title: BiDiFuse: a FIJI plugin for fusing bi-directionally recorded microscopic image volumes.
abstract: Deep tissue imaging is increasingly used for non-destructive interrogation of intact organs and small model organisms. An intuitive approach to increase the imaging depth by almost a factor of 2 is to record a sample from two sides and fuse both image stacks. However, imperfect three-dimensional alignment of both stacks presents a computational challenge. We have developed a FIJI plugin, called BiDiFuse, which merges bi-directionally recorded image stacks via 3D rigid transformations. The method is broadly applicable, considering it is compatible with all optical sectioning microscopes and it does not rely on fiducial markers for image registration.
  
  
  
  The method is freely available as a plugin for FIJI from https://github.com/JanDetrez/BiDiFuse/ CONTACT: winnok.devos@uantwerpen.be.
authors: Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium.
authors: Jan R
authors: JR
authors: Detrez
authors: Light Microscopy Facility & Laboratory of Neurophysiology, Faculty of Medicine, Free University of Brussels, 1070 Anderlecht, Belgium.
authors: Jean-Marie
authors: JM
authors: Vanderwinden
authors: Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium.|Department of Neuroscience, Janssen Research and Development, 2340 Beerse, Belgium.
authors: Michaël
authors: M
authors: Barbier
authors: Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium.
authors: Marlies
authors: M
authors: Verschuuren
authors: Department of Neuroscience, Janssen Research and Development, 2340 Beerse, Belgium.
authors: Rony
authors: R
authors: Nuydens
authors: Department of Neuroscience, Janssen Research and Development, 2340 Beerse, Belgium.
authors: Xavier
authors: X
authors: Langlois
authors: Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium.
authors: Jean-Pierre
authors: JP
authors: Timmermans
authors: Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium.|Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium.
authors: Winnok H
authors: WH
authors: De Vos
mesh_terms: D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional; D008853:Microscopy; D012984:Software