title: The benefit of thresholding carbon layers in electron tomographic tilt series by intensity downshifting.
abstract: When performing electron tomography, tilt series of images are often acquired from samples that contain unwanted carbonaceous material, such as an embedding resin, a thin carbon support film or hydrocarbon contamination. The presence of such layers can introduce artefacts in reconstructions, obscuring features of interest. Here, we illustrate the benefit of preprocessing a high-angle annular dark-field tomographic tilt series by thresholding unwanted low-density materials using a simple intensity downshifting procedure. The resulting tomograms have fewer artefacts and segmentation can be performed more accurately. We present two representative examples taken from studies of catalyst nanoparticles and amyloid plaque core material from the human brain.
authors.affiliation: Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica, Universidad de Cádiz, Puerto Real, Spain.
authors.forename: Lionel C
authors.initials: LC
authors.lastname: Gontard
authors.affiliation: Servicio de Microscopía Centro de Investigación, Tecnología e Innovación (CITIUS), Universidad de Sevilla, Sevilla, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Cintas
authors.affiliation: Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Jülich, Germany.
authors.forename: Rafal E Dunin
authors.initials: RE
authors.lastname: Borkowski
keywords: Carbon layers; electron tomography; image processing; intensity downshifting; tomogram segmentation