scholarly journals μSPIM: A Software Platform for Selective Plane Illumination Microscopy

2020 ◽  
Author(s):  
Daniel Saska ◽  
Paul Pichler ◽  
Chen Qian ◽  
Chrysia Pegasiou ◽  
Christopher L. Buckley ◽  
...  
Keyword(s):  
Optical Design ◽  
Light Sheet ◽  
Volumetric Imaging ◽  
Larval Zebrafish ◽  
Selective Plane Illumination Microscopy ◽  
Spatio Temporal ◽  
Set Up ◽  
Control And Synchronization ◽  
The Brain ◽  
Camera Shutter

AbstractSelective Plane Illumination Microscopy (SPIM) is a fluorescence imaging technique that allows volumetric imaging at high spatio-temporal resolution to monitor neural activity in live organisms such as larval zebrafish. A major challenge in the construction of a custom SPIM microscope is the control and synchronization of the various hardware components. Here we present a control toolset, μSPIM, built around the open-source MicroManager platform that has already been widely adopted for the control of microscopy hardware. Installation of μSPIM is relatively straightforward, involving a single C++ executable and a Java-based extension to Micro-Manager. Imaging protocols are defined through the μSPIM extension to Micro-Manager. The extension then synchronizes the camera shutter with the galvanometer mirrors to create a light-sheet that is scanned in the z-dimension, in synchrony with the imaging objective, to produce volumetric recordings. A key advantage of μSPIM is that a series of calibration procedures optimizes acquisition for a given set-up making it relatively independent of the optical design of the microscope, or the hardware used to build it. Two laser illumination arms can be used while also allowing for the introduction of illumination masks. μSPIM allows imaging of calcium activity throughout the brain of larval zebrafish at rates of 100 planes per second with single cell resolution as well as slower imaging to reconstruct cell populations, for example, in the cleared brains of mice.

scholarly journals 3D Interferometric Lattice Light-Sheet Imaging

2020 ◽  
Author(s):  
Bin Cao ◽  
Guanshi Wang ◽  
Jieru Li ◽  
Alexandros Pertsinidis
Keyword(s):  
Single Molecule ◽  
Super Resolution ◽  
Light Sheet ◽  
Detection Sensitivity ◽  
Live Cells ◽  
Background Suppression ◽  
Axial Resolution ◽  
Volumetric Imaging ◽  
Spatio Temporal ◽  
And Function

Understanding cellular structure and function requires live-cell imaging with high spatio-temporal resolution and high detection sensitivity. Direct visualization of molecular processes using single-molecule/super-resolution techniques has thus been transformative. However, extracting the highest-resolution 4D information possible from weak and dynamic fluorescence signals in live cells remains challenging. For example, some of the highest spatial resolution methods, e.g. interferometric (4Pi) approaches1-6 can be slow, require high peak excitation intensities that accelerate photobleaching or suffer from increased out-of-focus background. Selective-plane illumination (SPIM)7-12 reduces background, but most implementations typically feature modest spatial, especially axial, resolution. Here we develop 3D interferometric lattice light-sheet (3D-iLLS) imaging, a technique that overcomes many of these limitations. 3D-iLLS provides, by virtue of SPIM, low light levels and photobleaching, while providing increased background suppression and significantly improved volumetric imaging/sectioning capabilities through 4Pi interferometry. We demonstrate 3D-iLLS with axial resolution and single-particle localization precision down to <100nm (FWHM) and <10nm (1σ) respectively. 3D-iLLS paves the way for a fuller elucidation of sub-cellular phenomena by enhanced 4D resolution and SNR live imaging.

scholarly journals Spatio-temporal dynamics of cerebral capillary segments with stalling red blood cells

2017 ◽  
Vol 39 (5) ◽  
pp. 886-900 ◽  
Author(s):  
Şefik Evren Erdener ◽  
Jianbo Tang ◽  
Amir Sajjadi ◽  
Kıvılcım Kılıç ◽  
Sreekanth Kura ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Oct Angiography ◽  
Label Free ◽  
Systematic Analysis ◽  
Volumetric Imaging ◽  
Cerebral Capillary ◽  
Spatio Temporal ◽  
The Brain

Optical coherence tomography (OCT) allows label-free imaging of red blood cell (RBC) flux within capillaries with high spatio-temporal resolution. In this study, we utilized time-series OCT-angiography to demonstrate interruptions in capillary RBC flux in mouse brain in vivo. We noticed ∼7.5% of ∼200 capillaries had at least one stall in awake mice with chronic windows during a 9-min recording. At any instant, ∼0.45% of capillaries were stalled. Average stall duration was ∼15 s but could last over 1 min. Stalls were more frequent and longer lasting in acute window preparations. Further, isoflurane anesthesia in chronic preparations caused an increase in the number of stalls. In repeated imaging, the same segments had a tendency to stall again over a period of one month. In awake animals, functional stimulation decreased the observance of stalling events. Stalling segments were located distally, away from the first couple of arteriolar-side capillary branches and their average RBC and plasma velocities were lower than nonstalling capillaries within the same region. This first systematic analysis of capillary RBC stalls in the brain, enabled by rapid and continuous volumetric imaging of capillaries with OCT-angiography, will lead to future investigations of the potential role of stalling events in cerebral pathologies.

scholarly journals Synaptic Self-Organization of Spatio-Temporal Pattern Selectivity

2021 ◽  
Author(s):  
Mohammad Dehghani Habibabadi ◽  
Klaus Richard Pawelzik
Keyword(s):  
Synaptic Plasticity ◽  
Specific Pattern ◽  
Temporal Coding ◽  
Neuronal Coding ◽  
Temporal Mode ◽  
Spatio Temporal ◽  
Set Up ◽  
Spike Patterns ◽  
The Brain ◽  
Input Spike

Spiking model neurons can be set up to respond selectively to specific spatio-temporal spike patterns by optimization of their input weights. It is unknown, however, if existing synaptic plasticity mechanisms can achieve this temporal mode of neuronal coding and computation. Here it is shown that changes of synaptic efficacies which tend to balance excitatory and inhibitory synaptic inputs can make neurons sensitive to particular input spike patterns. Simulations demonstrate that a combination of Hebbian mechanisms, hetero-synaptic plasticity and synaptic scaling is sufficient for self-organizing sensitivity for spatio-temporal spike patterns that repeat in the input. In networks inclusion of hetero-synaptic plasticity leads to specialization and faithful representation of pattern sequences by a group of target neurons. Pattern detection is found to be robust against a range of distortions and noise. Furthermore, the resulting balance of excitatory and inhibitory inputs protects the memory for a specific pattern from being overwritten during ongoing learning when the pattern is not present. These results not only provide an explanation for experimental observations of balanced excitation and inhibition in cortex but also promote the plausibility of precise temporal coding in the brain.

scholarly journals Fast volumetric mapping of human brain slices

2020 ◽  
Author(s):  
Luca Pesce ◽  
Annunziatina Laurino ◽  
Vladislav Gavryusev ◽  
Giacomo Mazzamuto ◽  
Giuseppe Sancataldo ◽  
...  
Keyword(s):  
Human Brain ◽  
Brain Connectivity ◽  
Brain Slices ◽  
Light Sheet ◽  
Volumetric Imaging ◽  
Neuronal Markers ◽  
Light Sheet Microscopy ◽  
Inhibitory Population ◽  
Anatomical Information ◽  
The Brain

AbstractWe still lack a detailed map of the anatomical disposition of neurons in the human brain. A complete map would be an important step for deeply understanding the brain function, providing anatomical information useful to decipher the neuronal pattern in healthy and diseased conditions. Here, we present several important advances towards this goal, obtained by combining a new clearing method, advanced Light Sheet Microscopy and automated machinelearning based image analysis. We perform volumetric imaging of large sequentially stained human brain slices, labelled for two different neuronal markers NeuN and GAD67, discriminating the inhibitory population and reconstructing the brain connectivity.

scholarly journals Converting lateral scanning into axial focusing to speed up 3D microscopy

2020 ◽  
Author(s):  
Tonmoy Chakraborty ◽  
Bo-Jui Chang ◽  
Stephan Daetwyler ◽  
Etai Sapoznik ◽  
Bingying Chen ◽  
...  
Keyword(s):  
High Resolution ◽  
Spherical Aberration ◽  
Optical Design ◽  
Image Plane ◽  
Light Sheet ◽  
Volumetric Imaging ◽  
Light Sheet Microscopy ◽  
Scanning Rate ◽  
Order Of Magnitude ◽  
Axial Scanning

AbstractIn optical microscopy, the slow axial scanning rate of the objective or the sample has traditionally limited the speed of 3D volumetric imaging. Recently, by conjugating either a movable-mirror to the image plane or an electrotuneable lens (ETL) to the back-focal plane respectively, rapid axial scanning has been achieved. However, mechanical actuation of a mirror limits axial scanning rate (usually only 10-100 Hz for piezoelectric or voice coil based actuators), while ETLs introduce spherical and higher order aberrations, thereby preventing high-resolution imaging. Here, we introduce a novel optical design that can transform a lateral-scan motion into a spherical-aberration-free, high-resolution, rapid axial scan. Using a galvanometric mirror, we scan a laser beam laterally in a remote-focusing arm, which is then back-reflected from different heights of a mirror in image space. We characterize the optical performance of this remote focusing technique and use it to accelerate axially swept light-sheet microscopy (ASLM) by one order of magnitude, allowing the quantification of rapid vesicular dynamics in 3D.

scholarly journals Spatio-Temporal Hydrological Model Structure and Parametrization Analysis

2021 ◽  
Vol 9 (5) ◽  
pp. 467
Author(s):  
Mostafa Farrag ◽  
Gerald Corzo Perez ◽  
Dimitri Solomatine
Keyword(s):  
Hydrological Modeling ◽  
Model Building ◽  
Model Performance ◽  
Model Description ◽  
Generation Model ◽  
Model Structure ◽  
Runoff Generation ◽  
Spatial Sensitivity ◽  
Spatio Temporal ◽  
Set Up

Many grid-based spatial hydrological models suffer from the complexity of setting up a coherent spatial structure to calibrate such a complex, highly parameterized system. There are essential aspects of model-building to be taken into account: spatial resolution, the routing equation limitations, and calibration of spatial parameters, and their influence on modeling results, all are decisions that are often made without adequate analysis. In this research, an experimental analysis of grid discretization level, an analysis of processes integration, and the routing concepts are analyzed. The HBV-96 model is set up for each cell, and later on, cells are integrated into an interlinked modeling system (Hapi). The Jiboa River Basin in El Salvador is used as a case study. The first concept tested is the model structure temporal responses, which are highly linked to the runoff dynamics. By changing the runoff generation model description, we explore the responses to events. Two routing models are considered: Muskingum, which routes the runoff from each cell following the river network, and Maxbas, which routes the runoff directly to the outlet. The second concept is the spatial representation, where the model is built and tested for different spatial resolutions (500 m, 1 km, 2 km, and 4 km). The results show that the spatial sensitivity of the resolution is highly linked to the routing method, and it was found that routing sensitivity influenced the model performance more than the spatial discretization, and allowing for coarser discretization makes the model simpler and computationally faster. Slight performance improvement is gained by using different parameters’ values for each cell. It was found that the 2 km cell size corresponds to the least model error values. The proposed hydrological modeling codes have been published as open-source.

scholarly journals Spatio-temporal expectile regression models

2019 ◽  
Vol 20 (4) ◽  
pp. 386-409
Author(s):  
Elmar Spiegel ◽  
Thomas Kneib ◽  
Fabian Otto-Sobotka
Keyword(s):  
Tensor Product ◽  
Least Squares Regression ◽  
Expectile Regression ◽  
Specific Distribution ◽  
Weighted Means ◽  
Temporal Models ◽  
Error Terms ◽  
Spatio Temporal ◽  
Set Up ◽  
Main Effects

Spatio-temporal models are becoming increasingly popular in recent regression research. However, they usually rely on the assumption of a specific parametric distribution for the response and/or homoscedastic error terms. In this article, we propose to apply semiparametric expectile regression to model spatio-temporal effects beyond the mean. Besides the removal of the assumption of a specific distribution and homoscedasticity, with expectile regression the whole distribution of the response can be estimated. For the use of expectiles, we interpret them as weighted means and estimate them by established tools of (penalized) least squares regression. The spatio-temporal effect is set up as an interaction between time and space either based on trivariate tensor product P-splines or the tensor product of a Gaussian Markov random field and a univariate P-spline. Importantly, the model can easily be split up into main effects and interactions to facilitate interpretation. The method is presented along the analysis of spatio-temporal variation of temperatures in Germany from 1980 to 2014.

There are no A1 and A2 astrocytes in brain

2021 ◽  
Author(s):  
Shuang-qi Gao
Keyword(s):  
Endothelial Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Sorting ◽  
Reactive Astrocytes ◽  
Marker Genes ◽  
Set Up ◽  
The Brain

Abstract Objectives The subsets of astrocytes in the brain have not been fully elucidated. Using bulk RNA sequencing, reactive astrocytes were divided into A1 versus A2. However, using single-cell RNAseq (ScRNAseq), astrocytes were divided into over two subsets. Our aim was to set up the correspondence between the fluorescent-activated cell sorting (FACS)-bulk RNAseq and ScRNAseq data. Results We found that most of reactive astrocytes (RAs) marker genes were expressed in endothelial cells but not in astrocytes, suggesting those marker genes are not suitable for astrocytic activation. The absence of A1 and A2 astrocytes in the brain.

scholarly journals Regeneration, Plasticity, and Induced Molecular Programs in Adult Zebrafish Brain

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Mehmet Ilyas Cosacak ◽  
Christos Papadimitriou ◽  
Caghan Kizil
Keyword(s):  
Neural Plasticity ◽  
Molecular Mechanisms ◽  
Clinical Settings ◽  
Regenerative Capacity ◽  
Zebrafish Brain ◽  
Aquatic Vertebrates ◽  
Neural Stem Progenitor Cells ◽  
Set Up ◽  
Regenerative Therapies ◽  
The Brain

Regenerative capacity of the brain is a variable trait within animals. Aquatic vertebrates such as zebrafish have widespread ability to renew their brains upon damage, while mammals have—if not none—very limited overall regenerative competence. Underlying cause of such a disparity is not fully evident; however, one of the reasons could be activation of peculiar molecular programs, which might have specific roles after injury or damage, by the organisms that regenerate. If this hypothesis is correct, then there must be genes and pathways that (a) are expressed only after injury or damage in tissues, (b) are biologically and functionally relevant to restoration of neural tissue, and (c) are not detected in regenerating organisms. Presence of such programs might circumvent the initial detrimental effects of the damage and subsequently set up the stage for tissue redevelopment to take place by modulating the plasticity of the neural stem/progenitor cells. Additionally, if transferable, those “molecular mechanisms of regeneration” could open up new avenues for regenerative therapies of humans in clinical settings. This review focuses on the recent studies addressing injury/damage-induced molecular programs in zebrafish brain, underscoring the possibility of the presence of genes that could be used as biomarkers of neural plasticity and regeneration.

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