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

Abstract

Background: 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.

Results: 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.

Conclusion: 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.

Figure 1

TomoJ interface. A: ImageJ user interface as presented after launching TomoJ. Note that the toolbar differs from the standard ImageJ toolbar. The standard toolbar can be regained by using the "switch toolbar" button on the TomoJ interface. B: TomoJ interface divided into four regions. Top: global menus. Bottom (left to right): the regions devoted to automatic alignment, tools that require point selections, and 3D reconstruction. C: Data set window. The header includes the tilt-series name, the number of the visualized image in the total stack, the total number of images in the stack, the tilt angle corresponding to the visualized image, the image byte type, and the total memory occupied by the stack.

Figure 2

Comparison between phantom data and reconstruction. Slices 44, 54, 64, 74, and 84 of every volume are shown. Reconstructions were performed on noisy projections of a phantom (range: -50° to +50°, every 1°, vertical tilt axis). A: Original phantom. B: Reconstruction using the ART with 10 iterations and a relaxation coefficient of 0.01. C: Reconstruction using WBP. D: Reconstruction using the SIRT with 10 iterations and a relaxation coefficient of 1.