scholarly journals Accelerating multi-emitter localization in super-resolution localization microscopy with FPGA-GPU cooperative computation

2021 ◽  
Author(s):  
dan gui ◽  
Yunjiu Chen ◽  
Weibing Kuang ◽  
MINGTAO SHANG ◽  
Zhengxia WANG ◽  
...  
Keyword(s):  
Super Resolution ◽  
Localization Microscopy ◽  
Cooperative Computation ◽  
Emitter Localization

A literature review of localization methods and emergence of deep learning in single-molecule localization microscopy

2020 ◽  
Author(s):  
Anish Mukherjee
Keyword(s):  
Deep Learning ◽  
Single Molecule ◽  
Super Resolution ◽  
Point Sources ◽  
Learning Approaches ◽  
Localization Algorithm ◽  
Localization Microscopy ◽  
Trade Offs ◽  
Emitter Localization ◽  
Single Molecule Localization Microscopy

The quality of super-resolution images largely depends on the performance of the emitter localization algorithm used to localize point sources. In this article, an overview of the various techniques which are used to localize point sources in single-molecule localization microscopy are discussed and their performances are compared. This overview can help readers to select a localization technique for their application. Also, an overview is presented about the emergence of deep learning methods that are becoming popular in various stages of single-molecule localization microscopy. The state of the art deep learning approaches are compared to the traditional approaches and the trade-offs of selecting an algorithm for localization are discussed.

scholarly journals Divide and Conquer: Real-time maximum likelihood fitting of multiple emitters for super-resolution localization microscopy

2019 ◽  
Author(s):  
Luchang Li ◽  
Bo Xin ◽  
Weibing Kuang ◽  
Zhiwei Zhou ◽  
Zhen-Li Huang
Keyword(s):  
Image Processing ◽  
Real Time ◽  
Super Resolution ◽  
Large Cell ◽  
Field Of View ◽  
Divide And Conquer ◽  
Image Size ◽  
Localization Microscopy ◽  
Localization Algorithms ◽  
Emitter Localization

AbstractMulti-emitter localization has great potential for maximizing the imaging speed of super-resolution localization microscopy. However, the slow image analysis speed of reported multi-emitter localization algorithms limits their usage in mostly off-line image processing with small image size. Here we adopt the well-known divide and conquer strategy in computer science and present a fitting-based method called QC-STORM for fast multi-emitter localization. Using simulated and experimental data, we verify that QC-STORM is capable of providing real-time full image processing on raw images with 100 µm × 100 µm field of view and 10 ms exposure time, with comparable spatial resolution as the popular fitting-based ThunderSTORM and the up-to-date non-iterative WindSTORM. This study pushes the development and practical use of super-resolution localization microscopy in high-throughput or high-content imaging of cell-to-cell differences or discovering rare events in a large cell population.

scholarly journals Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes

2021 ◽  
Vol 22 (4) ◽  
pp. 1903
Author(s):  
Ivona Kubalová ◽  
Alžběta Němečková ◽  
Klaus Weisshart ◽  
Eva Hřibová ◽  
Veit Schubert
Keyword(s):  
Single Molecule ◽  
Imaging Techniques ◽  
Chromatin Condensation ◽  
Super Resolution ◽  
Stimulated Emission ◽  
Wide Field ◽  
Structured Illumination Microscopy ◽  
Metaphase Chromosomes ◽  
Localization Microscopy ◽  
Super Resolution 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.

scholarly journals Camera-based localization microscopy optimized with calibrated structured illumination

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.

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

PLoS ONE ◽  
2016 ◽  
Vol 11 (7) ◽  
pp. e0158884 ◽  
Author(s):  
Leila Nahidiazar ◽  
Alexandra V. Agronskaia ◽  
Jorrit Broertjes ◽  
Bram van den Broek ◽  
Kees Jalink
Keyword(s):  
Super Resolution ◽  
Localization Microscopy ◽  
Imaging Conditions

scholarly journals Super-resolution binding activated localization microscopy through reversible change of DNA conformation

Nucleus ◽  
2018 ◽  
Vol 9 (1) ◽  
pp. 182-189 ◽  
Author(s):  
Aleksander Szczurek ◽  
Udo Birk ◽  
Hans Knecht ◽  
Jurek Dobrucki ◽  
Sabine Mai ◽  
...  
Keyword(s):  
Super Resolution ◽  
Dna Conformation ◽  
Reversible Change ◽  
Localization Microscopy

Aberration Characterization and Correction in Super-Resolution Localization Microscopy

2017 ◽  
Vol 37 (3) ◽  
pp. 0318004
Author(s):  
赵泽宇 Zhao Zeyu ◽  
张肇宁 Zhang Zhaoning ◽  
黄振立 Huang Zhenli
Keyword(s):  
Super Resolution ◽  
Localization Microscopy

scholarly journals Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

2019 ◽  
Vol 16 (5) ◽  
pp. 387-395 ◽  
Author(s):  
Daniel Sage ◽  
Thanh-An Pham ◽  
Hazen Babcock ◽  
Tomas Lukes ◽  
Thomas Pengo ◽  
...  
Keyword(s):  
Single Molecule ◽  
Super Resolution ◽  
Localization Microscopy ◽  
Fight Club ◽  
2D And 3D ◽  
Single Molecule Localization Microscopy
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