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Open Access Software

TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy

Cédric MessaoudiI12, Thomas Boudier12, Carlos Oscar Sanchez Sorzano3 and Sergio Marco12*

Author Affiliations

1 Institut Curie. Section Recherche. Laboratoire d'Imagerie Intégrative. Centre Universitaire d'Orsay, 91405 Orsay CEDEX, France

2 INSERM U 759. Centre Universitaire d'Orsay. Bât 112. 91405 Orsay CEDEX, France

3 Bioengineering Lab, Escuela Politécnica Superior. Univ. San Pablo – CEU. Campus Urb. Montepríncipe s/n. 28668. Boadilla del Monte, Madrid, Spain

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BMC Bioinformatics 2007, 8:288  doi:10.1186/1471-2105-8-288

Published: 6 August 2007



Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomography fills the gap between high resolution structural methods (X-ray diffraction or nuclear magnetic resonance) and optical microscopy. We developed new software for transmission electron tomography, TomoJ. TomoJ is a plug-in for the now standard image analysis and processing software for optical microscopy, ImageJ.


TomoJ provides a user-friendly interface for alignment, reconstruction, and combination of multiple tomographic volumes and includes the most recent algorithms for volume reconstructions used in three-dimensional electron microscopy (the algebraic reconstruction technique and simultaneous iterative reconstruction technique) as well as the commonly used approach of weighted back-projection.


The software presented in this work is specifically designed for electron tomography. It has been written in Java as a plug-in for ImageJ and is distributed as freeware.