SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy

2015 ◽  
pp. btv576 ◽  
Author(s):  
Pavel Křížek ◽  
Tomáš Lukeš ◽  
Martin Ovesný ◽  
Karel Fliegel ◽  
Guy M. Hagen
Keyword(s):  
Fluorescence Microscopy ◽  
Structured Illumination ◽  
Matlab Toolbox

scholarly journals Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes

2020 ◽  
Author(s):  
Jiji Chen ◽  
Hideki Sasaki ◽  
Hoyin Lai ◽  
Yijun Su ◽  
Jiamin Liu ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Network Performance ◽  
Resolution Enhancement ◽  
Three Dimensional ◽  
Ground Truth ◽  
Time Lapse ◽  
Stimulated Emission ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Attention Networks

Abstract We demonstrate residual channel attention networks (RCAN) for restoring and enhancing volumetric time-lapse (4D) fluorescence microscopy data. First, we modify RCAN to handle image volumes, showing that our network enables denoising competitive with three other state-of-the-art neural networks. We use RCAN to restore noisy 4D super-resolution data, enabling image capture over tens of thousands of images (thousands of volumes) without apparent photobleaching. Second, using simulations we show that RCAN enables class-leading resolution enhancement, superior to other networks. Third, we exploit RCAN for denoising and resolution improvement in confocal microscopy, enabling ~2.5-fold lateral resolution enhancement using stimulated emission depletion (STED) microscopy ground truth. Fourth, we develop methods to improve spatial resolution in structured illumination microscopy using expansion microscopy ground truth, achieving improvements of ~1.4-fold laterally and ~3.4-fold axially. Finally, we characterize the limits of denoising and resolution enhancement, suggesting practical benchmarks for evaluating and further enhancing network performance.

scholarly journals Total Internal Reflection Fluorescence Microscopy (TIRFM) – novel techniques and applications

2020 ◽  
Vol 8 (11) ◽  
Author(s):  
Verena Richter ◽  
Michael Wagner ◽  
Herbert Schneckenburger
Keyword(s):  
Fluorescence Microscopy ◽  
Single Molecule ◽  
Total Internal Reflection ◽  
Plasma Membranes ◽  
Focal Adhesions ◽  
Internal Reflection ◽  
Total Internal Reflection Fluorescence ◽  
Thin Layers ◽  
Structured Illumination ◽  
Structured Illumination Microscopy

Total Internal Reflection Fluorescence Microscopy (TIRFM) has been established almost 40 years ago for studies of plasma membranes or membrane proximal sites of living cells. The method is based on light incidence at an angle above the critical angle of total internal reflection and generation of an evanescent electromagnetic field penetrating about 100 nm into a sample and permitting selective excitation of membrane proximal fluorophores. Two techniques are presented here: prism-type TIRFM and objective-type TIRFM with high aperture microscope objective lenses. Furthermore, numerous applications are summarized, e.g. measurement of focal adhesions, cell-substrate topology, endocytosis or exocytosis of vesicles as well as single molecule detection within thin layers. Finally, highly innovative combinations of TIRFM with Förster Resonance Energy Transfer (FRET) measurements as well as with Structured Illumination Microscopy (SIM) and fluorescence reader technologies are presented.

scholarly journals Efficient and Accurate Synapse Detection With Selective Structured Illumination Microscopy on the Putative Regions of Interest of Ultrathin Serial Sections

2021 ◽  
Vol 15 ◽  
Author(s):  
Gyeong Tae Kim ◽  
Sangkyu Bahn ◽  
Nari Kim ◽  
Joon Ho Choi ◽  
Jinseop S. Kim ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Fluorescence Microscopy ◽  
Neural Circuit ◽  
Molecular Characteristics ◽  
Imaging Method ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Gold Standard Method ◽  
Array Tomography ◽  
Synapse Detection

Critical determinants of synaptic functions include subcellular locations, input sources, and specific molecular characteristics. However, there is not yet a reliable and efficient method that can detect synapses. Electron microscopy is a gold-standard method to detect synapses due to its exceedingly high spatial resolution. However, it requires laborious and time-consuming sample preparation and lengthy imaging time with limited labeling methods. Recent advances in various fluorescence microscopy methods have highlighted fluorescence microscopy as a substitute for electron microscopy in reliable synapse detection in a large volume of neural circuits. In particular, array tomography has been verified as a useful tool for neural circuit reconstruction. To further improve array tomography, we developed a novel imaging method, called “structured illumination microscopy on the putative region of interest on ultrathin sections”, which enables efficient and accurate detection of synapses-of-interest. Briefly, based on low-magnification conventional fluorescence microscopy images, synapse candidacy was determined. Subsequently, the coordinates of the regions with candidate synapses were imaged using super-resolution structured illumination microscopy. Using this system, synapses from the high-order thalamic nucleus, the posterior medial nucleus in the barrel cortex were rapidly and accurately imaged.

Structured Illumination Fluorescence Microscopy: Diffraction-Limit Breaking Principle and Application in Life Science

2015 ◽  
Vol 52 (1) ◽  
pp. 010003 ◽  
Author(s):  
吴美瑞 Wu Meirui ◽  
杨西斌 Yang Xibin ◽  
熊大曦 Xiong Daxi ◽  
李辉 Li Hui ◽  
武晓东 Wu Xiaodong
Keyword(s):  
Fluorescence Microscopy ◽  
Life Science ◽  
Diffraction Limit ◽  
Structured Illumination

scholarly journals CryoSIM: super-resolution 3D structured illumination cryogenic fluorescence microscopy for correlated ultrastructural imaging

Optica ◽  
2020 ◽  
Vol 7 (7) ◽  
pp. 802 ◽  
Author(s):  
Michael A. Phillips ◽  
Maria Harkiolaki ◽  
David Miguel Susano Pinto ◽  
Richard M. Parton ◽  
Ana Palanca ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Super Resolution ◽  
Structured Illumination

scholarly journals Spatial calibration of structured illumination fluorescence microscopy using capillary tissue phantoms

2009 ◽  
Vol 72 (2) ◽  
pp. 85-92 ◽  
Author(s):  
Grace S. Lee ◽  
Lino F. Miele ◽  
Aslihan Turhan ◽  
Miao Lin ◽  
Dusan Hanidziar ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Structured Illumination ◽  
Tissue Phantoms ◽  
Spatial Calibration

scholarly journals Visualization of the Pollen Tube Cytoskeleton using Structured Illumination Fluorescence Microscopy

2006 ◽  
Vol 12 (S02) ◽  
pp. 438-439
Author(s):  
A Geitmann ◽  
O Gossot ◽  
R Zerzour
Keyword(s):  
Fluorescence Microscopy ◽  
Pollen Tube ◽  
Structured Illumination

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

scholarly journals Three-Dimensional Resolution Doubling in Wide-Field Fluorescence Microscopy by Structured Illumination

2008 ◽  
Vol 94 (12) ◽  
pp. 4957-4970 ◽  
Author(s):  
Mats G.L. Gustafsson ◽  
Lin Shao ◽  
Peter M. Carlton ◽  
C. J. Rachel Wang ◽  
Inna N. Golubovskaya ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Three Dimensional ◽  
Wide Field ◽  
Structured Illumination

scholarly journals Resolving the internal morphology of core–shell microgels with super-resolution fluorescence microscopy

2020 ◽  
Vol 2 (1) ◽  
pp. 323-331 ◽  
Author(s):  
Pia Otto ◽  
Stephan Bergmann ◽  
Alice Sandmeyer ◽  
Maxim Dirksen ◽  
Oliver Wrede ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Internal Structure ◽  
Single Molecule ◽  
Fluorescent Dyes ◽  
Super Resolution ◽  
Core Shell ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Internal Morphology

We investigate the internal structure of smart core–shell microgels by super-resolution fluorescence microscopy by combining of 3D single molecule localization and structured illumination microscopy using freely diffusing fluorescent dyes.

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