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This tool is supported wholly or in part by The Human Brain Project.

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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:
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

Because of the nature of electron microscope tomography, computer processor speed and memory are important´┐Żthe 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