Denoising of two-photon fluorescence images with Block-Matching 3D filtering

Danielyan, Aram; Wu, Yu-Wei; Shih, Pei‐Yu; Dembitskaya, Yulia; Semyanov, Alexey

doi:10.1016/j.ymeth.2014.03.010

Cited by 18 publications

(18 citation statements)

References 26 publications

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“…We are well aware that understanding NM toxicity needs more comprehensive, complex, and novel multi- and interdisciplinary approaches [ 9 – 23 ]. These are driven in many cases by furthering imaging techniques through more specific labeling and detection of the cellular fate of NMs as illustrated by (i) in vitro/in vivo fluorescence ([ 22 , 24 ]; Figure 1 ), synchrotron radiation-based (SR) Fourier transform infrared spectroscopy (FTIR) or X-ray fluorescence microscopy [ 25 ], or single photon emission computed tomography combined with X-ray computed tomography (SPECT-CT) imaging to study NM biodistribution at organ levels ( Figure 2 ); (ii) small-angle X-ray (SAXS; Figure 3 ) or neutron scattering [ 26 – 28 ], freeze-fracture combined transmission electron microscopy (FF-TEM) and sum-frequency generation (SFG) vibrational spectroscopy for determination of structure or membrane interactions of NMs [ 13 ], and in situ high-resolution TEM [ 29 ]; (iii) application of new sets of methodologies built on basic instrumentation and related expertise in combination with NM surface modifications and toxicity assaying. For example, alterations of dendrimers combined with high-resolution NMR, capillary electrophoresis, electrophysiology and computer-assisted modeling of membrane interactions [ 11 ] or the adjustment of chitosan-based NM combined with Fourier transform infrared (FTIR) spectroscopy, transmission electron microscopy (TEM), atomic force microscopy (AFM), flow cytometry and near-infrared (NIR) fluorescence spectroscopy in vivo [ 22 ] may also be critical to rigorously characterize NM traits and relate them to nanotoxicity parameters to be assessed.…”

Section: Promoting Awareness On Nms Through Novel Approaches and Tmentioning

confidence: 99%

The Janus Facet of Nanomaterials

Kardos

Jemnitz

Jablonkai

et al. 2015

BioMed Research International

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Application of nanoscale materials (NMs) displays a rapidly increasing trend in electronics, optics, chemical catalysis, biotechnology, and medicine due to versatile nature of NMs and easily adjustable physical, physicochemical, and chemical properties. However, the increasing abundance of NMs also poses significant new and emerging health and environmental risks. Despite growing efforts, understanding toxicity of NMs does not seem to cope with the demand, because NMs usually act entirely different from those of conventional small molecule drugs. Currently, large-scale application of available safety assessment protocols, as well as their furthering through case-by-case practice, is advisable. We define a standard work-scheme for nanotoxicity evaluation of NMs, comprising thorough characterization of structural, physical, physicochemical, and chemical traits, followed by measuring biodistribution in live tissue and blood combined with investigation of organ-specific effects especially regarding the function of the brain and the liver. We propose a range of biochemical, cellular, and immunological processes to be explored in order to provide information on the early effects of NMs on some basic physiological functions and chemical defense mechanisms. Together, these contributions give an overview with important implications for the understanding of many aspects of nanotoxicity.

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Section: Promoting Awareness On Nms Through Novel Approaches and Tmentioning

confidence: 99%

The Janus Facet of Nanomaterials

Kardos

Jemnitz

Jablonkai

et al. 2015

BioMed Research International

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“…Ca 2+ binding to calmodulin causes a conformational shift that changes the solvent exposure of the GFP and allows a fluorescence increase (Chen et al 2013). Earlier versions of GCaMP indicators had relatively low slow on-off kinetics and signal-to-noise ratio, which could however be improved by 3D Block-Matching filtering (Danielyan et al 2014). More recently, the development of the “ultrasensitive” GCaMP6 has improved neuronal event detection capability to single-spike resolution, though the off-kinetics remain somewhat slow (Chen et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Two-photon probes for in vivo multicolor microscopy of the structure and signals of brain cells

Ricard

Arroyo

et al. 2018

Brain Struct Funct

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Imaging the brain of living laboratory animals at a microscopic scale can be achieved by two-photon microscopy thanks to the high penetrability and low phototoxicity of the excitation wavelengths used. However, knowledge of the two-photon spectral properties of the myriad fluorescent probes is generally scarce and, for many, non-existent. In addition, the use of different measurement units in published reports further hinders the design of a comprehensive imaging experiment. In this review, we compile and homogenize the two-photon spectral properties of 280 fluorescent probes. We provide practical data, including the wavelengths for optimal two-photon excitation, the peak values of two-photon action cross section or molecular brightness, and the emission ranges. Beyond the spectroscopic description of these fluorophores, we discuss their binding to biological targets. This specificity allows in vivo imaging of cells, their processes, and even organelles and other subcellular structures in the brain. In addition to probes that monitor endogenous cell metabolism, studies of healthy and diseased brain benefit from the specific binding of certain probes to pathology-specific features, ranging from amyloid-β plaques to the autofluorescence of certain antibiotics. A special focus is placed on functional in vivo imaging using two-photon probes that sense specific ions or membrane potential, and that may be combined with optogenetic actuators. Being closely linked to their use, we examine the different routes of intravital delivery of these fluorescent probes according to the target. Finally, we discuss different approaches, strategies, and prerequisites for two-photon multicolor experiments in the brains of living laboratory animals.

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“…Filtering methods already find widespread use in 2P-LSM in two stages: frame averaging that takes place at acquisition time (equivalent to a linear, low-pass filter) followed by post-acquisition Gaussian (linear, low-pass) or median (nonlinear) filtering [ 7 – 9 ]. More complex de-noising algorithms have outperformed temporal averaging for the specialized case of calcium fluxes in a single focal plane [ 10 , 11 ] but rely on parametric models of signal and noise and have not been shown to be effective for de-noising 3D volumes over which parameters may vary. Thus, filtering strategies that can make similar improvements and can be applied over three-dimensional volumes have great promise for improving performance in 2P-LSM.…”

Section: Introductionmentioning

confidence: 99%

Spatiotemporal Rank Filtering Improves Image Quality Compared to Frame Averaging in 2-Photon Laser Scanning Microscopy

Pinkard¹,

Corbin²,

Krummel³

2016

PLoS ONE

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Live imaging of biological specimens using optical microscopy is limited by tradeoffs between spatial and temporal resolution, depth into intact samples, and phototoxicity. Two-photon laser scanning microscopy (2P-LSM), the gold standard for imaging turbid samples in vivo, has conventionally constructed images with sufficient signal-to-noise ratio (SNR) generated by sequential raster scans of the focal plane and temporal integration of the collected signals. Here, we describe spatiotemporal rank filtering, a nonlinear alternative to temporal integration, which makes more efficient use of collected photons by selectively reducing noise in 2P-LSM images during acquisition. This results in much higher SNR while preserving image edges and fine details. Practically, this allows for at least a four fold decrease in collection times, a substantial improvement for time-course imaging in biological systems.

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Denoising of two-photon fluorescence images with Block-Matching 3D filtering

Cited by 18 publications

References 26 publications

The Janus Facet of Nanomaterials

The Janus Facet of Nanomaterials

Two-photon probes for in vivo multicolor microscopy of the structure and signals of brain cells

Spatiotemporal Rank Filtering Improves Image Quality Compared to Frame Averaging in 2-Photon Laser Scanning Microscopy

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