D-CAT: Density and Clustering Annotation Tool for three dimensional electron microscopic volumes

The benefit of thresholding carbon layers in electron tomographic tilt series by intensity downshifting

“…In materials science, an increasing number of methods is now applied during a workflow to improve the quality of a tomographic reconstruction, including the use of: specific acquisition methods such as dual‐axis electron tomography (Tong et al ., ), full rotation specimen holders, focused ion beam milled specimens (Jarausch et al ., ) and impregnation methods (Gontard et al ., ); preprocessing to enhance and discretise image intensities, improve the alignment of a tomographic tilt series or perform sinogram enhancement (Batenburg et al ., ; Ortalan et al ., ; Cao et al ., ; Volkmann ; Bals et al ., ; Roelandts et al ., ; Scott et al ., ; Gontard, ); reconstruction algorithms that are faster and result in fewer missing wedge artefacts (Jinschek et al ., ; Leschner et al ., ; Lange et al ., ; Goris et al ., ; Roelandts et al ., ; Alpers et al ., ; Leary et al ., ; Van den Broek et al ., ); postprocessing of tomograms using approaches such as noise reduction (Frangakis et al ., ; Fernández & Li, ), thresholding, segmentation or automated feature identification (Gommes et al ., ; Batenburg & Sijbers, ; Friedrich et al ., ; Grothausmann et al ., ; Martínez‐Sánchez et al ., ; Lebbink et al ., ; Fernández, ). …”

“…postprocessing of tomograms using approaches such as noise reduction (Frangakis et al ., ; Fernández & Li, ), thresholding, segmentation or automated feature identification (Gommes et al ., ; Batenburg & Sijbers, ; Friedrich et al ., ; Grothausmann et al ., ; Martínez‐Sánchez et al ., ; Lebbink et al ., ; Fernández, ).…”

“…reconstruction algorithms that are faster and result in fewer missing wedge artefacts (Jinschek et al, 2008;Leschner et al, 2010;Lange et al, 2011;Goris et al, 2012;Roelandts et al, 2012;Alpers et al, 2013;Leary et al, 2013;Van den Broek et al, 2014); iv. postprocessing of tomograms using approaches such as noise reduction (Frangakis et al, 2001;Fernández & Li, 2009), thresholding, segmentation or automated feature identification (Gommes et al, 2005;Friedrich et al, 2009;Grothausmann et al, 2011;Martínez-Sánchez et al, 2011;Lebbink et al, 2012;Fernández, 2013).…”