The Role of Image Analysis Algorithms in Super-resolution Localization Microscopy

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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Camera-based localization microscopy optimized with calibrated structured illumination

Communications Physics ◽

10.1038/s42005-021-00546-y ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Martin Schmidt ◽

Adam C. Hundahl ◽

Henrik Flyvbjerg ◽

Rodolphe Marie ◽

Kim I. Mortensen

Keyword(s):

Data Analysis ◽

Super Resolution ◽

Wide Field ◽

Structured Illumination ◽

Uniform Illumination ◽

Localization Microscopy ◽

Localization And Tracking ◽

Field Imaging ◽

Wide Field Imaging ◽

Localization Information

AbstractUntil very recently, super-resolution localization and tracking of fluorescent particles used camera-based wide-field imaging with uniform illumination. Then it was demonstrated that structured illuminations encode additional localization information in images. The first demonstration of this uses scanning and hence suffers from limited throughput. This limitation was mitigated by fusing camera-based localization with wide-field structured illumination. Current implementations, however, use effectively only half the localization information that they encode in images. Here we demonstrate how all of this information may be exploited by careful calibration of the structured illumination. Our approach achieves maximal resolution for given structured illumination, has a simple data analysis, and applies to any structured illumination in principle. We demonstrate this with an only slightly modified wide-field microscope. Our protocol should boost the emerging field of high-precision localization with structured illumination.

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The Constantly Evolving Role of Medical Image Processing in Oncology: From Traditional Medical Image Processing to Imaging Biomarkers and Radiomics

Journal of Imaging ◽

10.3390/jimaging7080124 ◽

2021 ◽

Vol 7 (8) ◽

pp. 124

Author(s):

Kostas Marias

Keyword(s):

Image Processing ◽

Image Analysis ◽

Medical Image ◽

Biomarker Discovery ◽

Medical Image Processing ◽

Machine Learning Techniques ◽

Imaging Biomarker ◽

Imaging Biomarkers ◽

Precision Oncology

The role of medical image computing in oncology is growing stronger, not least due to the unprecedented advancement of computational AI techniques, providing a technological bridge between radiology and oncology, which could significantly accelerate the advancement of precision medicine throughout the cancer care continuum. Medical image processing has been an active field of research for more than three decades, focusing initially on traditional image analysis tasks such as registration segmentation, fusion, and contrast optimization. However, with the advancement of model-based medical image processing, the field of imaging biomarker discovery has focused on transforming functional imaging data into meaningful biomarkers that are able to provide insight into a tumor’s pathophysiology. More recently, the advancement of high-performance computing, in conjunction with the availability of large medical imaging datasets, has enabled the deployment of sophisticated machine learning techniques in the context of radiomics and deep learning modeling. This paper reviews and discusses the evolving role of image analysis and processing through the lens of the abovementioned developments, which hold promise for accelerating precision oncology, in the sense of improved diagnosis, prognosis, and treatment planning of cancer.

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The Role of Exopolysaccharides in Oral Biofilms

Journal of Dental Research ◽

10.1177/0022034519845001 ◽

2019 ◽

Vol 98 (7) ◽

pp. 739-745 ◽

Cited By ~ 7

Author(s):

C. Cugini ◽

M. Shanmugam ◽

N. Landge ◽

N. Ramasubbu

Keyword(s):

Biofilm Formation ◽

Bacterial Colonization ◽

Super Resolution ◽

Extracellular Proteins ◽

Extracellular Polysaccharides ◽

Oral Biofilms ◽

The Matrix ◽

Oral Microbes ◽

Biofilm Development

The oral cavity contains a rich consortium of exopolysaccharide-producing microbes. These extracellular polysaccharides comprise a major component of the oral biofilm. Together with extracellular proteins, DNA, and lipids, they form the biofilm matrix, which contributes to bacterial colonization, biofilm formation and maintenance, and pathogenesis. While a number of oral microbes have been studied in detail with regard to biofilm formation and pathogenesis, the exopolysaccharides have been well characterized for only select organisms, namely Streptococcus mutans and Aggregatibacter actinomycetemcomitans. Studies on the exopolysaccharides of other oral organisms, however, are in their infancy. In this review, we present the current research on exopolysaccharides of oral microbes regarding their biosynthesis, regulation, contributions to biofilm formation and stability of the matrix, and immune evasion. In addition, insight into the role of exopolysaccharides in biofilms is highlighted through the evaluation of emerging techniques such as pH probing of biofilm colonies, solid-state nuclear magnetic resonance for macromolecular interactions within biofilms, and super-resolution microscopy analysis of biofilm development. Finally, exopolysaccharide as a potential nutrient source for species within a biofilm is discussed.

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Optimizing Imaging Conditions for Demanding Multi-Color Super Resolution Localization Microscopy

PLoS ONE ◽

10.1371/journal.pone.0158884 ◽

2016 ◽

Vol 11 (7) ◽

pp. e0158884 ◽

Cited By ~ 77

Author(s):

Leila Nahidiazar ◽

Alexandra V. Agronskaia ◽

Jorrit Broertjes ◽

Bram van den Broek ◽

Kees Jalink

Keyword(s):

Super Resolution ◽

Localization Microscopy ◽

Imaging Conditions

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Germany and Russia Since Reunification: Continuity, Change, and the Role of Leaders

German Politics & Society ◽

10.3167/gps.2017.350103 ◽

2017 ◽

Vol 35 (1) ◽

pp. 42-62 ◽

Cited By ~ 1

Author(s):

Keyword(s):

Image Analysis ◽

International Relations ◽

The Political ◽

German Reunification ◽

The Past ◽

Personal Relations ◽

Economic Trends ◽

Economic Ties

How can we understand German-Russian relations since German reunification? Both the geopolitical positions of the two states and the political and economic ties between them have been transformed over the past twentyfive years. This paper will argue, however, that the role of the two countries’ leaders in shaping these relations has been surprisingly important. Building on the tradition of “first image” analysis in international relations, this paper shows that, along with larger political and economic trends, personal relations between these leaders have helped to set the tenor of bilateral ties. When the leaders were able to build trust and personal friendships, relations improved. Yet more recently, since 2012, relations have soured sharply. While there are obviously larger reasons for this, more negative personal ties between leaders have also played an important role. In short, just as issues of trust and friendship matter in personal ties, they also matter in International Relations.

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