scholarly journals High-resolution mapping and digital atlas of subcortical regions in the macaque monkey based on matched MAP-MRI and histology

2021 ◽  
Author(s):  
Kadharbatcha S Saleem ◽  
Alexandru V Avram ◽  
Daniel Glen ◽  
Cecil Chern-Chyi Yen ◽  
Frank Q Ye ◽  
...  
Keyword(s):  
High Resolution ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Brain Structures ◽  
Macaque Monkey ◽  
Three Dimensions ◽  
Brain Atlas ◽  
Fiber Tracts ◽  
Subcortical Regions ◽  
Deep Brain

Subcortical nuclei and other deep brain structures are known to play an important role in the regulation of the central and peripheral nervous systems. It can be difficult to identify and delineate many of these nuclei and their finer subdivisions in conventional MRI due to their small size, buried location, and often subtle contrast compared to neighboring tissue. To address this problem, we applied a multi-modal approach in ex vivo non-human primate (NHP) brain that includes high-resolution mean apparent propagator (MAP)-MRI and five different histological stains imaged with high-resolution microscopy in the brain of the same subject. By registering these high-dimensional MRI data to high-resolution histology data, we can map the location, boundaries, subdivisions, and micro-architectural features of subcortical gray matter regions in the macaque monkey brain. At high spatial resolution, diffusion MRI in general, and MAP-MRI in particular, can distinguish a large number of deep brain structures, including the larger and smaller white matter fiber tracts as well as architectonic features within various nuclei. Correlation with histology from the same brain enables a thorough validation of the structures identified with MAP-MRI. Moreover, anatomical details that are evident in images of MAP-MRI parameters are not visible in conventional T1-weighted images. We also derived subcortical template SC21 from segmented MRI slices in three-dimensions and registered this volume to a previously published anatomical template with cortical parcellation (Reveley et al., 2017; Saleem and Logothetis, 2012), thereby integrating the 3D segmentation of both cortical and subcortical regions into the same volume. This newly updated three-dimensional D99 digital brain atlas (V2.0) is intended for use as a reference standard for macaque neuroanatomical, functional, and connectional imaging studies, involving both cortical and subcortical targets. The SC21 and D99 digital templates are available as volumes and surfaces in standard NIFTI and GIFTI formats.

Confocal fluorescence microscopy with the tandem scanning light microscope

1989 ◽  
Vol 94 (4) ◽  
pp. 617-624
Author(s):  
S.J. Wright ◽  
J.S. Walker ◽  
H. Schatten ◽  
C. Simerly ◽  
J.J. McCarthy ◽  
...  
Keyword(s):  
High Resolution ◽  
Fluorescence Microscopy ◽  
Light Microscope ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Complex Structures ◽  
Charge Coupled Device ◽  
Confocal Fluorescence ◽  
Cooled Ccd ◽  
Cellular Components

Applications of the tandem scanning confocal microscope (TSM) to fluorescence microscopy and its ability to resolve fluorescent biological structures are described. The TSM, in conjunction with a cooled charge-coupled device (cooled CCD) and conventional epifluorescence light source and filter sets, provided high-resolution, confocal data, so that different fluorescent cellular components were distinguished in three dimensions within the same cell. One of the unique features of the TSM is the ability to image fluorochromes excited by ultraviolet light (e.g. Hoechst, DAPI) in addition to fluorescein and rhodamine. Since the illumination is dim, photobleaching is insignificant and prolonged viewing of living specimens is possible. Series of optical sections taken in the Z-axis with the TSM were reproduced as stereo images and three-dimensional reconstructions. These data show that the TSM is potentially a powerful tool in fluorescence microscopy for determining three-dimensional relationships of complex structures within cells labeled with multiple fluorochromes.

Three-dimensional reconstruction of metabolic data from quantitative autoradiography of rat brain

1984 ◽  
Vol 247 (3) ◽  
pp. E412-E419 ◽  
Author(s):  
L. S. Hibbard ◽  
R. A. Hawkins
Keyword(s):  
High Speed ◽  
Three Dimensional ◽  
Image Data ◽  
Brain Structures ◽  
Three Dimensions ◽  
Quantitative Autoradiography ◽  
Alignment Algorithm ◽  
Computer Methods ◽  
Mathematical Properties ◽  
Dimensional Reconstruction

Quantitative autoradiography is a powerful method for studying brain function by the determination of blood flow, glucose utilization, or transport of essential nutrients. Autoradiographic images contain vast amounts of potentially useful information, but conventional analyses can practically sample the data at only a small number of points arbitrarily chosen by the experimenter to represent discrete brain structures. To use image data more fully, computer methods for its acquisition, storage, quantitative analysis, and display are required. We have developed a system of computer programs that performs these tasks and has the following features: 1) editing and analysis of single images using interactive graphics, 2) an automatic image alignment algorithm that places images in register with one another using only the mathematical properties of the images themselves, 3) the calculation of mean images from equivalent images in different experimental serial image sets, 4) the calculation of difference images (e.g., experiment-minus-control) with the option to display only differences estimated to be statistically significant, and 5) the display of serial image metabolic maps reconstructed in three dimensions using a high-speed computer graphics system.

SEM Stop-Frame, Color, 3D Animation for Motion Pictures

1998 ◽  
Vol 4 (S2) ◽  
pp. 16-17
Author(s):  
David Scharf ◽  
Jacob Wilbrink ◽  
John A. Hunt
Keyword(s):  
High Resolution ◽  
Three Dimensional ◽  
Three Dimensions ◽  
3D Animation ◽  
Special Effects ◽  
Projection Screen ◽  
Traditional Format ◽  
Stereo Motion ◽  
Large Projection ◽  
Animation System

A stop-frame animation system has been developed for producing high-resolution, color and stereo motion picture animation sequences. The first of these sequences can be seen in the recently released IMAX 3D movies, “Four Million House Guests” a.k.a. “The Hidden Dimension”. IMAX movies have long been known for their breathtaking special effects that seem incredibly realistic because of the large projection screen (about 7 stories high) which is close to the entire audience, high resolution, and powerful audio effects. IMAX 3D is an extention to the traditional format that allows the audience to see three dimensional special effects with the aid of electronically shuttered viewing glasses. IMAX movies are an ideal medium to demonstrate the high resolution digital images that are possible with the SEM.The goal of the SEM movie project was to produce movie sequences where viewers feels like they are flying smoothly through micro-space past microscopic creatures and objects in three dimensions and in color.

scholarly journals Bathymetry of Northwest Greenland Using “Ocean Melting Greenland” (OMG) High-Resolution Airborne Gravity and Other Data

2019 ◽  
Vol 11 (2) ◽  
pp. 131 ◽  
Author(s):  
Lu An ◽  
Eric Rignot ◽  
Romain Millan ◽  
Kirsty Tinto ◽  
Josh Willis
Keyword(s):  
High Resolution ◽  
Continental Shelf ◽  
Gravity Data ◽  
Three Dimensional ◽  
Ice Sheet ◽  
Greenland Ice Sheet ◽  
Three Dimensions ◽  
Airborne Gravity ◽  
Lack Of Information ◽  
Sea Bed

Marine-terminating glaciers dominate the evolution of the Greenland Ice Sheet (GrIS) and its contribution to sea-level rise. Widespread glacier acceleration has been linked to the warming of ocean waters around the periphery of Greenland but a lack of information on the bathymetry of the continental shelf and glacial fjords has limited our ability to understand how subsurface, warm, salty ocean waters of Atlantic origin (AW) reach the glaciers and melt them from below. Here, we employ high-resolution, airborne gravity data (AIRGrav) in combination with multibeam echo sounding (MBES) data, to infer the bathymetry of the coastal areas of Northwest Greenland for NASA’s Ocean Melting Greenland (OMG) mission. High-resolution, AIRGrav data acquired on a 2 km spacing, 150 m ground clearance, with 1.5 mGal crossover error, is inverted in three dimensions to map the bathymetry. To constrain the inversion away from MBES data, we compare two methods: one based on the Direct Current (DC) shift of the gravity field (absolute minus observed gravity) and another based on the density of the bedrock. We evaluate and compare the two methods in areas with complete MBES coverage. We find the lowest standard error in bed elevation (±60 m) using the DC shift method. When applied to the entire coast of Northwest Greenland, the three-dimensional inversion reveals a complex network of connected sea bed channels, not known previously, that provide natural and varied pathways for AW to reach the glaciers across the continental shelf. The study demonstrates that the gravity approach offers an efficient and practical alternative to extensive ship mapping in ice-filled waters to obtain information critical to understanding and modeling ice-ocean interaction along ice sheet margins.

scholarly journals A new magnetic resonance-based technique for high-resolution quantification of amorphous and quasi-amorphous structures

2016 ◽  
Vol 13 (123) ◽  
pp. 20160589
Author(s):  
James Rafferty ◽  
Lance Farr ◽  
Tim James ◽  
David Chase ◽  
John Heinrich ◽  
...  
Keyword(s):  
Magnetic Resonance ◽  
High Resolution ◽  
Ex Vivo ◽  
Imaging Techniques ◽  
Three Dimensions ◽  
Small Scale ◽  
Micro Computed Tomography ◽  
Cross Sectional ◽  
Biological Structures ◽  
The One

We present a novel, high-resolution magnetic resonance technique, fine structure analysis (FSA) for the quantification and analysis of amorphous and quasi-amorphous biological structures. The one-dimensional technique is introduced mathematically and then applied to one simulated phantom, two physical phantoms and a set of ex vivo biological samples, scanned with interpoint spacings of 0.0038–0.195 mm and cross-sectional sizes of 3 × 3 or 5 × 5 mm. The simulated phantom and one of the physical phantoms consists of randomly arranged beads of known size in two and three dimensions, respectively. The second physical phantom was constructed by etching lines on Perspex. The ex vivo samples are human bone specimens. We show that for all three phantoms, the FSA technique is able to elucidate the average spacing of the structures present within each sample using structural spectroscopy, the smallest of which was 180 µm in size. We further show that in samples of trabecular bone, FSA is able to produce comparable results to micro-computed tomography, the current gold standard for measuring bone microstructure, but without the need for ionizing radiation. Many biological structures are too small to be captured by conventional, clinically deployed medical imaging techniques. FSA has the potential for use in the analysis of pathologies where such small-scale repeating structures are disrupted or their size, and spacing is otherwise altered.

Visualizing wood anatomy in three dimensions with high-resolution X-ray micro-tomography (μCT ) – a review –

IAWA Journal ◽  
2013 ◽  
Vol 34 (4) ◽  
pp. 408-424 ◽  
Author(s):  
Craig R. Brodersen
Keyword(s):  
High Resolution ◽  
Wood Anatomy ◽  
Data Extraction ◽  
Three Dimensional ◽  
Cell Types ◽  
Extraction Process ◽  
Three Dimensions ◽  
Wood Structures ◽  
X Ray ◽  
Micro Tomography

High-resolution X-ray micro-tomography (μCT) has emerged as one of the most promising new tools available to wood anatomists to study the three-dimensional organization of xylem networks. This non-destructive method faithfully reproduces the spatial relationships between the different cell types and allows the user to explore wood anatomy in new and innovative ways. With μCT imaging, the sample can be visualized in any plane and is not limited to a single section or exposed plane. Conventional CT software aids in the visualization of wood structures, and newly developed custom software can be used to rapidly automate the data extraction process, thereby accelerating the rate at which samples can be analyzed for research. In this review the origins of xylem reconstructions using traditional methods are discussed, as well as the current applications of μCT in plant biology and an overview of pertinent technical considerations associated with this technique. μCT imaging offers a new perspective on wood anatomy and highlights the importance of the relationships between wood structure and function.

scholarly journals Visualization and quantification of whole rat heart laminar structure using high-spatial resolution contrast-enhanced MRI

2012 ◽  
Vol 302 (1) ◽  
pp. H287-H298 ◽  
Author(s):  
Stephen H. Gilbert ◽  
David Benoist ◽  
Alan P. Benson ◽  
Ed White ◽  
Steven F. Tanner ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Rat Heart ◽  
High Spatial Resolution ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Structural Features ◽  
Isolated Rat Heart ◽  
Three Dimensions ◽  
Entire Volume ◽  
Branching Structures

It has been shown by histology that cardiac myocytes are organized into laminae and this structure is important in function, both influencing the spread of electrical activation and enabling myocardial thickening in systole by laminar sliding. We have carried out high-spatial resolution three-dimensional MRI of the ventricular myolaminae of the entire volume of the isolated rat heart after contrast perfusion [dimeglumine gadopentate (Gd-DTPA)]. Four ex vivo rat hearts were perfused with Gd-DTPA and fixative and high-spatial resolution MRI was performed on a 9.4T MRI system. After MRI, cryosectioning followed by histology was performed. Images from MRI and histology were aligned, described, and quantitatively compared. In the three-dimensional MR images we directly show the presence of laminae and demonstrate that these are highly branching and are absent from much of the subepicardium. We visualized these MRI volumes to demonstrate laminar architecture and quantitatively demonstrated that the structural features observed are similar to those imaged in histology. We showed qualitatively and quantitatively that laminar architecture is similar in the four hearts. MRI can be used to image the laminar architecture of ex vivo hearts in three dimensions, and the images produced are qualitatively and quantitatively comparable with histology. We have demonstrated in the rat that: 1) laminar architecture is consistent between hearts; 2) myolaminae are absent from much of the subepicardium; and 3) although localized orthotropy is present throughout the myocardium, tracked myolaminae are branching structures and do not have a discrete identity.

In-Lens Cryo-High Resolution Scanning Electron Microscopy: Methodologies for Molecular Imaging of Self-Assembled Organic Hydrogels

2003 ◽  
Vol 9 (4) ◽  
pp. 286-295 ◽  
Author(s):  
Robert P. Apkarian ◽  
Elizabeth R. Wright ◽  
Victor A. Seredyuk ◽  
Susan Eustis ◽  
L. Andrew Lyon ◽  
...  
Keyword(s):  
High Resolution ◽  
Low Temperature ◽  
Gemini Surfactants ◽  
High Vacuum ◽  
Three Dimensional ◽  
Three Dimensions ◽  
High Magnification ◽  
Vacuum Sublimation ◽  
Morphological Studies ◽  
Hydrogel Matrix

The micro- and nanoarchitectures of water-swollen hydrogels were routinely analyzed in three dimensions at very high resolution by two cryopreparation methods that provide stable low-temperature specimens for in-lens high magnification recordings. Gemini surfactants (gS), poly-N-isopropylacrylamides (p-NIP Am), and elastin-mimetic di- (db-E) and triblock (tb-E) copolymer proteins that form hydrogels have been routinely analyzed to the sub-10-nm level in a single day. After they were quench or high pressure frozen, samples in bulk planchets were subsequently chromium coated and observed at low temperature in an in-lens field emission SEM. Pre-equilibrated planchets (4–40°C) that hold 5–10 μl of hydrogel facilitate dynamic morphological studies above and below their transition temperatures. Rapidly frozen samples were fractured under liquid nitrogen, low-temperature metal coated, and observed in-lens to assess the dispersion characteristics of micelles and fragile colloidal assemblies within bulk frozen water. Utilizing the same planchet freezing system, the cryoetch-HRSEM technique removed bulk frozen water from the hydrogel matrix by low-temperature, high-vacuum sublimation. The remaining frozen solid-state sample faithfully represented the hydrogel matrix. Cryo- and cryoetch-HRSEM provided vast vistas of hydrogels at low and intermediate magnifications whereas high magnification recordings and anaglyphs (stereo images) provided a three-dimensional prospective and measurements on a molecular level.

scholarly journals DTI reveals whole-brain microstructural changes in the P301L mouse model of tauopathy

2020 ◽  
Author(s):  
Aidana Massalimova ◽  
Ruiqing Ni ◽  
Roger M. Nitsch ◽  
Marco Reisert ◽  
Dominik von Elverfeldt ◽  
...  
Keyword(s):  
White Matter ◽  
High Resolution ◽  
Mouse Model ◽  
Mouse Brain ◽  
Diffusion Tensor ◽  
Ex Vivo ◽  
Brain Regions ◽  
Brain Atlas ◽  
Microstructural Changes ◽  
Allen Mouse Brain Atlas

AbstractIntroductionIncreased expression of hyperphosphorylated tau and the formation of neurofibrillary tangles are associated with neuronal loss and white matter damage. Using high resolution ex vivo diffusion tensor imaging (DTI), we investigated microstructural changes in the white and grey matter in the P301L mouse model of human tauopathy at 8.5 months-of-age. For unbiased computational analysis, we implemented a pipeline for voxel-based analysis (VBA) and atlas-based analysis (ABA) of DTI mouse brain data.MethodsHemizygous and homozygous transgenic P301L mice and non-transgenic littermates were used. DTI data were acquired for generation of fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), axial diffusivity (AD) maps. VBA on the entire brain were performed using SPM8 and SPM Mouse toolbox. Initially, all DTI maps were co-registered with Allen mouse brain atlas to bring them to one common coordinate space. In VBA, co-registered DTI maps were normalized and smoothed in order to perform two-sample t-tests to compare hemizygotes with non-transgenic littermates, homozygotes with non-transgenic littermates, hemizygotes with homozygotes on each DTI parameter map. In ABA, the average values for selected regions-of-interests were computed with co-registered DTI maps and labels in Allen mouse brain atlas. After, the same two-sample t-tests were executed on the estimated average values.ResultsWe made reconstructed DTI data and VBA and ABA pipeline publicly available. With VBA, we found microstructural changes in the white matter in hemizygous P301L mice compared to non-transgenic littermates. In contrast, more pronounced and brain-wide spread changes were observed in VBA when comparing homozygous P301L mice with non-transgenic littermates. Statistical comparison of DTI metrics in selected brain regions by ABA corroborated findings from VBA. FA was found to be decreased in most brain regions, while MD, RD and AD were increased compared to hemizygotes and non-transgenic littermates.Discussion/ConclusionHigh resolution ex vivo DTI demonstrated brain-wide microstructural changes in the P301L mouse model of human tauopathy. The comparison between hemizygous and homozygous P301L mice revealed a gene-dose dependent effect on DTI metrics. The publicly available computational data analysis pipeline can provide a platform for future mechanistic and longitudinal studies.

Treatment of the gradient of defocus in images of tilted, thin crystals

1986 ◽  
Vol 44 ◽  
pp. 6-9
Author(s):  
R. Henderson ◽  
J.M. Baldwin
Keyword(s):  
Image Analysis ◽  
High Resolution ◽  
Electron Diffraction ◽  
Low Temperature ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Two Dimensional ◽  
Computer Image Analysis ◽  
Crystal Forms ◽  
Cell Dimensions

Bacteriorhodopsin, a membrane protein from Halobacteria, forms two-dimensional crystals which often have diameters of 20 microns. Several crystal forms have been obtained with cell dimensions of about 60 Å and diffraction to beyond 3 Å resolution. The structure of one of these crystal forms has recently been determined in projection at 3.5 Å resolution using images recorded at low temperature, together with computer image analysis methods that enable the averaging of information from areas of up to 1 micron in diameter. Electron diffraction intensities have also been recorded from tilted and untilted specimens providing three-dimensional amplitude measurements to 3 Å resolution. We are now analysing images from tilted specimens that should provide phases for the Fourier components of the structure to high resolution in three dimensions.

Sign in / Sign up

Export Citation Format

Share Document