Fast and accurate sCMOS noise correction for fluorescence microscopy.

Abstract:

:The rapid development of scientific CMOS (sCMOS) technology has greatly advanced optical microscopy for biomedical research with superior sensitivity, resolution, field-of-view, and frame rates. However, for sCMOS sensors, the parallel charge-voltage conversion and different responsivity at each pixel induces extra readout and pattern noise compared to charge-coupled devices (CCD) and electron-multiplying CCD (EM-CCD) sensors. This can produce artifacts, deteriorate imaging capability, and hinder quantification of fluorescent signals, thereby compromising strategies to reduce photo-damage to live samples. Here, we propose a content-adaptive algorithm for the automatic correction of sCMOS-related noise (ACsN) for fluorescence microscopy. ACsN combines camera physics and layered sparse filtering to significantly reduce the most relevant noise sources in a sCMOS sensor while preserving the fine details of the signal. The method improves the camera performance, enabling fast, low-light and quantitative optical microscopy with video-rate denoising for a broad range of imaging conditions and modalities.

journal_name

Nat Commun

journal_title

Nature communications

authors

Mandracchia B,Hua X,Guo C,Son J,Urner T,Jia S

doi

10.1038/s41467-019-13841-8

subject

Has Abstract

pub_date

2020-01-03 00:00:00

pages

94

issue

1

issn

2041-1723

pii

10.1038/s41467-019-13841-8

journal_volume

11

pub_type

杂志文章
  • Publisher Correction: CD146-HIF-1α hypoxic reprogramming drives vascular remodeling and pulmonary arterial hypertension.

    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: 已发布勘误

    doi:10.1038/s41467-019-12107-7

    authors: Luo Y,Teng X,Zhang L,Chen J,Liu Z,Chen X,Zhao S,Yang S,Feng J,Yan X

    更新日期:2019-09-05 00:00:00

  • Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation.

    abstract::The spatial organization of chromosomes has key functional roles, yet how chromosomes fold remains poorly understood at the single-molecule level. Here, we employ models of polymer physics to investigate DNA loci in human HCT116 and IMR90 wild-type and cohesin depleted cells. Model predictions on single-molecule struc...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17141-4

    authors: Conte M,Fiorillo L,Bianco S,Chiariello AM,Esposito A,Nicodemi M

    更新日期:2020-07-03 00:00:00

  • Anti-quenching NIR-II molecular fluorophores for in vivo high-contrast imaging and pH sensing.

    abstract::The contrast and sensitivity of in vivo fluorescence imaging has been revolutionized by molecular fluorophores operating in the second near-infrared window (NIR-II; 1000-1700 nm), but an ongoing challenge is the solvatochromism-caused quenching in aqueous solution for the long-wavelength absorbing fluorophores. Herein...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09043-x

    authors: Wang S,Fan Y,Li D,Sun C,Lei Z,Lu L,Wang T,Zhang F

    更新日期:2019-03-05 00:00:00

  • Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy.

    abstract::Genomic changes observed across treatment may result from either clonal evolution or geographically disparate sampling of heterogeneous tumors. Here we use computational modeling based on analysis of fifteen primary breast tumors and find that apparent clonal change between two tumor samples can frequently be explaine...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-08593-4

    authors: Caswell-Jin JL,McNamara K,Reiter JG,Sun R,Hu Z,Ma Z,Ding J,Suarez CJ,Tilk S,Raghavendra A,Forte V,Chin SF,Bardwell H,Provenzano E,Caldas C,Lang J,West R,Tripathy D,Press MF,Curtis C

    更新日期:2019-02-08 00:00:00

  • Ultrafast enzymatic digestion of proteins by microdroplet mass spectrometry.

    abstract::Enzymatic digestion for protein sequencing usually requires much time, and does not always result in high sequence coverage. Here we report the use of aqueous microdroplets to accelerate enzymatic reactions and, in particular, to improve protein sequencing. When a room temperature aqueous solution containing 10 µM myo...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-14877-x

    authors: Zhong X,Chen H,Zare RN

    更新日期:2020-02-26 00:00:00

  • Causal factors for seismicity near Azle, Texas.

    abstract::In November 2013, a series of earthquakes began along a mapped ancient fault system near Azle, Texas. Here we assess whether it is plausible that human activity caused these earthquakes. Analysis of both lake and groundwater variations near Azle shows that no significant stress changes were associated with the shallow...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7728

    authors: Hornbach MJ,DeShon HR,Ellsworth WL,Stump BW,Hayward C,Frohlich C,Oldham HR,Olson JE,Magnani MB,Brokaw C,Luetgert JH

    更新日期:2015-04-21 00:00:00

  • Accurate, scalable and integrative haplotype estimation.

    abstract::The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing dat...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13225-y

    authors: Delaneau O,Zagury JF,Robinson MR,Marchini JL,Dermitzakis ET

    更新日期:2019-11-28 00:00:00

  • Synthetic chimeric nucleases function for efficient genome editing.

    abstract::CRISPR-Cas systems have revolutionized genome editing across a broad range of biotechnological endeavors. Many CRISPR-Cas nucleases have been identified and engineered for improved capabilities. Given the modular structure of such enzymes, we hypothesized that engineering chimeric sequences would generate non-natural ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13500-y

    authors: Liu RM,Liang LL,Freed E,Chang H,Oh E,Liu ZY,Garst A,Eckert CA,Gill RT

    更新日期:2019-12-04 00:00:00

  • Intestinal microbiome composition and its relation to joint pain and inflammation.

    abstract::Macrophage-mediated inflammation is thought to have a causal role in osteoarthritis-related pain and severity, and has been suggested to be triggered by endotoxins produced by the gastrointestinal microbiome. Here we investigate the relationship between joint pain and the gastrointestinal microbiome composition, and o...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-12873-4

    authors: Boer CG,Radjabzadeh D,Medina-Gomez C,Garmaeva S,Schiphof D,Arp P,Koet T,Kurilshikov A,Fu J,Ikram MA,Bierma-Zeinstra S,Uitterlinden AG,Kraaij R,Zhernakova A,van Meurs JBJ

    更新日期:2019-10-25 00:00:00

  • Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process.

    abstract::Owing to their pathogenical role and unique ability to exist both as soluble proteins and transmembrane complexes, pore-forming toxins (PFTs) have been a focus of microbiologists and structural biologists for decades. PFTs are generally secreted as water-soluble monomers and subsequently bind the membrane of target ce...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12062

    authors: Iacovache I,De Carlo S,Cirauqui N,Dal Peraro M,van der Goot FG,Zuber B

    更新日期:2016-07-13 00:00:00

  • A threefold rise in widespread extreme rain events over central India.

    abstract::Socioeconomic challenges continue to mount for half a billion residents of central India because of a decline in the total rainfall and a concurrent rise in the magnitude and frequency of extreme rainfall events. Alongside a weakening monsoon circulation, the locally available moisture and the frequency of moisture-la...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00744-9

    authors: Roxy MK,Ghosh S,Pathak A,Athulya R,Mujumdar M,Murtugudde R,Terray P,Rajeevan M

    更新日期:2017-10-03 00:00:00

  • Distinct populations of cortical pyramidal neurons mediate drug reward and aversion.

    abstract::Processing within the anterior cingulate cortex (ACC) is crucial for the patterning of appropriate behavior, and ACC dysfunction following chronic drug use is thought to play a major role in drug addiction. However, cortical pyramidal projection neurons can be subdivided into two major types (intratelencephalic (IT) a...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-20526-0

    authors: Garcia AF,Crummy EA,Webb IG,Nooney MN,Ferguson SM

    更新日期:2021-01-08 00:00:00

  • Active control of anapole states by structuring the phase-change alloy Ge2Sb2Te5.

    abstract::High-index dielectric nanoparticles supporting a distinct series of Mie resonances have enabled a new class of optical antennas with unprecedented functionalities. The great wealth of multipolar responses has not only brought in new physical insight but also spurred practical applications. However, how to make such a ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-08057-1

    authors: Tian J,Luo H,Yang Y,Ding F,Qu Y,Zhao D,Qiu M,Bozhevolnyi SI

    更新日期:2019-01-23 00:00:00

  • Caloric restriction reduces age-related and all-cause mortality in rhesus monkeys.

    abstract::Caloric restriction (CR) without malnutrition increases longevity and delays the onset of age-associated disorders in short-lived species, from unicellular organisms to laboratory mice and rats. The value of CR as a tool to understand human ageing relies on translatability of CR's effects in primates. Here we show tha...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4557

    authors: Colman RJ,Beasley TM,Kemnitz JW,Johnson SC,Weindruch R,Anderson RM

    更新日期:2014-04-01 00:00:00

  • Information recovery from low coverage whole-genome bisulfite sequencing.

    abstract::The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important because even at the recommend 30X coverage for reference methylomes, up to 50% of high-resolution fea...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms11306

    authors: Libertini E,Heath SC,Hamoudi RA,Gut M,Ziller MJ,Czyz A,Ruotti V,Stunnenberg HG,Frontini M,Ouwehand WH,Meissner A,Gut IG,Beck S

    更新日期:2016-06-27 00:00:00

  • A gas-plastic elastomer that quickly self-heals damage with the aid of CO2 gas.

    abstract::Self-healing materials are highly desirable because they allow products to maintain their performance. Typical stimuli used for self-healing are heat and light, despite being unsuitable for materials used in certain products as heat can damage other components, and light cannot reach materials located within a product...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09826-2

    authors: Miwa Y,Taira K,Kurachi J,Udagawa T,Kutsumizu S

    更新日期:2019-04-23 00:00:00

  • Single-mode tunable laser emission in the single-exciton regime from colloidal nanocrystals.

    abstract::Whispering-gallery-mode resonators have been extensively used in conjunction with different materials for the development of a variety of photonic devices. Among the latter, hybrid structures, consisting of dielectric microspheres and colloidal core/shell semiconductor nanocrystals as gain media, have attracted intere...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3376

    authors: Grivas C,Li C,Andreakou P,Wang P,Ding M,Brambilla G,Manna L,Lagoudakis P

    更新日期:2013-01-01 00:00:00

  • Magnetic field induced quantum phases in a tensor network study of Kitaev magnets.

    abstract::Recent discovery of the half quantized thermal Hall conductivity in [Formula: see text]-RuCl[Formula: see text], a candidate material for the Kitaev spin liquid, suggests the presence of a highly entangled quantum state in external magnetic fields. This field induced phase appears between the low field zig-zag magneti...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15320-x

    authors: Lee HY,Kaneko R,Chern LE,Okubo T,Yamaji Y,Kawashima N,Kim YB

    更新日期:2020-04-02 00:00:00

  • High-performance p-channel transistors with transparent Zn doped-CuI.

    abstract::'Ideal' transparent p-type semiconductors are required for the integration of high-performance thin-film transistors (TFTs) and circuits. Although CuI has recently attracted attention owing to its excellent opto-electrical properties, solution processability, and low-temperature synthesis, the uncontrolled copper vaca...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18006-6

    authors: Liu A,Zhu H,Park WT,Kim SJ,Kim H,Kim MG,Noh YY

    更新日期:2020-08-27 00:00:00

  • Armadillo repeat containing 12 promotes neuroblastoma progression through interaction with retinoblastoma binding protein 4.

    abstract::Recent studies suggest the emerging roles of armadillo (ARM) family proteins in tumor progression. However, the functions and underlying mechanisms of ARM members in tumorigenesis and aggressiveness of neuroblastoma (NB) remain to be determined. Herein, we identify armadillo repeat containing 12 (ARMC12) as an ARM mem...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05286-2

    authors: Li D,Song H,Mei H,Fang E,Wang X,Yang F,Li H,Chen Y,Huang K,Zheng L,Tong Q

    更新日期:2018-07-19 00:00:00

  • Self-organization of Plk4 regulates symmetry breaking in centriole duplication.

    abstract::During centriole duplication, a single daughter centriole is formed next to the mother centriole. The molecular mechanism that determines a single duplication site remains a long-standing question. Here, we show that intrinsic self-organization of Plk4 is implicated in symmetry breaking in the process of centriole dup...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09847-x

    authors: Yamamoto S,Kitagawa D

    更新日期:2019-04-18 00:00:00

  • Origin of pressure-induced crystallization of Ce75Al25 metallic glass.

    abstract::Phase transitions in amorphous alloys under pressure are an important fundamental problem. Here we report on a first-principles study that reproduces the recently discovered pressure-induced crystallization of amorphous Ce100-xAlx (x<25) alloys and reveals an atomistic transformation mechanism. Contrary to common beli...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7493

    authors: Wu M,Tse JS,Wang SY,Wang CZ,Jiang JZ

    更新日期:2015-03-09 00:00:00

  • Structure and substrate selectivity of the 750-kDa α6β6 holoenzyme of geranyl-CoA carboxylase.

    abstract::Geranyl-CoA carboxylase (GCC) is essential for the growth of Pseudomonas organisms with geranic acid as the sole carbon source. GCC has the same domain organization and shares strong sequence conservation with the related biotin-dependent carboxylases 3-methylcrotonyl-CoA carboxylase (MCC) and propionyl-CoA carboxylas...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9986

    authors: Jurado AR,Huang CS,Zhang X,Zhou ZH,Tong L

    更新日期:2015-11-23 00:00:00

  • Polariton condensation and surface enhanced Raman in spherical ZnO microcrystals.

    abstract::Preparation and characterization of polariton Bose-Einstein condensates in micro-cavities of high quality are at the frontier of contemporary solid state physics. Here, we report on three-dimensional polariton condensation and confinement in pseudo-spherical ZnO microcrystals. The boundary of micro-spherical ZnO resem...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18666-4

    authors: Volkov VV,Oliver DJ,Perry CC

    更新日期:2020-09-30 00:00:00

  • Coil-globule transitions drive discontinuous volume conserving deformation in locally restrained gels.

    abstract::The equilibrium volume of a thermoresponsive polymer gel changes dramatically across a temperature due to the coil-globule transitions of the polymers. When cofacially oriented nanosheets are embedded in such a gel, the composite gel deforms at the temperature, without changing the volume, and the response time is con...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-04533-w

    authors: Yamamoto T,Masubuchi Y,Doi M

    更新日期:2018-05-25 00:00:00

  • A neural link between generosity and happiness.

    abstract::Generous behaviour is known to increase happiness, which could thereby motivate generosity. In this study, we use functional magnetic resonance imaging and a public pledge for future generosity to investigate the brain mechanisms that link generous behaviour with increases in happiness. Participants promised to spend ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15964

    authors: Park SQ,Kahnt T,Dogan A,Strang S,Fehr E,Tobler PN

    更新日期:2017-07-11 00:00:00

  • X-ray structure of a carpet-like antimicrobial defensin-phospholipid membrane disruption complex.

    abstract::Defensins are cationic antimicrobial peptides expressed throughout the plant and animal kingdoms as a first line of defense against pathogens. Membrane targeting and disruption is a crucial function of many defensins, however the precise mechanism remains unclear. Certain plant defensins form dimers that specifically ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-04434-y

    authors: Järvå M,Lay FT,Phan TK,Humble C,Poon IKH,Bleackley MR,Anderson MA,Hulett MD,Kvansakul M

    更新日期:2018-05-17 00:00:00

  • Somatodendritic consistency check for temporal feature segmentation.

    abstract::The brain identifies potentially salient features within continuous information streams to process hierarchical temporal events. This requires the compression of information streams, for which effective computational principles are yet to be explored. Backpropagating action potentials can induce synaptic plasticity in...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15367-w

    authors: Asabuki T,Fukai T

    更新日期:2020-03-25 00:00:00

  • Bivariate genome-wide association meta-analysis of pediatric musculoskeletal traits reveals pleiotropic effects at the SREBF1/TOM1L2 locus.

    abstract::Bone mineral density is known to be a heritable, polygenic trait whereas genetic variants contributing to lean mass variation remain largely unknown. We estimated the shared SNP heritability and performed a bivariate GWAS meta-analysis of total-body lean mass (TB-LM) and total-body less head bone mineral density (TBLH...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00108-3

    authors: Medina-Gomez C,Kemp JP,Dimou NL,Kreiner E,Chesi A,Zemel BS,Bønnelykke K,Boer CG,Ahluwalia TS,Bisgaard H,Evangelou E,Heppe DHM,Bonewald LF,Gorski JP,Ghanbari M,Demissie S,Duque G,Maurano MT,Kiel DP,Hsu YH,C J van d

    更新日期:2017-07-25 00:00:00

  • Adipose tissue NAPE-PLD controls fat mass development by altering the browning process and gut microbiota.

    abstract::Obesity is a pandemic disease associated with many metabolic alterations and involves several organs and systems. The endocannabinoid system (ECS) appears to be a key regulator of energy homeostasis and metabolism. Here we show that specific deletion of the ECS synthesizing enzyme, NAPE-PLD, in adipocytes induces obes...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7495

    authors: Geurts L,Everard A,Van Hul M,Essaghir A,Duparc T,Matamoros S,Plovier H,Castel J,Denis RG,Bergiers M,Druart C,Alhouayek M,Delzenne NM,Muccioli GG,Demoulin JB,Luquet S,Cani PD

    更新日期:2015-03-11 00:00:00