1. SPITFIR(e): A supermaneuverable algorithm for fast denoising and deconvolution of 3D fluorescence microscopy images and videos
- Author
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Sylvain Prigent, Hoai-Nam Nguyen, Ludovic Leconte, Cesar Augusto Valades-Cruz, Bassam Hajj, Jean Salamero, Charles Kervrann, Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Biologie Cellulaire et Cancer, Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Physico-Chimie Curie [Institut Curie] (PCC), Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), This work was jointly supported by the French National Research Agency (France-BioImaging ANR-10-INBS-04-07 and ANR-10-INBS-04-01, DALLISH-ANR-16-CE23-0005, LabEx Cell(n)Scale (ANR-11-LABX-0038) as part of the Idex PSL ANR-10-IDEX-0001-02) and Innopsys company. This work was also supported by ITMO Cancer (18CQ091)., L'institution (Inria) a financé les frais de publication pour que cet article soit en libre accès, and ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011)
- Subjects
regularization ,Multidisciplinary ,[INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV] ,sparsity ,[SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB] ,denoising ,[SDV.IB]Life Sciences [q-bio]/Bioengineering ,deconvolution ,optimization ,fluorescence microscopy ,[SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing - Abstract
Modern fluorescent microscopy imaging is still limited by the optical aberrations and the photon budget available in the specimen. A direct consequence is the necessity to develop flexible and “off-road” algorithms in order to recover structural details and improve spatial resolution, which is critical when restraining the illumination to low levels in order to limit photo-damages. Here, we report SPITFIR(e) a flexible method designed to accurately and quickly restore 2D–3D fluorescence microscopy images and videos (4D images). We designed a generic sparse-promoting regularizer to subtract undesirable out-of-focus background and we developed a primal-dual algorithm for fast optimization. SPITFIR(e) is a ”swiss-knife” method for practitioners as it adapts to any microscopy techniques, to various sources of signal degradation (noise, blur), to variable image contents, as well as to low signal-to-noise ratios. Our method outperforms existing state-of-the-art algorithms, and is more flexible than supervised deep-learning methods requiring ground truth datasets. The performance, the flexibility, and the ability to push the spatiotemporal resolution limit of sub-diffracted fluorescence microscopy techniques are demonstrated on experimental datasets acquired with various microscopy techniques from 3D spinning-disk confocal up to lattice light sheet microscopy.
- Published
- 2023
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