A visualization and segmentation toolbox for electron microscopy

• Published in: Journal of structural biology Vol. 164; no. 1; pp. 161 - 165
• Main Authors: Pruggnaller, Sabine, Mayr, Matthias, Frangakis, Achilleas S.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.10.2008
• Subjects: Electron microscopy toolbox; Image processing; Image Processing, Computer-Assisted; Imaging, Three-Dimensional; Microscopy, Electron - instrumentation; Segmentation; Software; Visualization; Electron microscopy toolbox; Visualization; Image processing; Segmentation
• ISSN: 1047-8477; 1095-8657
• DOI: 10.1016/j.jsb.2008.05.003

Three-dimensional image analysis includes image processing, segmentation and visualization operations, which facilitate the interpretation of data. We have developed a toolbox for three-dimensional (3D) electron microscopy (EM) in Amira, which is a commercial software package, used by many laboratories. Our toolbox integrates a number of established procedures specifically tailored for 3D EM. These include input-output, filtering, segmentation, visualization and ray-tracing functions, which can be accessed directly from a user-friendly pop-up menu. They allow performing denoising and segmentation tasks directly in Amira, without the need of other programs, and ultimately allow the visualization of the results at photo-realistic quality with ray-tracing. They also allow a direct interaction with the data, such that, e.g., sub-tomograms can be directly extracted, or segmentation areas can be interactively selected. The implemented functions are fast, reliable and intuitive, yielding a comprehensive package for visualization in EM.