the electron beam.
EM3D features an integrated graphical user interface that automates most of the initial alignment and reconstruction of the tilt-series data to form a 3D volume. These functions seamlessly connect with segmentation and model-generation tools that permit the user to easily and reliably extract specific structural components from the reconstructed volume. The 3D models can then be visualized and manipulated using an extensive package of surface- and volume-rendering techniques.
EM3D also provides a set of analysis tools to quantify structural information from the models, including their moments, proximity relationships, and spatial reliability. Altogether, EM3D facilitates the analysis of 3D cell structure at the full resolution of a reconstructed volume (2-3 nm).
- NIfTI-1 support
- David Ress, Mark Harlow, David Yip, Robert Marshall, Cornelia Koch-Stoschek, Mira Raman and Uel J. McMahan
- The McMahan lab: email@example.com
- Free download after registration.
- How to get
- Register and download from website
- Current version
- EM3D V. 1.2
- Current version release date
- Nov. 30, 2005
- Open source
- Available free of charge
EM3D runs under IDL virtual machine (free download from http://www.rsinc.com/idlvm/).
Because of the nature of electron microscope tomography, computer processor speed and memory are important�the more, the better. Systems should have minimum 1.5 - 2 Ghz processor(s) and 2GB or more of memory.
- Technical publications
Ress, D., Harlow, M.L., Schwarz, M., Marshall, R.M., and U.J. Mc Mahan. Automatic acquisition of fiducial markers and alignment of images in tilt series for electron tomography. J. Electron Microscopy 48: 277-287, 1999
Ress, D.B., Harlow, M.L., Marshall, R.M. and McMahan, U.J. Methods for generating high-resolution structural models from electron microscope tomography data. Structure: 12 (10):1763-1774, 2004.
Ress, D., Harlow, M.L., Marshall, R.A., and McMahan, U.J. Optimized Method for Isodensity Surface Models Obtained with Electron Microscope Tomography Data. Engineering in Medicine and Biology Society, 2003. Proceedings of the 25th Annual International Conference of IEEE. pp. 774-777, 2003.
- Applications publications
Harlow, M.L., Ress, D., Stoschek, A., Marshall, R.M. and McMahan, U.J. The architecture of active zone material at the frog's neuromuscular junction. Nature 409:479-484, 2001
Petersen, J.D., Chen, X., Vinada, L., Dosemeci, A., Lisman, J.E., and Reese, T.S. Distribution of postsynaptic density (PSD)-95 and Ca2+/calmodulin-dependent protein kinase II at the PSD. J. Neuroscience, 23: 11270-11278, 2003.
- Other information
- alignment, analysis, electron microscope tomography, HBP supported, microscopy, model generation, reconstruction, segmentation, surface analysis, surface-and volume-rendering, visualization, volume
- IDL, Linux, MacOS, UNIX, Windows
- IATR listing last updated
- 30 Jan 2006
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