scholarly journals A real-time compression library for microscopy images

2017 ◽  
Author(s):  
Bálint Balázs ◽  
Joran Deschamps ◽  
Marvin Albert ◽  
Jonas Ries ◽  
Lars Hufnagel
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Imaging Techniques ◽  
Intrinsic Noise ◽  
Light Sheet ◽  
Localization Microscopy ◽  
Time Compression ◽  
Light Sheet Microscopy ◽  
Microscopy Images ◽  
Single Molecule Localization Microscopy

AbstractFluorescence imaging techniques such as single molecule localization microscopy, high-content screening and light-sheet microscopy are producing ever-larger datasets, which poses increasing challenges in data handling and data sharing. Here, we introduce a real-time compression library that allows for very fast (beyond 1 GB/s) compression and de-compression of microscopy datasets during acquisition. In addition to an efficient lossless mode, our algorithm also includes a lossy option, which limits pixel deviations to the intrinsic noise level of the image and yields compression ratio of up to 100-fold. We present a detailed performance analysis of the different compression modes for various biological samples and imaging modalities.

scholarly journals Hessian single molecule localization microscopy using sCMOS camera

2018 ◽  
Author(s):  
Fudong Xue ◽  
Wenting He ◽  
Fan Xu ◽  
Mingshu Zhang ◽  
Liangyi Chen ◽  
...  
Keyword(s):  
Single Molecule ◽  
Signal To Noise Ratio ◽  
Imaging Techniques ◽  
Super Resolution ◽  
Fast Imaging ◽  
Large Field ◽  
Localization Microscopy ◽  
Readout Noise ◽  
Single Pixel ◽  
Single Molecule Localization Microscopy

AbstractSingle-molecule localization microscopy (SMLM) has the highest spatial resolution among the existing super-resolution (SR) imaging techniques, but its temporal resolution needs further improvement. An sCMOS camera can effectively increase the imaging rate due to its large field of view and fast imaging speed. Using an sCMOS camera for SMLM imaging can significantly improve the imaging time resolution, but the unique single pixel-dependent readout noise of sCMOS cameras severely limits their application in SMLM imaging. This paper develops a Hessian-based SMLM (Hessian-SMLM) method that can correct the variance, gain and offset of a single pixel of a camera and effectively eliminate the pixel-dependent readout noise of sCMOS cameras, especially when the signal-to-noise ratio is low. Using Hessian SMLM to image mEos3.2-labeled actin was able to significantly reduce the artifacts due to camera noise.

scholarly journals 3D Structure From 2D Microscopy Images Using Deep Learning

2021 ◽  
Vol 1 ◽  
Author(s):  
Benjamin Blundell ◽  
Christian Sieben ◽  
Suliana Manley ◽  
Ed Rosten ◽  
QueeLim Ch’ng ◽  
...  
Keyword(s):  
Deep Learning ◽  
Single Molecule ◽  
Structural Model ◽  
Protein Complexes ◽  
3D Structure ◽  
Data Set ◽  
Localization Microscopy ◽  
Single Structure ◽  
Microscopy Images ◽  
Single Molecule Localization Microscopy

Understanding the structure of a protein complex is crucial in determining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional. Recent advances in Artificial Intelligence have been applied to this problem, primarily using voxel based approaches to analyse sets of electron microscopy images. Here we present a deep learning solution for reconstructing the protein complexes from a number of 2D single molecule localization microscopy images, with the solution being completely unconstrained. Our convolutional neural network coupled with a differentiable renderer predicts pose and derives a single structure. After training, the network is discarded, with the output of this method being a structural model which fits the data-set. We demonstrate the performance of our system on two protein complexes: CEP152 (which comprises part of the proximal toroid of the centriole) and centrioles.

scholarly journals Hochaufgelöste Visualisierung einzelner Moleküle auf ganzen Zellen

BIOspektrum ◽  
2020 ◽  
Vol 26 (7) ◽  
pp. 735-738
Author(s):  
Jan Schlegel ◽  
Markus Sauer
Keyword(s):  
Single Molecule ◽  
Three Dimensional ◽  
Light Sheet ◽  
Localization Microscopy ◽  
Adhesion Receptor ◽  
Whole Cells ◽  
Analysis Techniques ◽  
Complex Interactions ◽  
Different Parts ◽  
Single Molecule Localization Microscopy

AbstractBiological systems are dynamic and three-dimensional but many techniques allow only static and two-dimensional observation of cells. We used three-dimensional (3D) lattice light-sheet single-molecule localization microscopy (dSTORM) to investigate the complex interactions and distribution of single molecules in the plasma membrane of whole cells. Different receptor densities of the adhesion receptor CD56 at different parts of the cell highlight the importance and need of three-dimensional observation and analysis techniques.

scholarly journals Single-Molecule Localization Microscopy to Study Protein Organization in the Filamentous Fungus Trichoderma atroviride

Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3199
Author(s):  
Alexander W.A.F. Reismann ◽  
Lea Atanasova ◽  
Susanne Zeilinger ◽  
Gerhard J. Schütz
Keyword(s):  
Single Molecule ◽  
Filamentous Fungus ◽  
Mammalian Cells ◽  
Hyphal Growth ◽  
Trichoderma Atroviride ◽  
Localization Microscopy ◽  
Family Protein ◽  
Mycoparasitic Fungus ◽  
Microscopy Images ◽  
Single Molecule Localization Microscopy

Single-molecule localization microscopy has boosted our understanding of biological samples by offering access to subdiffraction resolution using fluorescence microscopy methods. While in standard mammalian cells this approach has found wide-spread use, its application to filamentous fungi has been scarce. This is mainly due to experimental challenges that lead to high amounts of background signal because of ample autofluorescence. Here, we report the optimization of labeling, imaging and data analysis protocols to yield the first single-molecule localization microscopy images of the filamentous fungus Trichoderma atroviride. As an example, we show the spatial distribution of the Sur7 tetraspanin-family protein Sfp2 required for hyphal growth and cell wall stability in this mycoparasitic fungus.

scholarly journals Oblique plane single-molecule localization microscopy for thick samples

2018 ◽  
Author(s):  
Jeongmin Kim ◽  
Michal Wojcik ◽  
Yuan Wang ◽  
Ke Xu ◽  
Xiang Zhang
Keyword(s):  
Fluorescence Detection ◽  
Single Molecule ◽  
Tissue Sample ◽  
Super Resolution ◽  
Light Sheet ◽  
Localization Microscopy ◽  
Isotropic Resolution ◽  
Fluorescent Beads ◽  
Imaging Depth ◽  
Single Molecule Localization Microscopy

We introduce single-molecule oblique plane microscopy (obSTORM) to directly image oblique sections of thick samples into depth without lengthy axial stack acquisition. Using oblique light-sheet illumination and oblique fluorescence detection, obSTORM offers uniform super-resolution throughout imaging depth in diverse biological specimens from cells to tissues. In particular, we demonstrate an isotropic resolution of ∼51 nm over a depth of 32 μm for a tissue sample, and comparable resolution over a depth of 100 μm using fluorescent beads.

Single-Molecule Imaging of Active Mitochondrial Nitroreductases using a Photo-Crosslinking Fluorescent Sensor

2019 ◽  
Author(s):  
Zacharias Thiel ◽  
Pablo Rivera-Fuentes
Keyword(s):  
Subcellular Localization ◽  
Fluorescent Probe ◽  
Single Molecule ◽  
Mammalian Cells ◽  
Fluorescent Sensor ◽  
Biological Functions ◽  
Localization Microscopy ◽  
Drug Activation ◽  
Nitroreductase Activity ◽  
Single Molecule Localization Microscopy

Many biomacromolecules are known to cluster in microdomains with specific subcellular localization. In the case of enzymes, this clustering greatly defines their biological functions. Nitroreductases are enzymes capable of reducing nitro groups to amines and play a role in detoxification and pro-drug activation. Although nitroreductase activity has been detected in mammalian cells, the subcellular localization of this activity remains incompletely characterized. Here, we report a fluorescent probe that enables super-resolved imaging of pools of nitroreductase activity within mitochondria. This probe is activated sequentially by nitroreductases and light to give a photo-crosslinked adduct of active enzymes. In combination with a general photoactivatable marker of mitochondria, we performed two-color, threedimensional, single-molecule localization microscopy. These experiments allowed us to image the sub-mitochondrial organization of microdomains of nitroreductase activity.<br>

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