Divide and conquer: real-time maximum likelihood fitting of multiple emitters for super-resolution localization microscopy

Li, Luchang; Xin, Bo; Kuang, Weibing; Zhou, Zhiwei; Huang, Zhen-Li

doi:10.1364/oe.27.021029

Cited by 29 publications

(19 citation statements)

References 37 publications

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“…In this case, the center of gravity can be determined to a higher precision than the Gauss fit of the PSF would allow. Even the positions of multi-emitters can be accurately fit by special algorithms with minor sacrifices in the localization precision [21]. With such a sparse excitation regime, thousands of images must be recorded and combined into the final SMLM image.…”

Section: Introductionmentioning

confidence: 99%

Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes

Kubalová

Němečková

Weißhart

et al. 2021

IJMS

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The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200–250 nm laterally, ~500–700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4′,6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.

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Section: Introductionmentioning

confidence: 99%

Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes

Kubalová

Němečková

Weißhart

et al. 2021

IJMS

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“…Dense emitter localization algorithms are more accurate for localizing overlapping dense emitters ( Holden et al, 2011 ), except that it is computationally intensive and slow ( Sage et al, 2019 ). High-speed algorithms for emitters with moderate or high density ( Li et al, 2019 ; Ma et al, 2019 ; Xu et al, 2020 ) have recently become available.…”

Section: Brief Overview Of Smlm Imaging Systemmentioning

confidence: 99%

Probing Chromatin Compaction and Its Epigenetic States in situ With Single-Molecule Localization-Based Super-Resolution Microscopy

Liu

2021

Front. Cell Dev. Biol.

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Chromatin organization play a vital role in gene regulation and genome maintenance in normal biological processes and in response to environmental insults. Disruption of chromatin organization imposes a significant effect on many cellular processes and is often associated with a range of pathological processes such as aging and cancer. Extensive attention has been attracted to understand the structural and functional studies of chromatin architecture. Biochemical assays coupled with the state-of-the-art genomic technologies have been traditionally used to probe chromatin architecture. Recent advances in single molecule localization microscopy (SMLM) open up new opportunities to directly visualize higher-order chromatin architecture, its compaction status and its functional states at nanometer resolution in the intact cells or tissue. In this review, we will first discuss the recent technical advantages and challenges of using SMLM to image chromatin architecture. Next, we will focus on the recent applications of SMLM for structural and functional studies to probe chromatin architecture in key cellular processes. Finally, we will provide our perspectives on the recent development and potential applications of super-resolution imaging of chromatin architecture in improving our understanding in diseases.

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“…In the past decade, a number of localization algorithms have been developed in the literature on the basis of a variety of criteria and objectives, including but not limited to localization of single emitters in single frames : (d)STORM 4 , Octan 5 , FluoroBancroft 6 , Gaussian fitting 7 , PeakSelector 8 , SOFI 9 , DAOSTORM 10 , maximum likelihood 11 , and palm3d 12 , localization of multiple emitters in single frames : 3D-DAOSTORM 13 , compressed sensing 14 , fast maximum likelihood 15 , RadialSymmetry 16 , PeakFit 17 , PALMER 18 , RapidSTORM 19 , least-square fitting with the 3D Gibson-Lanni point spread function (PSF) 20 , PC-PALM 21 , fast compressed sensing 22 , Easy-DHPSF 23 , 3D-WTM 24 , RainSTORM 25 , WaveTracer 26 , μManager 27 , ThunderSTORM 28 , FALCON 29 , MIATool 30 , AO-STORM 31 , state space 32 , TVSTORM 33 , ADCG 34 , Cspline 35 , ALM 36 , SMAP 37 , UNLOC 38 , sparse Bayesian learning 39 , LSTR 40 , FCEG 41 , WinSTORM 42 , and QC-STORM 43 , localization of multiple emitters in multiple frames : 3B analysis 44 , deconSTORM 45 , spatiotemporal decomposition and association 46 , and nonnegative matrix factorization 47 . In addition, the recent approaches include cloud computing 48 , clustering analysis 49 , 50 , big data analysis 51 , correlation analysis 52 , HAWK 53 to alleviate artifacts detectable by the Fourier ring co...…”

Section: Introductionmentioning

confidence: 99%

“…Among the localization algorithms in the literature, only a few exploit temporal correlation by jointly utilizing multiple data frames or the entire data movie in estimation of emitter locations 44 – 47 . The majority of localization algorithms 1 – 43 estimate emitter locations from each single data frame independently or by the frame-by-frame localization (FFL). Thus, most localization nanoscopy images are FFL images.…”

Section: Introductionmentioning

confidence: 99%

“…The temporal correlation is still contained in the FFL image, which if exploited, shall improve the localization accuracy of estimated emitter locations and the quality of nanoscopy image as well. The algorithms UNLOC 38 and QC-STORM 43 detect and reconnect the estimated locations that might be generated from the same emitter in consecutive frames in order to improve localization accuracy. It is interesting to know the potentially maximum improvement of quality that can be obtained by exploitation of the temporal correlation in an FFL image.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Potential quality improvement of stochastic optical localization nanoscopy images obtained by frame by frame localization algorithms

Sun

2020

Sci Rep

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A data movie of stochastic optical localization nanoscopy contains spatial and temporal correlations, both providing information of emitter locations. The majority of localization algorithms in the literature estimate emitter locations by frame-by-frame localization (FFL), which exploit only the spatial correlation and leave the temporal correlation into the FFL nanoscopy images. The temporal correlation contained in the FFL images, if exploited, can improve the localization accuracy and the image quality. In this paper, we analyze the properties of the FFL images in terms of root mean square minimum distance (RMSMD) and root mean square error (RMSE). It is shown that RMSMD and RMSE can be potentially reduced by a maximum fold equal to the square root of the average number of activations per emitter. Analyzed and revealed are also several statistical properties of RMSMD and RMSE and their relationship with respect to a large number of data frames, bias and variance of localization errors, small localization errors, sample drift, and the worst FFL image. Numerical examples are taken and the results confirm the prediction of analysis. The ideas about how to develop an algorithm to exploit the temporal correlation of FFL images are also briefly discussed. The results suggest development of two kinds of localization algorithms: the algorithms that can exploit the temporal correlation of FFL images and the unbiased localization algorithms.

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Divide and conquer: real-time maximum likelihood fitting of multiple emitters for super-resolution localization microscopy

Cited by 29 publications

References 37 publications

Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes

Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes

Probing Chromatin Compaction and Its Epigenetic States in situ With Single-Molecule Localization-Based Super-Resolution Microscopy

Potential quality improvement of stochastic optical localization nanoscopy images obtained by frame by frame localization algorithms

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