scholarly journals Histology-based average template of the marmoset cortex with probabilistic localization of cytoarchitectural areas

2020 ◽  
Author(s):  
Piotr Majka ◽  
Sylwia Bednarek ◽  
Jonathan M. Chan ◽  
Natalia Jermakow ◽  
Cirong Liu ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Quantitative Information ◽  
List Type ◽  
Spatial Transformations ◽  
Common Reference ◽  
Probabilistic Mapping ◽  
Reference Space ◽  
Magnetic Resonance Imaging Mri ◽  
The Individual ◽  
Brain Atlases

AbstractThe rapid adoption of marmosets in neuroscience has created a demand for three dimensional (3D) atlases of the brain of this species to facilitate data integration in a common reference space. We report on a new open access template of the marmoset cortex (the Nencki–Monash, or NM template), representing a morphological average of 20 brains of young adult individuals, obtained by 3D reconstructions generated from Nissl-stained serial sections. The method used to generate the template takes into account morphological features of the individual brains, as well as the borders of clearly defined cytoarchitectural areas. This has resulted in a resource which allows direct estimates of the most likely coordinates of each cortical area, as well as quantification of the margins of error involved in assigning voxels to areas, and preserves quantitative information about the laminar structure of the cortex. We provide spatial transformations between the NM and other available marmoset brain templates, thus enabling integration with magnetic resonance imaging (MRI) and tracer-based connectivity data. The NM template combines some of the main advantages of histology-based atlases (e.g. information about the cytoarchitectural structure) with features more commonly associated with MRI-based templates (isotropic nature of the dataset, and probabilistic analyses). The underlying workflow may be found useful in the future development of brain atlases that incorporate information about the variability of areas in species for which it may be impractical to ensure homogeneity of the sample in terms of age, sex and genetic background.Graphical abstractHighlightsA 3D template of the marmoset cortex representing the average of 20 individuals.The template is based on Nissl stain and preserves information about cortical layers.Probabilistic mapping of areas, cortical thickness, and layer intensity profiles.Includes spatial transformations to other marmoset brain atlases.AbbreviationsFor a list of areas and their abbreviations see Table S2.

scholarly journals Pore structure 3-D imaging by synchrotron micro-tomography of graupel grains

2010 ◽  
Vol 3 (6) ◽  
pp. 4761-4789
Author(s):  
F. Enzmann ◽  
M. M. Miedaner ◽  
M. Kersten ◽  
N. von Blohn ◽  
S. K. Mitra ◽  
...  
Keyword(s):  
Pore Structure ◽  
Three Dimensional ◽  
Liquid Nitrogen Temperature ◽  
Growth Conditions ◽  
Quantitative Information ◽  
Original Structure ◽  
Bubble Structure ◽  
Micro Tomography ◽  
The Individual

Abstract. Three dimensional air bubble structure including size distribution, concentration and spatial distribution are important clues in identifying the growth regime of graupel and hailstone. For imaging of the bubble structure, a cryo-stage was developed to adapt to the standard setup of the SLS X04SA tomography beamline (actually replaced by the TOMCAT beamline) at the Swiss Light Source synchrotron facility to the requirements of ice particle micro-tomography. The cryo-stage setup provides for the first time 3-D-data on the individual inner pore shape delineation down to μm spatial (voxel) resolution of sub-mm small naturally as well as wind tunnel rimed graupel particles. Special care must be taken for maintaining a cooling chain between sampling and measurement. It must be kept at liquid nitrogen temperature (77 K) until measurement of the original structure at the μm spatial scale. However, even at that temperature there is no chance to preserve any ice bubble structure at sub-μm spatial resolution due to the Kelvin effect. In natural graupel grains, Y-shaped morphology of air-filled pores was found. This morphology transformed into smaller and rounded voids well-known from literature when the ice particle was annealed for as short as half an hour at 265 K and must, therefore, be regarded as artificial rather than representing the in situ pore structure. With the new synchrotron tomography approach, quantitative information on the in situ pore structure statistics within individual samples representative for a known or, thus, deduced growth mode or history can be derived, in particular if combined with airplane sampling in the troposphere at in situ growth conditions.

scholarly journals An improved multiple-frequency method for measuring in situ target strengths

2005 ◽  
Vol 62 (8) ◽  
pp. 1636-1646 ◽  
Author(s):  
Stéphane G. Conti ◽  
David A. Demer ◽  
Michael A. Soule ◽  
Jean H.E. Conti
Keyword(s):  
Reference System ◽  
Three Dimensional ◽  
Previous Method ◽  
Target Strength ◽  
System Transformation ◽  
Multiple Frequency ◽  
Frequency Method ◽  
Multiple Targets ◽  
Common Reference ◽  
The Individual

Abstract Refinements have been made to the multiple-frequency method for rejecting overlapping echoes when making target-strength measurements with split-beam echosounders described in Demer et al. (1999). The technique requires that echoes, simultaneously detected with two or more adjacent split-beam transducers of different frequencies, pass multiple-target rejection algorithms at each frequency, and characterize virtually identical three-dimensional target coordinates. To translate the coordinates into a common reference system for comparison, the previous method only considered relative transducer positions and assumed that the beam axes of the transducers were parallel. The method was improved by first, optimizing the accuracy and precision of the range and angular measurements of the individual frequency detections; and second, precisely determining acoustically the relative positions and angular orientations of the transducers, thus completely describing the reference-system transformation(s). Algorithms are presented for accurately and precisely estimating the transformation parameters, and efficiently rejecting multiple targets while retaining measurements of most single targets. These improvements are demonstrated through simulations, controlled test-tank experiments, and shipboard measurements using 38- and 120-kHz split-beam transducers. The results indicate that the improved multiple-frequency TS method can reject more than 97% of multiple targets, while allowing 99% of the resolvable single targets to be measured.

scholarly journals Visualizing anatomically registered data with Brainrender

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Federico Claudi ◽  
Adam L Tyson ◽  
Luigi Petrucco ◽  
Troy W Margrie ◽  
Ruben Portugues ◽  
...  
Keyword(s):  
Imaging Techniques ◽  
Three Dimensional ◽  
Multidimensional Data ◽  
Data Types ◽  
Model Species ◽  
Common Reference ◽  
Multidimensional Datasets ◽  
Interactive Data ◽  
Python Package ◽  
Brain Atlases

Three-dimensional (3D) digital brain atlases and high-throughput brain wide imaging techniques generate large multidimensional datasets that can be registered to a common reference frame. Generating insights from such datasets depends critically on visualization and interactive data exploration, but this a challenging task. Currently available software is dedicated to single atlases, model species or data types, and generating 3D renderings that merge anatomically registered data from diverse sources requires extensive development and programming skills. Here, we present brainrender: an open-source Python package for interactive visualization of multidimensional datasets registered to brain atlases. Brainrender facilitates the creation of complex renderings with different data types in the same visualization and enables seamless use of different atlas sources. High-quality visualizations can be used interactively and exported as high-resolution figures and animated videos. By facilitating the visualization of anatomically registered data, brainrender should accelerate the analysis, interpretation, and dissemination of brain-wide multidimensional data.

scholarly journals Brainrender: a python-based software for visualizing anatomically registered data

2020 ◽  
Author(s):  
Federico Claudi ◽  
Adam L. Tyson ◽  
Luigi Petrucco ◽  
Troy W. Margrie ◽  
Ruben Portugues ◽  
...  
Keyword(s):  
High Resolution ◽  
Imaging Techniques ◽  
Three Dimensional ◽  
Multidimensional Data ◽  
Data Types ◽  
Common Reference ◽  
Multidimensional Datasets ◽  
Code Base ◽  
Different Sources ◽  
Brain Atlases

The recent development of high-resolution three-dimensional (3D) digital brain atlases and high-throughput brain wide imaging techniques has fueled the generation of large datasets that can be registered to a common reference frame. This registration facilitates integrating data from different sources and resolutions to assemble rich multidimensional datasets. Generating insights from these new types of datasets depends critically on the ability to easily visualize and explore the data in an interactive manner. This is, however, a challenging task. Currently available software is dedicated to single atlases, model species or data types, and generating 3D renderings that merge anatomically registered data from diverse sources requires extensive development and programming skills. To address this challenge, we have developed brainrender: a generic, open-source Python package for simultaneous and interactive visualization of multidimensional datasets registered to brain atlases. Brainrender has been designed to facilitate the creation of complex custom renderings and can be used programmatically or through a graphical user interface. It can easily render different data types in the same visualization, including user-generated data, and enables seamless use of different brain atlases using the same code base. In addition, brainrender generates high-quality visualizations that can be used interactively and exported as high-resolution figures and animated videos. By facilitating the visualization of anatomically registered data, brainrender should accelerate the analysis, interpretation, and dissemination of brain-wide multidimensional data.

Semi-automated methods for 3-D reconstruction of macromolecular complexes

1995 ◽  
Vol 53 ◽  
pp. 42-43
Author(s):  
B. Carragher ◽  
M. Whittaker
Keyword(s):  
Three Dimensional ◽  
Time Saving ◽  
Macromolecular Complexes ◽  
Symmetry Properties ◽  
Dimensional Reconstruction ◽  
Experienced Operator ◽  
Projection Images ◽  
The Individual ◽  
Natural Symmetry

Techniques for three-dimensional reconstruction of macromolecular complexes from electron micrographs have been successfully used for many years. These include methods which take advantage of the natural symmetry properties of the structure (for example helical or icosahedral) as well as those that use single axis or other tilting geometries to reconstruct from a set of projection images. These techniques have traditionally relied on a very experienced operator to manually perform the often numerous and time consuming steps required to obtain the final reconstruction. While the guidance and oversight of an experienced and critical operator will always be an essential component of these techniques, recent advances in computer technology, microprocessor controlled microscopes and the availability of high quality CCD cameras have provided the means to automate many of the individual steps.During the acquisition of data automation provides benefits not only in terms of convenience and time saving but also in circumstances where manual procedures limit the quality of the final reconstruction.

Diffraction contrast of dislocations in icosahedral quasicrystals

1990 ◽  
Vol 48 (4) ◽  
pp. 454-455
Author(s):  
K. Urban ◽  
Z. Zhang ◽  
M. Wollgarten ◽  
D. Gratias
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Complete Characterization ◽  
Extinction Condition ◽  
Burgers Vector ◽  
Diffraction Contrast ◽  
Lattice Geometry ◽  
Reference Space ◽  
Icosahedral Quasicrystals ◽  
The One

Recently dislocations have been observed by electron microscopy in the icosahedral quasicrystalline (IQ) phase of Al65Cu20Fe15. These dislocations exhibit diffraction contrast similar to that known for dislocations in conventional crystals. The contrast becomes extinct for certain diffraction vectors g. In the following the basis of electron diffraction contrast of dislocations in the IQ phase is described. Taking account of the six-dimensional nature of the Burgers vector a “strong” and a “weak” extinction condition are found.Dislocations in quasicrystals canot be described on the basis of simple shear or insertion of a lattice plane only. In order to achieve a complete characterization of these dislocations it is advantageous to make use of the one to one correspondence of the lattice geometry in our three-dimensional space (R3) and that in the six-dimensional reference space (R6) where full periodicity is recovered . Therefore the contrast extinction condition has to be written as gpbp + gobo = 0 (1). The diffraction vector g and the Burgers vector b decompose into two vectors gp, bp and go, bo in, respectively, the physical and the orthogonal three-dimensional sub-spaces of R6.

Phonetic iconicity in the evaluative morphology of a sample of Indo-European, Niger-Congo and Austronesian languages

2010 ◽  
Vol 3 (2) ◽  
pp. 156-180 ◽  
Author(s):  
Renáta Gregová ◽  
Lívia Körtvélyessy ◽  
Július Zimmermann
Keyword(s):  
Three Dimensional ◽  
Sound Symbolism ◽  
Three Dimensional Model ◽  
Austronesian Languages ◽  
Place Of Articulation ◽  
European Languages ◽  
Phonetic Symbolism ◽  
The Individual ◽  
Core Vocabulary

Universals Archive (Universal #1926) indicates a universal tendency for sound symbolism in reference to the expression of diminutives and augmentatives. The research ( Štekauer et al. 2009 ) carried out on European languages has not proved the tendency at all. Therefore, our research was extended to cover three language families – Indo-European, Niger-Congo and Austronesian. A three-step analysis examining different aspects of phonetic symbolism was carried out on a core vocabulary of 35 lexical items. A research sample was selected out of 60 languages. The evaluative markers were analyzed according to both phonetic classification of vowels and consonants and Ultan's and Niewenhuis' conclusions on the dominance of palatal and post-alveolar consonants in diminutive markers. Finally, the data obtained in our sample languages was evaluated by means of a three-dimensional model illustrating the place of articulation of the individual segments.

Computed Tomography and Magnetic Resonance Imaging-aided Diagnosis of Primary Essential Cutis Verticis Gyrata: A Case Report with 5-year Follow-up and Review of the Literature

2019 ◽  
Vol 15 (9) ◽  
pp. 906-910
Author(s):  
Hongzhang Zhu ◽  
Shi-Ting Feng ◽  
Xingqi Zhang ◽  
Zunfu Ke ◽  
Ruixi Zeng ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
Magnetic Resonance ◽  
Three Dimensional ◽  
Stable Condition ◽  
Resonance Imaging ◽  
Mri Findings ◽  
Cutis Verticis Gyrata ◽  
Essential Form ◽  
History Of ◽  
Magnetic Resonance Imaging Mri

Background: Cutis Verticis Gyrata (CVG) is a rare skin disease caused by overgrowth of the scalp, presenting as cerebriform folds and wrinkles. CVG can be classified into two forms: primary (essential and non-essential) and secondary. The primary non-essential form is often associated with neurological and ophthalmological abnormalities, while the primary essential form occurs without associated comorbidities. Discussion: We report on a rare case of primary essential CVG with a 4-year history of normal-colored scalp skin mass in the parietal-occipital region without symptom in a 34-year-old male patient, retrospectively summarizing his pathological and Computer Tomography (CT) and magnetic resonance imaging (MRI) findings. The major clinical observations on the CT and MR sectional images include a thickened dermis and excessive growth of the scalp, forming the characteristic scalp folds. With the help of CT and MRI Three-dimensional (3D) reconstruction techniques, the characteristic skin changes could be displayed intuitively, providing more evidence for a diagnosis of CVG. At the 5-year followup, there were no obvious changes in the lesion. Conclusion: Based on our observations, we propose that not all patients with primary essential CVG need surgical intervention, and continuous clinical observation should be an appropriate therapy for those in stable condition.

scholarly journals Towards Tracking of Deep Brain Stimulation Electrodes Using an Integrated Magnetometer

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2670
Author(s):  
Thomas Quirin ◽  
Corentin Féry ◽  
Dorian Vogel ◽  
Céline Vergne ◽  
Mathieu Sarracanie ◽  
...  
Keyword(s):  
Deep Brain Stimulation ◽  
Brain Stimulation ◽  
Mean Absolute Error ◽  
Tracking System ◽  
Three Dimensional ◽  
Absolute Error ◽  
Magnetic Tracking ◽  
Magnetic Camera ◽  
Magnetic Resonance Imaging Mri ◽  
Deep Brain

This paper presents a tracking system using magnetometers, possibly integrable in a deep brain stimulation (DBS) electrode. DBS is a treatment for movement disorders where the position of the implant is of prime importance. Positioning challenges during the surgery could be addressed thanks to a magnetic tracking. The system proposed in this paper, complementary to existing procedures, has been designed to bridge preoperative clinical imaging with DBS surgery, allowing the surgeon to increase his/her control on the implantation trajectory. Here the magnetic source required for tracking consists of three coils, and is experimentally mapped. This mapping has been performed with an in-house three-dimensional magnetic camera. The system demonstrates how magnetometers integrated directly at the tip of a DBS electrode, might improve treatment by monitoring the position during and after the surgery. The three-dimensional operation without line of sight has been demonstrated using a reference obtained with magnetic resonance imaging (MRI) of a simplified brain model. We observed experimentally a mean absolute error of 1.35 mm and an Euclidean error of 3.07 mm. Several areas of improvement to target errors below 1 mm are also discussed.

scholarly journals A detailed analysis of anatomical plausibility of crossed and uncrossed streamline rendition of the dentato-rubro-thalamic tract (DRT(T)) in a commercial stereotactic planning system

2021 ◽  
Author(s):  
Volker A. Coenen ◽  
Bastian E. Sajonz ◽  
Peter C. Reinacher ◽  
Christoph P. Kaller ◽  
Horst Urbach ◽  
...  
Keyword(s):  
Surgical Planning ◽  
Ground Truth ◽  
Planning System ◽  
Single Subject ◽  
Fiber Structure ◽  
Native Space ◽  
Volume Of Interest ◽  
Mri Scans ◽  
Magnetic Resonance Imaging Mri ◽  
The Individual

Abstract Background An increasing number of neurosurgeons use display of the dentato-rubro-thalamic tract (DRT) based on diffusion weighted imaging (dMRI) as basis for their routine planning of stimulation or lesioning approaches in stereotactic tremor surgery. An evaluation of the anatomical validity of the display of the DRT with respect to modern stereotactic planning systems and across different tracking environments has not been performed. Methods Distinct dMRI and anatomical magnetic resonance imaging (MRI) data of high and low quality from 9 subjects were used. Six subjects had repeated MRI scans and therefore entered the analysis twice. Standardized DICOM structure templates for volume of interest definition were applied in native space for all investigations. For tracking BrainLab Elements (BrainLab, Munich, Germany), two tensor deterministic tracking (FT2), MRtrix IFOD2 (https://www.mrtrix.org), and a global tracking (GT) approach were used to compare the display of the uncrossed (DRTu) and crossed (DRTx) fiber structure after transformation into MNI space. The resulting streamlines were investigated for congruence, reproducibility, anatomical validity, and penetration of anatomical way point structures. Results In general, the DRTu can be depicted with good quality (as judged by waypoints). FT2 (surgical) and GT (neuroscientific) show high congruence. While GT shows partly reproducible results for DRTx, the crossed pathway cannot be reliably reconstructed with the other (iFOD2 and FT2) algorithms. Conclusion Since a direct anatomical comparison is difficult in the individual subjects, we chose a comparison with two research tracking environments as the best possible “ground truth.” FT2 is useful especially because of its manual editing possibilities of cutting erroneous fibers on the single subject level. An uncertainty of 2 mm as mean displacement of DRTu is expectable and should be respected when using this approach for surgical planning. Tractographic renditions of the DRTx on the single subject level seem to be still illusive.

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