An adaptive non-local means filter for denoising live-cell images and improving particle detection

Yang, Lei; Parton, Richard M.; Ball, Graeme; Qiu, Zhen; Greenaway, A. H.; Davis, Ilan; Lu, Weiping

doi:10.1016/j.jsb.2010.06.019

Cited by 53 publications

(44 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The average donor channel image was created from images with the 532 nm excitation, and the average acceptor image was created from images with the 635 nm excitation. Both images were filtered to enhance fluorescent spots and converted to images of fluorescent spot probabilities (25). Spots with probability above a set value were fit with a two…”

Section: Discussionmentioning

confidence: 99%

DNA-Endonuclease Complex Dynamics by Simultaneous FRET and Fluorophore Intensity in Evanescent Field

Tutkus

Marčiulionis

Sasnauskas

et al. 2017

Biophysical Journal

View full text Add to dashboard Cite

The single-molecule Fö rster resonance energy transfer (FRET) is a powerful tool to study interactions and conformational changes of biological molecules in the distance range from a few to 10 nm. In this study, we demonstrate a method to augment this range with longer distances. The method is based on the intensity changes of a tethered fluorophore, diffusing in the exponentially decaying evanescent excitation field. In combination with FRET it allowed us to reveal and characterize the dynamics of what had been inaccessible conformations of the DNA-protein complex. Our model system, restriction enzyme Ecl18kI, interacts with a FRET pair-labeled DNA fragment to form two different DNA loop conformations. The DNA-protein interaction geometry is such that the efficient FRET is expected for one of these conformations-''antiparallel'' loop. In the alternative ''parallel'' loop, the expected distance between the dyes is outside the range accessible by FRET. Therefore, ''antiparallel'' looping is observed in a single-molecule time trajectory as discrete transitions to a state of high FRET efficiency. At the same time, transitions to a high-intensity state of the directly excited acceptor fluorophore on a DNA tether are due to a change of its average position in the evanescent field of excitation and can be associated with a loop of either ''parallel'' or ''antiparallel'' configuration. Simultaneous analysis of FRET and acceptor intensity trajectories then allows us to discriminate different DNA loop conformations and access the average lifetimes of different states.

show abstract

Section: Discussionmentioning

confidence: 99%

DNA-Endonuclease Complex Dynamics by Simultaneous FRET and Fluorophore Intensity in Evanescent Field

Tutkus

Marčiulionis

Sasnauskas

et al. 2017

Biophysical Journal

View full text Add to dashboard Cite

show abstract

“…The denoising method becomes adaptive, i.e., the adaptive NLM (ANLM), when an NLM method adapts its h parameter values based on the characteristics of the image. 22,26,29,36,37 Previous studies have suggested that the optimal values for h could be selected to be proportional to the noise variation. 22,25 For an image with an unknown true noise variation, the noise level, σðx i Þ, at voxel x i , could be estimated by computing the minimal Euclidean distance of the weighted average of all blocks neighboring the voxel x i E Q -T A R G E T ; t e m p : i n t r a l i n k -; e 0 0 4 ; 3 2 6 ; 6 0 9…”

Section: Basics Of Nonlocal Means-based Denoisingmentioning

confidence: 99%

Adaptive anatomical preservation optimal denoising for radiation therapy daily MRI

et al. 2017

View full text Add to dashboard Cite

, "Adaptive anatomical preservation optimal denoising for radiation therapy daily MRI," J. Med. Imag. 4(3), 034004 (2017), doi: 10.1117/1.JMI.4.3.034004. Abstract. Low-field magnetic resonance imaging (MRI) has recently been integrated with radiation therapy systems to provide image guidance for daily cancer radiation treatments. The main benefit of the low-field strength is minimal electron return effects. The main disadvantage of low-field strength is increased image noise compared to diagnostic MRIs conducted at 1.5 T or higher. The increased image noise affects both the discernibility of soft tissues and the accuracy of further image processing tasks for both clinical and research applications, such as tumor tracking, feature analysis, image segmentation, and image registration. An innovative method, adaptive anatomical preservation optimal denoising (AAPOD), was developed for optimal image denoising, i.e., to maximally reduce noise while preserving the tissue boundaries. AAPOD employs a series of adaptive nonlocal mean (ANLM) denoising trials with increasing denoising filter strength (i.e., the block similarity filtering parameter in the ANLM algorithm), and then detects the tissue boundary losses on the differences of sequentially denoised images using a zero-crossing edge detection method. The optimal denoising filter strength per voxel is determined by identifying the denoising filter strength value at which boundary losses start to appear around the voxel. The final denoising result is generated by applying the ANLM denoising method with the optimal per-voxel denoising filter strengths. The experimental results demonstrated that AAPOD was capable of reducing noise adaptively and optimally while avoiding tissue boundary losses. AAPOD is useful for improving the quality of MRIs with low-contrast-to-noise ratios and could be applied to other medical imaging modalities, e.g., computed tomography.

show abstract

“…Patch-based filter (PBF) [4,11] is a state-of-the-art development of NLM filter in which the sizes of the searching windows are adaptively selected. However, for low SNR images containing particle-like features, such as fluorescence live-cell images with mixed Poisson-Gaussian noise contaminations [1][2][3][4], the Euclidean distance measured in greyscale images may not be robust for preserving the features [12]. Consequently, NLM filter and other algorithms that are based on this measurement can lead to loss of information and artefacts in denoised images.…”

Section: Introductionmentioning

confidence: 99%

A 2D+t Feature-preserving Non-local Means Filter for Image Denoising and Improved Detection of Small and Weak Particles

Yang¹,

Parton²,

Ball³

et al. 2010

Procedings of the British Machine Vision Conference 2010

Self Cite

View full text Add to dashboard Cite

A feature-preserving non-local means (FP-NLM) filter has been developed recently for denoising images containing small and weak particlelike objects. It explores the commonly used non-local means filter to employ two similarity measurements taken in the original greyscale image and a feature image which measures the particle probability in the original image. In this paper, we report a new approach to image mapping for constructing the feature image by incorporating both spatial and temporal (2D+t) characteristics of objects. We present a 2D+t FP-NLM filter based on the improved particle probability image. Experiments show that the new filter can achieve better balance between particle enhancement and background smoothing for images under severe noise contamination and has a greater capability in detecting particles of interest in such environments.

show abstract

An adaptive non-local means filter for denoising live-cell images and improving particle detection

Cited by 53 publications

References 30 publications

DNA-Endonuclease Complex Dynamics by Simultaneous FRET and Fluorophore Intensity in Evanescent Field

DNA-Endonuclease Complex Dynamics by Simultaneous FRET and Fluorophore Intensity in Evanescent Field

Adaptive anatomical preservation optimal denoising for radiation therapy daily MRI

A 2D+t Feature-preserving Non-local Means Filter for Image Denoising and Improved Detection of Small and Weak Particles

Contact Info

Product

Resources

About