Amira (in collaboration with the Zuse Institute Berlin )

Amira is a commercial software platform for 3D and 4D data analysis, modeling and visualization of biological data. The Zuse Institute Berlin is a research institute in Berlin Germany that applies mathematics and computer science to extend the capabilities of Amira. We are collaborating with the Department of Visualization and Data Analysis at the Zuse Institute Berlin to refine an algorithm for the semi-automatic and automatic segmentation of microtubules from electron tomography data.

Please see the following paper for a more detailed description of the tool:

  • Weber B, Greenan G, Prohaska S, Baum D, Hege HC, Müller-Reichert T, Hyman AA, Verbavatz JM. Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos. J Struct Biol. 2012 May;178(2):129-38.
  • Weber B, Tranfield EM, Höög JL, Baum D, Antony C, Hyman T, Verbavatz JM, Prohaska S. Automated Stitching of Microtubule Centerlines across Serial Electron Tomograms. PLoS One. 2014 Dec 1;9(12):e113222.


Imod is open-source collection of data reconstruction, processing and segmentation programs in 2D and 3D. This extensive suite of programs has been developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the Boulder Laboratory for 3-D Electron Microscopy of Cells. The tools are under continuous development and there is an active international community working together to provide continuous input and improvement suggestions.

Within the Electron Microscopy Facility at the Instituto Gulbenkian de Ciência IMOD is used for the 3D reconstruction of electron tomography data and data segmentation and modeling.

There is a wealth of information on the website and very helpful introductory tutorials can be found here, including some introductory videos.

Please see the following papers for a more detailed description of the tool:

  • Kremer J.R., D.N. Mastronarde and J.R. McIntosh (1996) Computer visualization of three-dimensional image data using IMOD J. Struct. Biol. 116:71-76;
  • Mastronarde, D.N. (1997) Dual-axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 120:343-352.

Image J

ImageJ is a Java-based freeware platform that uses a great array of plugins and macros tailored for individual objectives and problems. Scientists in need of a solution have built many of these tools and the built-in editor allows customization of existing tools. The program can handle images from many different imagining sources, and in 2D, and 3D.

Within the Electron Microscopy Facility at the Instituto Gulbenkian de Ciência ImageJ is used for visualization and analysis of TEM micrographs. ImageJ is also used for alignment of images from fluorescence microscopy and electron microscopy that are combined together in correlative light and electron microscopy protocols.