title: Optimizing the 3D-reconstruction technique for serial block-face scanning electron microscopy.
abstract: BACKGROUND
  Elucidating the anatomy of neuronal circuits and localizing the synaptic connections between neurons, can give us important insights in how the neuronal circuits work. We are using serial block-face scanning electron microscopy (SBEM) to investigate the anatomy of a collision detection circuit including the Lobula Giant Movement Detector (LGMD) neuron in the locust, Locusta migratoria. For this, thousands of serial electron micrographs are produced that allow us to trace the neuronal branching pattern.
  
  
  METHODS
  The reconstruction of neurons was previously done manually by drawing cell outlines of each cell in each image separately. This approach was very time consuming and troublesome. To make the process more efficient a new interactive software was developed. It uses the contrast between the neuron under investigation and its surrounding for semi-automatic segmentation.
  
  
  RESULTS
  For segmentation the user sets starting regions manually and the algorithm automatically selects a volume within the neuron until the edges corresponding to the neuronal outline are reached. Internally the algorithm optimizes a 3D active contour segmentation model formulated as a cost function taking the SEM image edges into account. This reduced the reconstruction time, while staying close to the manual reference segmentation result.
  
  
  METHODS
  Our algorithm is easy to use for a fast segmentation process, unlike previous methods it does not require image training nor an extended computing capacity.
  
  
  CONCLUSIONS
  Our semi-automatic segmentation algorithm led to a dramatic reduction in processing time for the 3D-reconstruction of identified neurons.
authors.affiliation: Institute of Cell Biology, Histology and Embryology, Research Unit Electron Microscopic Techniques, Medical University of Graz, Harrachgasse 21, 8010 Graz, Austria.
authors.forename: Stefan
authors.initials: S
authors.lastname: Wernitznig
authors.affiliation: Institute of Cell Biology, Histology and Embryology, Research Unit Electron Microscopic Techniques, Medical University of Graz, Harrachgasse 21, 8010 Graz, Austria.
authors.forename: Mariella
authors.initials: M
authors.lastname: Sele
authors.affiliation: Ludwig Boltzmann Institute for Clinical Forensic Imaging, Universitätsplatz 4, 8010 Graz, Austria; Institute for Computer Graphics and Vision, BioTechMed-Graz, Graz University of Technology, Inffeldgasse 16, 8010 Graz, Austria.
authors.forename: Martin
authors.initials: M
authors.lastname: Urschler
authors.affiliation: Institute for Electron Microscopy and Nanoanalysis, NAWI Graz, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria.
authors.forename: Armin
authors.initials: A
authors.lastname: Zankel
authors.affiliation: Institute for Electron Microscopy and Nanoanalysis, NAWI Graz, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria.
authors.forename: Peter
authors.initials: P
authors.lastname: Pölt
authors.affiliation: Newcastle University, Institute of Neuroscience, Framlington Place, NE2 4HH Newcastle upon Tyne, UK.
authors.forename: F Claire
authors.initials: FC
authors.lastname: Rind
authors.affiliation: Institute of Cell Biology, Histology and Embryology, Research Unit Electron Microscopic Techniques, Medical University of Graz, Harrachgasse 21, 8010 Graz, Austria. Electronic address: gerd.leitinger@medunigraz.at.
authors.forename: Gerd
authors.initials: G
authors.lastname: Leitinger
mesh_terms: D000818:Animals; D006110:Grasshoppers; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008855:Microscopy, Electron, Scanning / Q000379:methods*; D009474:Neurons / Q000648:ultrastructure*
keywords: 3D-reconstruction; Locust; Semi-automatic segmentation; Serial block-face scanning electron microscopy