title: A visualization and segmentation toolbox for electron microscopy.
abstract: 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.
authors.affiliation: Department of Computational and Structural Biology, European Molecular Biology Laboratory, Meyerhofstr 1, 69117 Heidelberg, Germany. pruggnal@embl.de
authors.forename: Sabine
authors.initials: S
authors.lastname: Pruggnaller
authors.forename: Matthias
authors.initials: M
authors.lastname: Mayr
authors.forename: Achilleas S
authors.initials: AS
authors.lastname: Frangakis
mesh_terms: D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional; D008854:Microscopy, Electron / Q000295:instrumentation*; D012984:Software