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High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio.

ABSTRACT: Four-dimensional fluorescence microscopy--which records 3D image information as a function of time--provides an unbiased way of tracking dynamic behavior of subcellular components in living samples and capturing key events in complex macromolecular processes. Unfortunately, the combination of phototoxicity and photobleaching can severely limit the density or duration of sampling, thereby limiting the biological information that can be obtained. Although widefield microscopy provides a very light-efficient way of imaging, obtaining high-quality reconstructions requires deconvolution to remove optical aberrations. Unfortunately, most deconvolution methods perform very poorly at low signal-to-noise ratios, thereby requiring moderate photon doses to obtain acceptable resolution. We present a unique deconvolution method that combines an entropy-based regularization function with kernels that can exploit general spatial characteristics of the fluorescence image to push the required dose to extreme low levels, resulting in an enabling technology for high-resolution in vivo biological imaging.

SUBMITTER: Arigovindan M

PROVIDER: S-EPMC3808589 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

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High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio.

Arigovindan Muthuvel M Fung Jennifer C JC Elnatan Daniel D Mennella Vito V Chan Yee-Hung Mark YH Pollard Michael M Branlund Eric E Sedat John W JW Agard David A DA

Proceedings of the National Academy of Sciences of the United States of America 20131008 43

Four-dimensional fluorescence microscopy--which records 3D image information as a function of time--provides an unbiased way of tracking dynamic behavior of subcellular components in living samples and capturing key events in complex macromolecular processes. Unfortunately, the combination of phototoxicity and photobleaching can severely limit the density or duration of sampling, thereby limiting the biological information that can be obtained. Although widefield microscopy provides a very light ...[more]

PMID: 24106307

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Project description:MotivationTarget-specific hybridization depends on oligo-probe characteristics that improve hybridization specificity and minimize genome-wide cross-hybridization. Interplay between specific hybridization and genome-wide cross-hybridization has been insufficiently studied, despite its crucial role in efficient probe design and in data analysis.ResultsIn this study, we defined hybridization specificity as a ratio between oligo target-specific hybridization and oligo genome-wide cross-hybridization. A microarray database, derived from the Genomic Comparison Hybridization (GCH) experiment and performed using the Affymetrix platform, contains two different types of probes. The first type of oligo-probes does not have a specific target on the genome and their hybridization signals are derived from genome-wide cross-hybridization alone. The second type includes oligonucleotides that have a specific target on the genomic DNA and their signals are derived from specific and cross-hybridization components combined together in a total signal. A comparative analysis of hybridization specificity of oligo-probes, as well as their nucleotide sequences and thermodynamic features was performed on the database. The comparison has revealed that hybridization specificity was negatively affected by low stability of the fully-paired oligo-target duplex, stable probe self-folding, G-rich content, including GGG motifs, low sequence complexity and nucleotide composition symmetry.ConclusionFiltering out the probes with defined 'negative' characteristics significantly increases specific hybridization and dramatically decreasing genome-wide cross-hybridization. Selected oligo-probes have two times higher hybridization specificity on average, compared to the probes that were filtered from the analysis by applying suggested cutoff thresholds to the described parameters. A new approach for efficient oligo-probe design is described in our study.Contactshabalin@ncbi.nlm.nih.gov or olga.matveeva@gmail.comSupplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio.

Publications

High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio.

Similar Datasets

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