BiDiFuse: a FIJI plugin for fusing bi-directionally recorded microscopic image volumes

• Published in: Bioinformatics (Oxford, England) Vol. 32; no. 23; pp. 3691 - 3693
• Main Authors: Detrez, Jan R, Vanderwinden, Jean-Marie, Barbier, Michaël, Verschuuren, Marlies, Nuydens, Rony, Langlois, Xavier, Timmermans, Jean-Pierre, De Vos, Winnok H
• Format: Journal Article
• Language: English
• Published: England 01-12-2016
• Subjects: Humans; Image Processing, Computer-Assisted - methods; Imaging, Three-Dimensional; Microscopy; Software
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btw515

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: [e-mail].