Optical Property Analyses of Plant Cells for Adaptive Optics Microscopy

Tamada, Yosuke; Murata, Takashi; Hattori, Masayuki; Oya, Shin; Hayano, Yutaka; Kamei, Yasuhiro

doi:10.1080/15599612.2014.901455

Cited by 27 publications

(11 citation statements)

References 37 publications

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“…Alternatively, spectral unmixing can be used to separate each contribution [34]. Furthermore, chloroplasts, mitochondria, starch granules and the cell wall are all light-scattering structures [35][36][37]. Collectively, background light absorbing, emitting and scattering factors reduce both excitation and signal detection efficiencies in whole-mount fresh tissues.…”

Section: Important Considerations Prior To Imagingmentioning

confidence: 99%

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Dumur

Duncan

Graumann

et al. 2019

Nucleus

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The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. Abbreviations: 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel

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Section: Important Considerations Prior To Imagingmentioning

confidence: 99%

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Dumur

Duncan

Graumann

et al. 2019

Nucleus

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“…The value D∕r 0 denotes the number of turbulent cells aligning on the aperture diameter, frequently used to indicate the degree of image degradation. The residual wavefront error after AO correction was σ AO ¼ 0.16 rad, theoretically yielding a Strehl ratio, r ST ¼ expð−σ 2 AO Þ of 0.98. 5 This is the same level reported by Tao et al 7 However, Strehl ratios measured from the observed images ought to be lower than those derived from residual phase errors on the sensor.…”

Section: Defocus Aberrationmentioning

confidence: 99%

“…Parts of the foggy components may have arisen from the diffusion of light occurring on the etched surface of the coverslip, where about half the wavelength of depth enhanced the diffractive errors. 2,17 Figures 7(g)-7(i) show the AO-corrected images. As expected, bead images of 1.0-μm diameter around the reference patterns became finer such that their individual shapes were distinguishable as being spherical.…”

Section: Higher-order Aberrationsmentioning

confidence: 99%

“…Thus, the observed images may be blurred. [1][2][3] Adaptive optics (AO) can resolve such situations, and various AO *Address all correspondence to Noriaki Miura, miuranr@mail.kitami-it.ac.jp systems have been developed for biological microscopy. 4 A number of pioneering AO systems for microscopy have adopted indirect methods of phase-error measurement, including methods that use image metrics, and these have been successfully employed in biological applications.…”

Section: Introductionmentioning

confidence: 99%

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Imaging performance of microscopy adaptive-optics system using scene-based wavefront sensing

et al. 2020

Self Cite

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. Significance: A scene-based adaptive-optics (AO) system is developed and a method for investigating its imaging performance is proposed. The system enables derivation of Strehl ratios from observed images via collaboration with computer simulations. The resultant Strehl ratios are comparable with those of other current AO systems. Aim: For versatile and noninvasive AO microscopy, a scene-based wavefront-sensing technique working on a Shack–Hartmann wavefront sensor is developed in a modal control system. The purpose of the research is to clarify the imaging performance of the AO system via the derivation of Strehl ratios from observed images toward applications in microscopy of living cells and tissues. Approach: Two imaging metrics that can be directly measured from observed images (i.e., an energy concentration ratio and unbiased maximum ratio) are defined and related to the Strehl ratio via computer simulations. Experiments are conducted using artificial targets to measure the imaging metrics, which are then converted to Strehl ratios. Results: The resultant Strehl ratios are and 0.5 in the cases of defocus and higher aberrations, respectively. The half-widths at half-maximum of the AO-corrected bead images are favorably comparable to those of on-focus images under simple defocus aberration, and the AO system works both under bright-field illumination and on fluorescent bead images. Conclusions: The proposed scene-based AO system is expected to work with a Strehl ratio of more than 0.5 when applied to high-resolution live imaging of cells and tissues under bright-field and fluorescence microscopies.

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“…It is interesting to note that PSAs with higher numbers of images tend to be more robust against phase unwrapping failures which may arise due to combinations of modulation between reference and object beams, and mechanical vibrations. The literature indicates typical refractive indices of the cell wall (n = 1.41−1.52) for flowering plants, 28 cytoplasm (n = 1.36 − 1.39), nucleus (n = 1.355 − 1.65) and nucleolus (n = 1.375 − 1.385) for animal cells. 29,30 These values are numerically consistent; however, it should be noted that the uncertainty in refractive index limits the ability to accurately quantify the thickness of organelles in many cases; additionally, preparation of the sample between microscope slides may also affect the thicknesses measured.…”

Section: Phase Measurement From a Biological Samplementioning

confidence: 99%

A flexible quantitative phase imaging microscope for label-free imaging of thick biological specimens using aperture masks

Seniya

Towers

2019

Preprint

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A flexible quantitative phase imaging microscope is reported that offers new capabilities in terms of phase measurement from both thin and thick biological specimens. The method utilises Zernike's phase contrast approach for label-free imaging with a Twymann-Green based phase shifting module in the back focal plane. The interfering wave fronts are manipulated by laser cut apertures to form the scattered and non-scattered fields. The design is flexible and low-cost. It is shown that the bandwidth of the optical source can be optimised to enable larger optical path differences to be measured whilst giving essentially speckle free imaging. Phase maps of the cell membrane, nucleus and nucleolus of transparent epidermis cells of Allium cepa have been examined as proof of concept. Measurements from a range of glass beads confirm the optical path difference capability. The implementation of the phase shifting module is < 10% of the cost of that using a spatial light modulator whilst delivering equivalent phase resolution.

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Optical Property Analyses of Plant Cells for Adaptive Optics Microscopy

Cited by 27 publications

References 37 publications

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Imaging performance of microscopy adaptive-optics system using scene-based wavefront sensing

A flexible quantitative phase imaging microscope for label-free imaging of thick biological specimens using aperture masks

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