scholarly journals Post hoc Correction of Chromatic Aberrations in Large-Scale Volumetric Images in Confocal Microscopy

2021 ◽  
Vol 15 ◽  
Author(s):  
Marcus N. Leiwe ◽  
Satoshi Fujimoto ◽  
Takeshi Imai
Keyword(s):  
Confocal Microscopy ◽  
Large Scale ◽  
Chromatic Aberration ◽  
Multicolor Imaging ◽  
Volumetric Images ◽  
Chromatic Aberrations ◽  
Correction Program ◽  
Confocal Images ◽  
Post Hoc ◽  
The Brain

Over the last decade, tissue-clearing techniques have expanded the scale of volumetric fluorescence imaging of the brain, allowing for the comprehensive analysis of neuronal circuits at a millimeter scale. Multicolor imaging is particularly powerful for circuit tracing with fluorescence microscopy. However, multicolor imaging of large samples often suffers from chromatic aberration, where different excitation wavelengths of light have different focal points. In this study, we evaluated chromatic aberrations for representative objective lenses and a clearing agent with confocal microscopy and found that axial aberration is particularly problematic. Moreover, the axial chromatic aberrations were often depth-dependent. Therefore, we developed a program that is able to align depths for different fluorescence channels based on reference samples with fluorescent beads or data from guide stars within biological samples. We showed that this correction program can successfully correct chromatic aberrations found in confocal images of multicolor-labeled brain tissues. Our simple post hoc correction strategy is useful to obtain large-scale multicolor images of cleared tissues with minimal chromatic aberrations.

The Reduction of Chromatic Aberrations Due to Instrumental Instabilities

1971 ◽  
Vol 29 ◽  
pp. 14-15
Author(s):  
J. S. Lally ◽  
R. Evans
Keyword(s):  
Electron Microscope ◽  
High Voltage ◽  
Focal Length ◽  
Chromatic Aberration ◽  
Objective Lens ◽  
Usual Practice ◽  
Voltage Electron ◽  
Short Focal Length ◽  
Chromatic Aberrations ◽  
Electron Microscopes

One of the instrumental factors often limiting the resolution of the electron microscope is image defocussing due to changes in accelerating voltage or objective lens current. This factor is particularly important in high voltage electron microscopes both because of the higher voltages and lens currents required but also because of the inherently longer focal lengths, i.e. 6 mm in contrast to 1.5-2.2 mm for modern short focal length objectives.The usual practice in commercial electron microscopes is to design separately stabilized accelerating voltage and lens supplies. In this case chromatic aberration in the image is caused by the random and independent fluctuations of both the high voltage and objective lens current.

New Aspects in the Design of Electron Optical Magnification Systems

1972 ◽  
Vol 30 ◽  
pp. 606-607
Author(s):  
Willem H.J. Andersen
Keyword(s):  
Electron Microscope ◽  
Imaging System ◽  
Chromatic Aberration ◽  
Research Tool ◽  
Energy Losses ◽  
Objective Lens ◽  
Theoretical Limit ◽  
Optical Magnification ◽  
Chromatic Aberrations ◽  
High Degree

Electron microscope design, and particularly the design of the imaging system, has reached a high degree of perfection. Present objective lenses perform up to their theoretical limit, while the whole imaging system, consisting of three or four lenses, provides very wide ranges of magnification and diffraction camera length with virtually no distortion of the image. Evolution of the electron microscope in to a routine research tool in which objects of steadily increasing thickness are investigated, has made it necessary for the designer to pay special attention to the chromatic aberrations of the magnification system (as distinct from the chromatic aberration of the objective lens). These chromatic aberrations cause edge un-sharpness of the image due to electrons which have suffered energy losses in the object.There exist two kinds of chromatic aberration of the magnification system; the chromatic change of magnification, characterized by the coefficient Cm, and the chromatic change of rotation given by Cp.

Toward The Simultaneous Correction of Spherical and Chromatic Aberration in Electron Optics by Means of an Electrostatic Electron Mirror

1990 ◽  
Vol 48 (1) ◽  
pp. 206-207
Author(s):  
Gertrude. F. Rempfer
Keyword(s):  
Chromatic Aberration ◽  
Transverse Magnetic ◽  
Objective Lens ◽  
Ion Imaging ◽  
Corrected Image ◽  
Electric And Magnetic Fields ◽  
Chromatic Aberrations ◽  
Improved Performance ◽  
Electron Microscopes ◽  
Image Planes

Optimum performance in electron and ion imaging instruments, such as electron microscopes and probe-forming instruments, in most cases depends on a compromise either between imaging errors due to spherical and chromatic aberrations and the diffraction error or between the imaging errors and the current in the image. These compromises result in the use of very small angular apertures. Reducing the spherical and chromatic aberration coefficients would permit the use of larger apertures with resulting improved performance, granted that other problems such as incorrect operation of the instrument or spurious disturbances do not interfere. One approach to correcting aberrations which has been investigated extensively is through the use of multipole electric and magnetic fields. Another approach involves the use of foil windows. However, a practical system for correcting spherical and chromatic aberration is not yet available.Our approach to correction of spherical and chromatic aberration makes use of an electrostatic electron mirror. Early studies of the properties of electron mirrors were done by Recknagel. More recently my colleagues and I have studied the properties of the hyperbolic electron mirror as a function of the ratio of accelerating voltage to mirror voltage. The spherical and chromatic aberration coefficients of the mirror are of opposite sign (overcorrected) from those of electron lenses (undercorrected). This important property invites one to find a way to incorporate a correcting mirror in an electron microscope. Unfortunately, the parts of the beam heading toward and away from the mirror must be separated. A transverse magnetic field can separate the beams, but in general the deflection aberrations degrade the image. The key to avoiding the detrimental effects of deflection aberrations is to have deflections take place at image planes. Our separating system is shown in Fig. 1. Deflections take place at the separating magnet and also at two additional magnetic deflectors. The uncorrected magnified image formed by the objective lens is focused in the first deflector, and relay lenses transfer the image to the separating magnet. The interface lens and the hyperbolic mirror acting in zoom fashion return the corrected image to the separating magnet, and the second set of relay lenses transfers the image to the final deflector, where the beam is deflected onto the projection axis.

Implantable neural interfaces

2018 ◽  
Author(s):  
Stefano Vassanelli
Keyword(s):  
Brain Function ◽  
Large Scale ◽  
Ionic Channels ◽  
Patch Clamp Technique ◽  
Advantages And Disadvantages ◽  
Optogenetic Stimulation ◽  
Physical Interfaces ◽  
The Brain

Establishing direct communication with the brain through physical interfaces is a fundamental strategy to investigate brain function. Starting with the patch-clamp technique in the seventies, neuroscience has moved from detailed characterization of ionic channels to the analysis of single neurons and, more recently, microcircuits in brain neuronal networks. Development of new biohybrid probes with electrodes for recording and stimulating neurons in the living animal is a natural consequence of this trend. The recent introduction of optogenetic stimulation and advanced high-resolution large-scale electrical recording approaches demonstrates this need. Brain implants for real-time neurophysiology are also opening new avenues for neuroprosthetics to restore brain function after injury or in neurological disorders. This chapter provides an overview on existing and emergent neurophysiology technologies with particular focus on those intended to interface neuronal microcircuits in vivo. Chemical, electrical, and optogenetic-based interfaces are presented, with an analysis of advantages and disadvantages of the different technical approaches.

What Has Direct Cortical and Subcortical Electrostimulation Taught Us about Neurolinguistics?

2019 ◽  
pp. 185-211
Author(s):  
Hugues Duffau
Keyword(s):  
White Matter ◽  
Large Scale ◽  
Functional Neuroimaging ◽  
Great Accuracy ◽  
Subcortical White Matter ◽  
Cerebral Lesions ◽  
Physiological Basis ◽  
Postoperative Mri ◽  
The Brain

Investigating the neural and physiological basis of language is one of the most important challenges in neurosciences. Direct electrical stimulation (DES), usually performed in awake patients during surgery for cerebral lesions, is a reliable tool for detecting both cortical and subcortical (white matter and deep grey nuclei) regions crucial for cognitive functions, especially language. DES transiently interacts locally with a small cortical or axonal site, but also nonlocally, as the focal perturbation will disrupt the entire subnetwork sustaining a given function. Thus, in contrast to functional neuroimaging, DES represents a unique opportunity to identify with great accuracy and reproducibility, in vivo in humans, the structures that are actually indispensable to the function, by inducing a transient virtual lesion based on the inhibition of a subcircuit lasting a few seconds. Currently, this is the sole technique that is able to directly investigate the functional role of white matter tracts in humans. Thus, combining transient disturbances elicited by DES with the anatomical data provided by pre- and postoperative MRI enables to achieve reliable anatomo-functional correlations, supporting a network organization of the brain, and leading to the reappraisal of models of language representation. Finally, combining serial peri-operative functional neuroimaging and online intraoperative DES allows the study of mechanisms underlying neuroplasticity. This chapter critically reviews the basic principles of DES, its advantages and limitations, and what DES can reveal about the neural foundations of language, that is, the large-scale distribution of language areas in the brain, their connectivity, and their ability to reorganize.

scholarly journals Content-Based Estimation of Brain MRI Tilt in Three Orthogonal Directions

2021 ◽  
Author(s):  
Pooja Prabhu ◽  
A. K. Karunakar ◽  
Sanjib Sinha ◽  
N. Mariyappa ◽  
G. K. Bhargava ◽  
...  
Keyword(s):  
Large Scale ◽  
Brain Mri ◽  
Similarity Measures ◽  
Principal Component ◽  
Brain Anatomy ◽  
Morphological Operations ◽  
Mr Images ◽  
Tilt Correction ◽  
Brain Mr Images ◽  
The Brain

AbstractIn a general scenario, the brain images acquired from magnetic resonance imaging (MRI) may experience tilt, distorting brain MR images. The tilt experienced by the brain MR images may result in misalignment during image registration for medical applications. Manually correcting (or estimating) the tilt on a large scale is time-consuming, expensive, and needs brain anatomy expertise. Thus, there is a need for an automatic way of performing tilt correction in three orthogonal directions (X, Y, Z). The proposed work aims to correct the tilt automatically by measuring the pitch angle, yaw angle, and roll angle in X-axis, Z-axis, and Y-axis, respectively. For correction of the tilt around the Z-axis (pointing to the superior direction), image processing techniques, principal component analysis, and similarity measures are used. Also, for correction of the tilt around the X-axis (pointing to the right direction), morphological operations, and tilt correction around the Y-axis (pointing to the anterior direction), orthogonal regression is used. The proposed approach was applied to adjust the tilt observed in the T1- and T2-weighted MR images. The simulation study with the proposed algorithm yielded an error of 0.40 ± 0.09°, and it outperformed the other existing studies. The tilt angle (in degrees) obtained is ranged from 6.2 ± 3.94, 2.35 ± 2.61, and 5 ± 4.36 in X-, Z-, and Y-directions, respectively, by using the proposed algorithm. The proposed work corrects the tilt more accurately and robustly when compared with existing studies.

A new method to predict anomaly in brain network based on graph deep learning

2020 ◽  
Vol 31 (6) ◽  
pp. 681-689
Author(s):  
Jalal Mirakhorli ◽  
Hamidreza Amindavar ◽  
Mojgan Mirakhorli
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Brain Plasticity ◽  
Brain Network ◽  
High Order ◽  
Brain Diseases ◽  
Simultaneous Occurrence ◽  
Generative Adversarial Network ◽  
The Brain ◽  
Brain Connections

AbstractFunctional magnetic resonance imaging a neuroimaging technique which is used in brain disorders and dysfunction studies, has been improved in recent years by mapping the topology of the brain connections, named connectopic mapping. Based on the fact that healthy and unhealthy brain regions and functions differ slightly, studying the complex topology of the functional and structural networks in the human brain is too complicated considering the growth of evaluation measures. One of the applications of irregular graph deep learning is to analyze the human cognitive functions related to the gene expression and related distributed spatial patterns. Since a variety of brain solutions can be dynamically held in the neuronal networks of the brain with different activity patterns and functional connectivity, both node-centric and graph-centric tasks are involved in this application. In this study, we used an individual generative model and high order graph analysis for the region of interest recognition areas of the brain with abnormal connection during performing certain tasks and resting-state or decompose irregular observations. Accordingly, a high order framework of Variational Graph Autoencoder with a Gaussian distributer was proposed in the paper to analyze the functional data in brain imaging studies in which Generative Adversarial Network is employed for optimizing the latent space in the process of learning strong non-rigid graphs among large scale data. Furthermore, the possible modes of correlations were distinguished in abnormal brain connections. Our goal was to find the degree of correlation between the affected regions and their simultaneous occurrence over time. We can take advantage of this to diagnose brain diseases or show the ability of the nervous system to modify brain topology at all angles and brain plasticity according to input stimuli. In this study, we particularly focused on Alzheimer’s disease.

scholarly journals Engineered glycomaterial implants orchestrate large-scale functional repair of brain tissue chronically after severe traumatic brain injury

2021 ◽  
Vol 7 (10) ◽  
pp. eabe0207
Author(s):  
Charles-Francois V. Latchoumane ◽  
Martha I. Betancur ◽  
Gregory A. Simchick ◽  
Min Kyoung Sun ◽  
Rameen Forghani ◽  
...  
Keyword(s):  
Traumatic Brain Injury ◽  
Brain Injury ◽  
Severe Traumatic Brain Injury ◽  
Large Scale ◽  
Growth Factor Signaling ◽  
Neuronal Circuit ◽  
Reach To Grasp ◽  
Function Recovery ◽  
Cellular Repair ◽  
The Brain

Severe traumatic brain injury (sTBI) survivors experience permanent functional disabilities due to significant volume loss and the brain’s poor capacity to regenerate. Chondroitin sulfate glycosaminoglycans (CS-GAGs) are key regulators of growth factor signaling and neural stem cell homeostasis in the brain. However, the efficacy of engineered CS (eCS) matrices in mediating structural and functional recovery chronically after sTBI has not been investigated. We report that neurotrophic factor functionalized acellular eCS matrices implanted into the rat M1 region acutely after sTBI significantly enhanced cellular repair and gross motor function recovery when compared to controls 20 weeks after sTBI. Animals subjected to M2 region injuries followed by eCS matrix implantations demonstrated the significant recovery of “reach-to-grasp” function. This was attributed to enhanced volumetric vascularization, activity-regulated cytoskeleton (Arc) protein expression, and perilesional sensorimotor connectivity. These findings indicate that eCS matrices implanted acutely after sTBI can support complex cellular, vascular, and neuronal circuit repair chronically after sTBI.

Brain stem – from general view to computational model based on switchboard rules of operation

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Włodzisław Duch ◽  
Dariusz Mikołajewski
Keyword(s):  
Brain Stem ◽  
Large Scale ◽  
Ionic Channels ◽  
General View ◽  
The Central Nervous System ◽  
Network States ◽  
Large Scale Simulations ◽  
Influence Of Noise ◽  
The Brain ◽  
Sufficient Precision

Abstract Despite great progress in understanding the functions and structures of the central nervous system (CNS) the brain stem remains one of the least understood systems. We know that the brain stem acts as a decision station preparing the organism to act in a specific way, but such functions are rather difficult to model with sufficient precision to replicate experimental data due to the scarcity of data and complexity of large-scale simulations of brain stem structures. The approach proposed in this article retains some ideas of previous models, and provides more precise computational realization that enables qualitative interpretation of the functions played by different network states. Simulations are aimed primarily at the investigation of general switching mechanisms which may be executed in brain stem neural networks, as far as studying how the aforementioned mechanisms depend on basic neural network features: basic ionic channels, accommodation, and the influence of noise.

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