A software tool for tomographic axial superresolution in STED microscopy

Koho, Sami; Deguchi, Takahiro; Hänninen, Pekka

doi:10.1111/jmi.12287

Cited by 10 publications

(9 citation statements)

References 26 publications

(53 reference statements)

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“…However, as reaching the full convergence may take a large amount of iterations, we proposed two more practical thresholds based on the rate of change of the effective resolution (−1 nm it −1 and −0.2 nm it −1 ). We compared the FRC metric against two previously published ones τ 1 and η k 17–19,34 .…”

Section: Methodsmentioning

confidence: 99%

Fourier ring correlation simplifies image restoration in fluorescence microscopy

et al. 2019

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Fourier ring correlation (FRC) has recently gained popularity among fluorescence microscopists as a straightforward and objective method to measure the effective image resolution. While the knowledge of the numeric resolution value is helpful in e.g., interpreting imaging results, much more practical use can be made of FRC analysis—in this article we propose blind image restoration methods enabled by it. We apply FRC to perform image de-noising by frequency domain filtering. We propose novel blind linear and non-linear image deconvolution methods that use FRC to estimate the effective point-spread-function, directly from the images. We show how FRC can be used as a powerful metric to observe the progress of iterative deconvolution. We also address two important limitations in FRC that may be of more general interest: how to make FRC work with single images (within certain practical limits) and with three-dimensional images with highly anisotropic resolution.

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Section: Methodsmentioning

confidence: 99%

Fourier ring correlation simplifies image restoration in fluorescence microscopy

et al. 2019

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“…We also defined an alternative threshold for stopping the iteration, based on the rate of change of the effective resolution (1µm/it) in our example. We compared our metric against two previously published ones τ 1 and η k [31,32,33].…”

Section: Methodsmentioning

confidence: 99%

Fourier Ring Correlation Simplifies Image Restoration in Fluorescence Microscopy

Koho

Tortarolo

Castello

et al. 2019

Preprint

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Fourier ring correlation (FRC) has recently gained some popularity among (super-resolution) fluorescence microscopists as a straightforward and objective method to measure the effective resolution of a microscopy image. While the knowledge of the numeric resolution value is helpful in e.g. interpreting imaging results, much more practical use can be made of FRC analysis -in this article we propose novel blind image restoration methods enabled by it. We apply FRC to perform image de-noising by frequency domain filtering. We propose novel blind linear and non-linear image deconvolution methods that use FRC to estimate the effective point-spread-function, directly from the images, with no need for prior knowledge of the instrument or sample characteristics. The deconvolution is shown to work exquisitely with both twoand three-dimensional images. We also show how FRC can be used as a powerful metric to observe the progress of iterative deconvolution. While developing the image restoration methods, we also addressed two important limitations in FRC that are of more general interest: how to make FRC work with single images and with three-dimensional images with anisotropic resolution.(1)

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“…Image Correlation : An automatic image correlation method was created, based on our own SuperTomo software that was originally developed for tomographic STED image reconstruction, but contains powerful image registration functions that can be easily applied elsewhere. For the CLEM application, the registration functionality of SuperTomo was expanded to 2D images.…”

Section: Methodsmentioning

confidence: 99%

“…Otherwise the image registration implementation was kept the same as in ref. . The different spatial transformations together with various image similarity metrics that have been implemented in SuperTomo, such as normalized cross correlation, mutual information, and mean squared difference, allowed to tune the image correlation settings quite flexibly.…”

Section: Methodsmentioning

confidence: 99%

“…The potential of the FNDs is further highlighted in a live cell experiment, in which cells containing FNDs and mitochondrial marker dye (MitoTracker) were first imaged on a confocal microscope, after which the sample was prepared for, and imaged with TEM. The multimodal images were correlated with our own open‐source SuperTomo software, except for the live cell data for which a custom MatLab script was created.…”

Section: Introductionmentioning

confidence: 99%

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STED‐TEM Correlative Microscopy Leveraging Nanodiamonds as Intracellular Dual‐Contrast Markers

Prabhakar

Peurla

Koho

et al. 2017

Small

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Development of fluorescent and electron dense markers is essential for the implementation of correlative light and electron microscopy, as dual-contrast landmarks are required to match the details in the multimodal images. Here, a novel method for correlative microscopy that utilizes fluorescent nanodiamonds (FNDs) as dual-contrast probes is reported. It is demonstrated how the FNDs can be used as dual-contrast labels-and together with automatic image registration tool SuperTomo, for precise image correlation-in high-resolution stimulated emission depletion (STED)/confocal and transmission electron microscopy (TEM) correlative microscopy experiments. It is shown how FNDs can be employed in experiments with both live and fixed cells as well as simple test samples. The fluorescence imaging can be performed either before TEM imaging or after, as the robust FNDs survive the TEM sample preparation and can be imaged with STED and other fluorescence microscopes directly on the TEM grids.

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A software tool for tomographic axial superresolution in STED microscopy

Cited by 10 publications

References 26 publications

Fourier ring correlation simplifies image restoration in fluorescence microscopy

Fourier ring correlation simplifies image restoration in fluorescence microscopy

Fourier Ring Correlation Simplifies Image Restoration in Fluorescence Microscopy

STED‐TEM Correlative Microscopy Leveraging Nanodiamonds as Intracellular Dual‐Contrast Markers

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