Fourier ring correlation simplifies image restoration in fluorescence microscopy.

Abstract:

:Fourier ring correlation (FRC) has recently gained popularity among fluorescence microscopists as a straightforward and objective method to measure the effective image resolution. While the knowledge of the numeric resolution value is helpful in e.g., interpreting imaging results, much more practical use can be made of FRC analysis-in this article we propose blind image restoration methods enabled by it. We apply FRC to perform image de-noising by frequency domain filtering. We propose novel blind linear and non-linear image deconvolution methods that use FRC to estimate the effective point-spread-function, directly from the images. We show how FRC can be used as a powerful metric to observe the progress of iterative deconvolution. We also address two important limitations in FRC that may be of more general interest: how to make FRC work with single images (within certain practical limits) and with three-dimensional images with highly anisotropic resolution.

journal_name

Nat Commun

journal_title

Nature communications

authors

Koho S,Tortarolo G,Castello M,Deguchi T,Diaspro A,Vicidomini G

doi

10.1038/s41467-019-11024-z

subject

Has Abstract

pub_date

2019-07-15 00:00:00

pages

3103

issue

1

issn

2041-1723

pii

10.1038/s41467-019-11024-z

journal_volume

10

pub_type

杂志文章
  • Large-scale self-organization of reconfigurable topological defect networks in nematic liquid crystals.

    abstract::Topological defects in nematic liquid crystals are ubiquitous. The defects are important in understanding the fundamental properties of the systems, as well as in practical applications, such as colloidal self-assembly, optical vortex generation and templates for molecular self-assembly. Usually, spatially and tempora...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13238

    authors: Sasaki Y,Jampani VSR,Tanaka C,Sakurai N,Sakane S,Le KV,Araoka F,Orihara H

    更新日期:2016-11-07 00:00:00

  • Control of chrysanthemum flowering through integration with an aging pathway.

    abstract::Age, as a threshold of floral competence acquisition, prevents precocious flowering when there is insufficient biomass, and ensures flowering independent of environmental conditions; however, the underlying regulatory mechanisms are largely unknown. In this study, silencing the expression of a nuclear factor gene, CmN...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00812-0

    authors: Wei Q,Ma C,Xu Y,Wang T,Chen Y,Lü J,Zhang L,Jiang CZ,Hong B,Gao J

    更新日期:2017-10-10 00:00:00

  • Tumor-associated B-cells induce tumor heterogeneity and therapy resistance.

    abstract::In melanoma, therapies with inhibitors to oncogenic BRAFV600E are highly effective but responses are often short-lived due to the emergence of drug-resistant tumor subpopulations. We describe here a mechanism of acquired drug resistance through the tumor microenvironment, which is mediated by human tumor-associated B ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00452-4

    authors: Somasundaram R,Zhang G,Fukunaga-Kalabis M,Perego M,Krepler C,Xu X,Wagner C,Hristova D,Zhang J,Tian T,Wei Z,Liu Q,Garg K,Griss J,Hards R,Maurer M,Hafner C,Mayerhöfer M,Karanikas G,Jalili A,Bauer-Pohl V,Weihsengru

    更新日期:2017-09-19 00:00:00

  • The structural basis of promiscuity in small multidrug resistance transporters.

    abstract::By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pr...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19820-8

    authors: Kermani AA,Macdonald CB,Burata OE,Ben Koff B,Koide A,Denbaum E,Koide S,Stockbridge RB

    更新日期:2020-11-27 00:00:00

  • Self-assembly of DNA nanotubes with controllable diameters.

    abstract::The synthesis of DNA nanotubes is an important area in nanobiotechnology. Different methods to assemble DNA nanotubes have been reported, and control over the width of the nanotubes has been achieved by programmed subunits of DNA tiles. Here we report the self-assembly of DNA nanotubes with controllable diameters. The...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1535

    authors: Wilner OI,Orbach R,Henning A,Teller C,Yehezkeli O,Mertig M,Harries D,Willner I

    更新日期:2011-11-15 00:00:00

  • Emergence of orbital angular moment at van Hove singularity in graphene/h-BN moiré superlattice.

    abstract::Bloch electrons lacking inversion symmetry exhibit orbital magnetic moments owing to the rotation around their center of mass; this moment induces a valley splitting in a magnetic field. For the graphene/h-BN moiré superlattice, inversion symmetry is broken by the h-BN. The superlattice potential generates a series of...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19043-x

    authors: Moriya R,Kinoshita K,Crosse JA,Watanabe K,Taniguchi T,Masubuchi S,Moon P,Koshino M,Machida T

    更新日期:2020-10-23 00:00:00

  • Formation and diversification of a paradigm biosynthetic gene cluster in plants.

    abstract::Numerous examples of biosynthetic gene clusters (BGCs), including for compounds of agricultural and medicinal importance, have now been discovered in plant genomes. However, little is known about how these complex traits are assembled and diversified. Here, we examine a large number of variants within and between spec...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19153-6

    authors: Liu Z,Cheema J,Vigouroux M,Hill L,Reed J,Paajanen P,Yant L,Osbourn A

    更新日期:2020-10-23 00:00:00

  • Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis.

    abstract::Epilepsy is one of the most common neurological disorders, yet its pathophysiology is poorly understood due to the high complexity of affected neuronal circuits. To identify dysfunctional neuronal subtypes underlying seizure activity in the human brain, we have performed single-nucleus transcriptomics analysis of >110...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18752-7

    authors: Pfisterer U,Petukhov V,Demharter S,Meichsner J,Thompson JJ,Batiuk MY,Asenjo-Martinez A,Vasistha NA,Thakur A,Mikkelsen J,Adorjan I,Pinborg LH,Pers TH,von Engelhardt J,Kharchenko PV,Khodosevich K

    更新日期:2020-10-07 00:00:00

  • Author Correction: RNAs coordinate nuclear envelope assembly and DNA replication through ELYS recruitment to chromatin.

    abstract::In the original version of this Article, the affiliation details for Antoine Aze, Michalis Fragkos, Stéphane Bocquet, Julien Cau and Marcel Méchali incorrectly omitted 'CNRS and the University of Montpellier'. This has now been corrected in both the PDF and HTML versions of the Article. ...

    journal_title:Nature communications

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41467-018-02968-9

    authors: Aze A,Fragkos M,Bocquet S,Cau J,Méchali M

    更新日期:2018-02-05 00:00:00

  • Author Correction: The effects of mutational processes and selection on driver mutations across cancer types.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature communications

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41467-020-15800-0

    authors: Temko D,Tomlinson IPM,Severini S,Schuster-Böckler B,Graham TA

    更新日期:2020-04-20 00:00:00

  • Bending rules for animal propulsion.

    abstract::Animal propulsors such as wings and fins bend during motion and these bending patterns are believed to contribute to the high efficiency of animal movements compared with those of man-made designs. However, efforts to implement flexible designs have been met with contradictory performance results. Consequently, there ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4293

    authors: Lucas KN,Johnson N,Beaulieu WT,Cathcart E,Tirrell G,Colin SP,Gemmell BJ,Dabiri JO,Costello JH

    更新日期:2014-01-01 00:00:00

  • Shape-memory effects in molecular crystals.

    abstract::Molecular crystals can be bent elastically by expansion or plastically by delamination into slabs that glide along slip planes. Here we report that upon bending, terephthalic acid crystals can undergo a mechanically induced phase transition without delamination and their overall crystal integrity is retained. Such pla...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-11612-z

    authors: Ahmed E,Karothu DP,Warren M,Naumov P

    更新日期:2019-08-19 00:00:00

  • Overcoming ultraviolet light instability of sensitized TiO₂ with meso-superstructured organometal tri-halide perovskite solar cells.

    abstract::The power conversion efficiency of hybrid solid-state solar cells has more than doubled from 7 to 15% over the past year. This is largely as a result of the incorporation of organometallic trihalide perovskite absorbers into these devices. But, as promising as this development is, long-term operational stability is ju...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3885

    authors: Leijtens T,Eperon GE,Pathak S,Abate A,Lee MM,Snaith HJ

    更新日期:2013-01-01 00:00:00

  • Structural basis for the recognition and degradation of host TRIM proteins by Salmonella effector SopA.

    abstract::The hallmark of Salmonella Typhimurium infection is an acute intestinal inflammatory response, which is mediated through the action of secreted bacterial effector proteins. The pro-inflammatory Salmonella effector SopA is a HECT-like E3 ligase, which was previously proposed to activate host RING ligases TRIM56 and TRI...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14004

    authors: Fiskin E,Bhogaraju S,Herhaus L,Kalayil S,Hahn M,Dikic I

    更新日期:2017-01-13 00:00:00

  • Src family kinases Fyn and Lyn are constitutively activated and mediate plasmacytoid dendritic cell responses.

    abstract::Plasmacytoid dendritic cells (pDC) are type I interferon-producing cells with critical functions in a number of human illnesses; however, their molecular regulation is incompletely understood. Here we show the role of Src family kinases (SFK) in mouse and human pDCs. pDCs express Fyn and Lyn and their activating resid...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14830

    authors: Dallari S,Macal M,Loureiro ME,Jo Y,Swanson L,Hesser C,Ghosh P,Zuniga EI

    更新日期:2017-04-03 00:00:00

  • Late Na(+) current and protracted electrical recovery are critical determinants of the aging myopathy.

    abstract::The aging myopathy manifests itself with diastolic dysfunction and preserved ejection fraction. We raised the possibility that, in a mouse model of physiological aging, defects in electromechanical properties of cardiomyocytes are important determinants of the diastolic characteristics of the myocardium, independently...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9803

    authors: Signore S,Sorrentino A,Borghetti G,Cannata A,Meo M,Zhou Y,Kannappan R,Pasqualini F,O'Malley H,Sundman M,Tsigkas N,Zhang E,Arranto C,Mangiaracina C,Isobe K,Sena BF,Kim J,Goichberg P,Nahrendorf M,Isom LL,Leri A,An

    更新日期:2015-11-06 00:00:00

  • Tuning the activities of cuprous oxide nanostructures via the oxide-metal interaction.

    abstract::Despite tremendous importance in catalysis, the design of oxide-metal interface has been hampered by the limited understanding of the nature of interfacial sites and the oxide-metal interaction (OMI). Through construction of well-defined Cu2O/Pt, Cu2O/Ag and Cu2O/Au interfaces, we find that Cu2O nanostructures (NSs) o...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15965-8

    authors: Huang W,Liu Q,Zhou Z,Li Y,Ling Y,Wang Y,Tu Y,Wang B,Zhou X,Deng D,Yang B,Yang Y,Liu Z,Bao X,Yang F

    更新日期:2020-05-08 00:00:00

  • Planar Hall effect and anisotropic magnetoresistance in polar-polar interface of LaVO3-KTaO3 with strong spin-orbit coupling.

    abstract::Among the perovskite oxide family, KTaO3 (KTO) has recently attracted considerable interest as a possible system for the realization of the Rashba effect. In this work, we report a novel conducting interface by placing KTO with another insulator, LaVO3 (LVO) and report planar Hall effect (PHE) and anisotropic magnetor...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-14689-z

    authors: Wadehra N,Tomar R,Varma RM,Gopal RK,Singh Y,Dattagupta S,Chakraverty S

    更新日期:2020-02-13 00:00:00

  • Landscape topography structures the soil microbiome in arctic polygonal tundra.

    abstract::In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03089-z

    authors: Taş N,Prestat E,Wang S,Wu Y,Ulrich C,Kneafsey T,Tringe SG,Torn MS,Hubbard SS,Jansson JK

    更新日期:2018-02-22 00:00:00

  • STING-dependent paracriny shapes apoptotic priming of breast tumors in response to anti-mitotic treatment.

    abstract::A fascinating but uncharacterized action of antimitotic chemotherapy is to collectively prime cancer cells to apoptotic mitochondrial outer membrane permeabilization (MOMP), while impacting only on cycling cell subsets. Here, we show that a proapoptotic secretory phenotype is induced by activation of cGAS/STING in can...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13689-y

    authors: Lohard S,Bourgeois N,Maillet L,Gautier F,Fétiveau A,Lasla H,Nguyen F,Vuillier C,Dumont A,Moreau-Aubry A,Frapin M,David L,Loussouarn D,Kerdraon O,Campone M,Jézéquel P,Juin PP,Barillé-Nion S

    更新日期:2020-01-14 00:00:00

  • Using metacommunity ecology to understand environmental metabolomes.

    abstract::Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a the...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19989-y

    authors: Danczak RE,Chu RK,Fansler SJ,Goldman AE,Graham EB,Tfaily MM,Toyoda J,Stegen JC

    更新日期:2020-12-11 00:00:00

  • Genetic architecture of epigenetic and neuronal ageing rates in human brain regions.

    abstract::Identifying genes regulating the pace of epigenetic ageing represents a new frontier in genome-wide association studies (GWASs). Here using 1,796 brain samples from 1,163 individuals, we carry out a GWAS of two DNA methylation-based biomarkers of brain age: the epigenetic ageing rate and estimated proportion of neuron...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15353

    authors: Lu AT,Hannon E,Levine ME,Crimmins EM,Lunnon K,Mill J,Geschwind DH,Horvath S

    更新日期:2017-05-18 00:00:00

  • CSN6 drives carcinogenesis by positively regulating Myc stability.

    abstract::Cullin-RING ubiquitin ligases (CRLs) are critical in ubiquitinating Myc, while COP9 signalosome (CSN) controls neddylation of Cullin in CRL. The mechanistic link between Cullin neddylation and Myc ubiquitination/degradation is unclear. Here we show that Myc is a target of the CSN subunit 6 (CSN6)-Cullin signalling axi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6384

    authors: Chen J,Shin JH,Zhao R,Phan L,Wang H,Xue Y,Post SM,Ho Choi H,Chen JS,Wang E,Zhou Z,Tseng C,Gully C,Velazquez-Torres G,Fuentes-Mattei E,Yeung G,Qiao Y,Chou PC,Su CH,Hsieh YC,Hsu SL,Ohshiro K,Shaikenov T,Wang H

    更新日期:2014-11-14 00:00:00

  • Tipping elements in the human intestinal ecosystem.

    abstract::The microbial communities living in the human intestine can have profound impact on our well-being and health. However, we have limited understanding of the mechanisms that control this complex ecosystem. Here, based on a deep phylogenetic analysis of the intestinal microbiota in a thousand western adults, we identify...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5344

    authors: Lahti L,Salojärvi J,Salonen A,Scheffer M,de Vos WM

    更新日期:2014-07-08 00:00:00

  • CtIP fusion to Cas9 enhances transgene integration by homology-dependent repair.

    abstract::In genome editing with CRISPR-Cas9, transgene integration often remains challenging. Here, we present an approach for increasing the efficiency of transgene integration by homology-dependent repair (HDR). CtIP, a key protein in early steps of homologous recombination, is fused to Cas9 and stimulates transgene integrat...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03475-7

    authors: Charpentier M,Khedher AHY,Menoret S,Brion A,Lamribet K,Dardillac E,Boix C,Perrouault L,Tesson L,Geny S,De Cian A,Itier JM,Anegon I,Lopez B,Giovannangeli C,Concordet JP

    更新日期:2018-03-19 00:00:00

  • Deviation from high-entropy configurations in the atomic distributions of a multi-principal-element alloy.

    abstract::The alloy-design strategy of combining multiple elements in near-equimolar ratios has shown great potential for producing exceptional engineering materials, often known as 'high-entropy alloys'. Understanding the elemental distribution, and, thus, the evolution of the configurational entropy during solidification, is ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6964

    authors: Santodonato LJ,Zhang Y,Feygenson M,Parish CM,Gao MC,Weber RJ,Neuefeind JC,Tang Z,Liaw PK

    更新日期:2015-01-20 00:00:00

  • Functional genetic encoding of sulfotyrosine in mammalian cells.

    abstract::Protein tyrosine O-sulfation (PTS) plays a crucial role in extracellular biomolecular interactions that dictate various cellular processes. It also involves in the development of many human diseases. Regardless of recent progress, our current understanding of PTS is still in its infancy. To promote and facilitate rele...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18629-9

    authors: He X,Chen Y,Beltran DG,Kelly M,Ma B,Lawrie J,Wang F,Dodds E,Zhang L,Guo J,Niu W

    更新日期:2020-09-24 00:00:00

  • Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development.

    abstract::The breast cancer susceptibility gene BRCA1 is well known for its function in double-strand break (DSB) DNA repair. While BRCA1 is also implicated in transcriptional regulation, the physiological significance remains unclear. COBRA1 (also known as NELF-B) is a BRCA1-binding protein that regulates RNA polymerase II (RN...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10913

    authors: Nair SJ,Zhang X,Chiang HC,Jahid MJ,Wang Y,Garza P,April C,Salathia N,Banerjee T,Alenazi FS,Ruan J,Fan JB,Parvin JD,Jin VX,Hu Y,Li R

    更新日期:2016-03-04 00:00:00

  • Millimetre-long transport of photogenerated carriers in topological insulators.

    abstract::Excitons are spin integer particles that are predicted to condense into a coherent quantum state at sufficiently low temperature. Here by using photocurrent imaging we report experimental evidence of formation and efficient transport of non-equilibrium excitons in Bi2-xSbxSe3 nanoribbons. The photocurrent distribution...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13711-3

    authors: Hou Y,Wang R,Xiao R,McClintock L,Clark Travaglini H,Paulus Francia J,Fetsch H,Erten O,Savrasov SY,Wang B,Rossi A,Vishik I,Rotenberg E,Yu D

    更新日期:2019-12-16 00:00:00

  • An experimental test on the probability of extinction of new genetic variants.

    abstract::In 1927, J.B.S. Haldane reasoned that the probability of fixation of new beneficial alleles is twice their fitness effect. This result, later generalized by M. Kimura, has since become the cornerstone of modern population genetics. There is no experimental test of Haldane's insight that new beneficial alleles are lost...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3417

    authors: Chelo IM,Nédli J,Gordo I,Teotónio H

    更新日期:2013-01-01 00:00:00