Wavelet-based image fusion in multi-view three-dimensional microscopy

• Published in: Bioinformatics Vol. 28; no. 2; pp. 238 - 245
• Main Authors: Rubio-Guivernau, Jose L., Gurchenkov, Vasily, Luengo-Oroz, Miguel A., Duloquin, Louise, Bourgine, Paul, Santos, Andres, Peyrieras, Nadine, Ledesma-Carbayo, Maria J.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.01.2012; Oxford University Press (OUP)
• Subjects: Animals; Biological and medical sciences; Danio rerio; Echinoidea; Fundamental and applied biological sciences. Psychology; General aspects; Humans; Image Processing, Computer-Assisted; Life Sciences; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Microscopy, Fluorescence; Neurons and Cognition; Sea Urchins - embryology; Software; Zebrafish - embryology; Microscopy; Image processing; Image
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btr609

Motivation: Multi-view microscopy techniques such as Light-Sheet Fluorescence Microscopy (LSFM) are powerful tools for 3D + time studies of live embryos in developmental biology. The sample is imaged from several points of view, acquiring a set of 3D views that are then combined or fused in order to overcome their individual limitations. Views fusion is still an open problem despite recent contributions in the field. Results: We developed a wavelet-based multi-view fusion method that, due to wavelet decomposition properties, is able to combine the complementary directional information from all available views into a single volume. Our method is demonstrated on LSFM acquisitions from live sea urchin and zebrafish embryos. The fusion results show improved overall contrast and details when compared with any of the acquired volumes. The proposed method does not need knowledge of the system's point spread function (PSF) and performs better than other existing PSF independent fusion methods. Availability and Implementation: The described method was implemented in Matlab (The Mathworks, Inc., USA) and a graphic user interface was developed in Java. The software, together with two sample datasets, is available at http://www.die.upm.es/im/software/SPIMFusionGUI.zip A public release, free of charge for non-commercial use, is planned after the publication of this article. Contact: jlrubio@die.upm.es; nadine.peyrieras@inaf.cnrs-gif.fr; mledesma@die.upm.es Supplementary Information: Supplementary data are available at Bioinformatics online.