scholarly journals SpineJ : A software tool for quantitative analysis of nanoscale spine morphology

2019 ◽  
Author(s):  
Florian Levet ◽  
Jan Tønnesen ◽  
Valentin Nägerl ◽  
Jean-Baptiste Sibarita
Keyword(s):  
Super Resolution ◽  
Software Tool ◽  
Neuronal Function ◽  
Spine Morphology ◽  
Nanoscale Structures ◽  
Structural Details ◽  
User Friendly ◽  
Super Resolution Microscopy ◽  
Friendly Graphical User Interface ◽  
Imagej Plugin

AbstractSuper-resolution microscopy provides diffraction-unlimited optical access to the intricate morphology of neurons in living brain tissue, resolving their finest structural details, which are critical for neuronal function. However, as existing image analysis software tools have been developed for diffraction-limited images, they are generally not well suited for quantifying nanoscale structures like dendritic spines. We present SpineJ, a semi-automatic ImageJ plugin that is specifically designed for this purpose. SpineJ comes with an intuitive and user-friendly graphical user interface, facilitating fast, accurate, and unbiased analysis of spine morphology.

scholarly journals Expansion stimulated emission depletion microscopy (ExSTED)

2018 ◽  
Author(s):  
Mengfei Gao ◽  
Riccardo Maraspini ◽  
Oliver Beutel ◽  
Amin Zehtabian ◽  
Britta Eickholt ◽  
...  
Keyword(s):  
Excited State ◽  
Optical Resolution ◽  
Super Resolution ◽  
Stimulated Emission ◽  
High Fidelity ◽  
Sted Microscopy ◽  
Structural Details ◽  
Stimulated Emission Depletion ◽  
Conventional Microscopy ◽  
Super Resolution Microscopy

AbstractStimulated emission depletion (STED) microscopy is routinely used to resolve the ultra-structure of cells with a ∼10-fold higher resolution compared to diffraction limited imaging. While STED microscopy is based on preparing the excited state of fluorescent probes with light, the recently developed expansion microscopy (ExM) provides sub-diffraction resolution by physically enlarging the sample before microscopy. Expansion of fixed cells by crosslinking and swelling of hydrogels easily enlarges the sample ∼4-fold and hence increases the effective optical resolution by this factor. To overcome the current limits of these complimentary approaches, we here combined ExM with STED (ExSTED) and demonstrate an increase in resolution of up to 30-fold compared to conventional microscopy (<10 nm lateral and ∼50 nm isotropic). While the increase in resolution is straight forward, we found that high fidelity labelling via multi-epitopes is required to obtain emitter densities that allow to resolve ultra-structural details with ExSTED. Our work provides a robust template for super resolution microscopy of entire cells in the ten nanometer range.

scholarly journals Enhanced super-resolution microscopy by extreme value based emitter recovery

2018 ◽  
Author(s):  
Hongqiang Ma ◽  
Wei Jiang ◽  
Jianquan Xu ◽  
Yang Liu
Keyword(s):  
Super Resolution ◽  
Extreme Value ◽  
New Approach ◽  
Manual Adjustment ◽  
Imaging Characteristics ◽  
Nanoscale Imaging ◽  
Super Resolution Microscopy ◽  
Adjustment Of Parameters ◽  
Imagej Plugin

ABSTRACTSuper-resolution localization microscopy allows visualization of biological structure at nanoscale resolution. However, the presence of heterogeneous background can degrade the nanoscale resolution by tens of nanometers and introduce significant image artifacts. Here we develop a new approach, referred to as extreme value based emitter recovery (EVER), to accurately recover the distorted fluorescent emitters from heterogeneous background. Through numerical simulation and biological experiments, we demonstrate that EVER significantly improves the accuracy and fidelity of the reconstructed super-resolution image for a wide variety of imaging characteristics. EVER requires no manual adjustment of parameters and is implemented as an easy-to-use ImageJ plugin that can immediately enhance the quality of super-resolution images. Our method paves the way for accurate nanoscale imaging of samples with heterogeneous background fluorescence, such as thicker tissue and cells.

Expansion Microscopy: Scalable and Convenient Super-Resolution Microscopy

2019 ◽  
Vol 35 (1) ◽  
pp. 683-701 ◽  
Author(s):  
Paul W. Tillberg ◽  
Fei Chen
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Imaging Techniques ◽  
Super Resolution ◽  
Resolving Power ◽  
Relative Ease ◽  
Nanoscale Structures ◽  
Physical Form ◽  
Tissue Specimens ◽  
Super Resolution Microscopy

Expansion microscopy (ExM) is a physical form of magnification that increases the effective resolving power of any microscope. Here, we describe the fundamental principles of ExM, as well as how recently developed ExM variants build upon and apply those principles. We examine applications of ExM in cell and developmental biology for the study of nanoscale structures as well as ExM's potential for scalable mapping of nanoscale structures across large sample volumes. Finally, we explore how the unique anchoring and hydrogel embedding properties enable postexpansion molecular interrogation in a purified chemical environment. ExM promises to play an important role complementary to emerging live-cell imaging techniques, because of its relative ease of adoption and modification and its compatibility with tissue specimens up to at least 200 μm thick.

scholarly journals Structural and Functional Modulation of Perineuronal Nets: In Search of Important Players with Highlight on Tenascins

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1345
Author(s):  
Ana Jakovljević ◽  
Milena Tucić ◽  
Michaela Blažiková ◽  
Andrej Korenić ◽  
Yannis Missirlis ◽  
...  
Keyword(s):  
Synaptic Plasticity ◽  
Brain Plasticity ◽  
Super Resolution ◽  
Perineuronal Nets ◽  
Optimal Conditions ◽  
Neuronal Function ◽  
Specialized Form ◽  
Functional Modulation ◽  
Super Resolution Microscopy ◽  
The Brain

The extracellular matrix (ECM) of the brain plays a crucial role in providing optimal conditions for neuronal function. Interactions between neurons and a specialized form of ECM, perineuronal nets (PNN), are considered a key mechanism for the regulation of brain plasticity. Such an assembly of interconnected structural and regulatory molecules has a prominent role in the control of synaptic plasticity. In this review, we discuss novel ways of studying the interplay between PNN and its regulatory components, particularly tenascins, in the processes of synaptic plasticity, mechanotransduction, and neurogenesis. Since enhanced neuronal activity promotes PNN degradation, it is possible to study PNN remodeling as a dynamical change in the expression and organization of its constituents that is reflected in its ultrastructure. The discovery of these subtle modifications is enabled by the development of super-resolution microscopy and advanced methods of image analysis.

scholarly journals A Method for Quantifying Molecular Interactions Using Stochastic Modelling and Super-Resolution Microscopy

2017 ◽  
Author(s):  
Keria Bermudez-Hernandez ◽  
Sarah Keegan ◽  
Donna R. Whelan ◽  
Dylan A. Reid ◽  
Jennifer Zagelbaum ◽  
...  
Keyword(s):  
Super Resolution ◽  
Stochastic Modelling ◽  
Analytical Form ◽  
Molecular Clusters ◽  
Interaction Factor ◽  
Cluster Density ◽  
Super Resolution Microscopy ◽  
The Relationship ◽  
Microscopy Images ◽  
Imagej Plugin

AbstractWe introduce the Interaction Factor (IF), a measure for quantifying the interaction of molecular clusters in super-resolution microscopy images. The IF is robust in the sense that it is independent of cluster density, and it only depends on the extent of the pair-wise interaction between different types of molecular clusters in the image. The IF for a single or a collection of images is estimated by first using stochastic modelling where the locations of clusters in the images are repeatedly randomized to estimate the distribution of the overlaps between the clusters in the absence of interaction (IF=0). Second, an analytical form of the relationship between IF and the overlap (which has the random overlap as its only parameter) is used to estimate the IF for the experimentally observed overlap. The advantage of IF compared to conventional methods to quantify interaction in microscopy images is that it is insensitive to changing cluster density and is an absolute measure of interaction, making the interpretation of experiments easier. We validate the IF method by using both simulated and experimental data and provide an ImageJ plugin for determining the IF of an image.

BiofilmQ, a software tool for quantiative image analysis of microbial biofilm communities

2020 ◽  
Author(s):  
Hannah Jeckel ◽  
Raimo Hartmann ◽  
Eric Jelli ◽  
Knut Drescher ◽  
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Software Tool ◽  
Image Cytometry ◽  
Microbial Life ◽  
Space And Time ◽  
Life On Earth ◽  
User Friendly ◽  
Friendly Graphical User Interface ◽  
Three Dimensional Space

&lt;p&gt;Biofilms are now considered to be the most abundant form of microbial life on Earth, playing critical roles in biogeochemical cycles, agriculture, and health care. Phenotypic and genotypic variations in biofilms generally occur in three-dimensional space and time, and biofilms are therefore often investigated using microscopy. However, the quantitative analysis of microscopy images presents a key obstacle in phenotyping biofilm communities and single-cell heterogeneity inside biofilms. Here, we present BiofilmQ, a comprehensive image cytometry software tool for the automated high-throughput quantification and visualization of 3D and 2D community properties in space and time. Using BiofilmQ does not require prior knowledge of programming or image processing and provides a user-friendly graphical user interface, resulting in editable publication-quality figures. BiofilmQ is designed for handling fluorescence images of any spatially structured microbial community and growth geometry, including microscopic, mesoscopic, macroscopic colonies and aggregates, as well as bacterial biofilms in the context of eukaryotic hosts.&lt;/p&gt;

scholarly journals Enhanced super-resolution microscopy by extreme value based emitter recovery

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongqiang Ma ◽  
Wei Jiang ◽  
Jianquan Xu ◽  
Yang Liu
Keyword(s):  
Super Resolution ◽  
Extreme Value ◽  
Biological Structure ◽  
Manual Adjustment ◽  
Imaging Characteristics ◽  
Nanoscale Imaging ◽  
Super Resolution Microscopy ◽  
Adjustment Of Parameters ◽  
Imagej Plugin

AbstractSuper-resolution localization microscopy allows visualization of biological structure at nanoscale resolution. However, the presence of heterogeneous background can degrade the nanoscale resolution by tens of nanometers and introduce significant image artifacts. Here we investigate and validate an efficient approach, referred to as extreme value-based emitter recovery (EVER), to accurately recover the distorted fluorescent emitters from heterogeneous background. Through numerical simulation and biological experiments, we validated the accuracy of EVER in improving the fidelity of the reconstructed super-resolution image for a wide variety of imaging characteristics. EVER requires no manual adjustment of parameters and has been implemented as an easy-to-use ImageJ plugin that can immediately enhance the quality of reconstructed super-resolution images. This method is validated as an efficient way for robust nanoscale imaging of samples with heterogeneous background fluorescence, such as thicker tissue and cells.

scholarly journals Neuronal Localization of SENP Proteins with Super Resolution Microscopy

2020 ◽  
Vol 10 (11) ◽  
pp. 778
Author(s):  
Luca Colnaghi ◽  
Andrea Conz ◽  
Luca Russo ◽  
Clara A. Musi ◽  
Luana Fioriti ◽  
...  
Keyword(s):  
Super Resolution ◽  
Structured Illumination ◽  
Neuronal Function ◽  
Structured Illumination Microscopy ◽  
Synaptic Markers ◽  
Specific Protease ◽  
Fine Regulation ◽  
And Function ◽  
Super Resolution Microscopy ◽  
First Time

SUMOylation of proteins plays a key role in modulating neuronal function. For this reason, the balance between protein SUMOylation and deSUMOylation requires fine regulation to guarantee the homeostasis of neural tissue. While extensive research has been carried out on the localization and function of small ubiquitin-related modifier (SUMO) variants in neurons, less attention has been paid to the SUMO-specific isopeptidases that constitute the human SUMO-specific isopeptidase (SENP)/Ubiquitin-Specific Protease (ULP) cysteine protease family (SENP1-3 and SENP5-7). Here, for the first time, we studied the localization of SENP1, SENP6, and SENP7 in cultured hippocampal primary neurons at a super resolution detail level, with structured illumination microscopy (SIM). We found that the deSUMOylases partially colocalize with pre- and post-synaptic markers such as synaptophysin and drebrin. Thus, further confirming the presence with synaptic markers of the negative regulators of the SUMOylation machinery.

A software tool for STED-AFM correlative super-resolution microscopy

2015 ◽  
Author(s):  
Sami Koho ◽  
Takahiro Deguchi ◽  
Madis Löhmus ◽  
Tuomas Näreoja ◽  
Pekka E. Hänninen
Keyword(s):  
Super Resolution ◽  
Software Tool ◽  
Super Resolution Microscopy

Super-Resolution Microscopy in Studying the Structure and Function of the Cell Nucleus

Acta Naturae ◽  
2017 ◽  
Vol 9 (4) ◽  
pp. 42-51
Author(s):  
S. S. Ryabichko ◽  
◽  
A. N. Ibragimov ◽  
L. A. Lebedeva ◽  
E. N. Kozlov ◽  
...  
Keyword(s):  
Cell Nucleus ◽  
Super Resolution ◽  
Structure And Function ◽  
And Function ◽  
Super Resolution Microscopy
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