scholarly journals Automated Reconstruction of a Serial-Section EM Drosophila Brain with Flood-Filling Networks and Local Realignment

2019 ◽  
Author(s):  
Peter H. Li ◽  
Larry F. Lindsey ◽  
Michał Januszewski ◽  
Zhihao Zheng ◽  
Alexander Shakeel Bates ◽  
...  
Keyword(s):  
Serial Section ◽  
Neural Circuitry ◽  
Global Alignment ◽  
Serial Sections ◽  
Transmission Electron ◽  
Order Of Magnitude ◽  
Local Realignment ◽  
Drosophila Brain ◽  
Health And Disease ◽  
Single Synapse

AbstractReconstruction of neural circuitry at single-synapse resolution is a key target for improving understanding of the nervous system in health and disease. Serial section transmission electron microscopy (ssTEM) is among the most prolific imaging methods employed in pursuit of such reconstructions. We demonstrate how Flood-Filling Networks (FFNs) can be used to computationally segment a forty-teravoxel whole-brain Drosophila ssTEM volume. To compensate for data irregularities and imperfect global alignment, FFNs were combined with procedures that locally re-align serial sections as well as dynamically adjust and synthesize image content. The proposed approach produced a largely merger-free segmentation of the entire ssTEM Drosophila brain, which we make freely available. As compared to manual tracing using an efficient skeletonization strategy, the segmentation enabled circuit reconstruction and analysis workflows that were an order of magnitude faster.

scholarly journals Automated Reconstruction of a Serial-Section EM Drosophila Brain with Flood-Filling Networks and Local Realignment

2019 ◽  
Vol 25 (S2) ◽  
pp. 1364-1365 ◽  
Author(s):  
Peter H. Li ◽  
Larry F. Lindsey ◽  
Michał Januszewski ◽  
Mike Tyka ◽  
Jeremy Maitin-Shepard ◽  
...  
Keyword(s):  
Serial Section ◽  
Local Realignment ◽  
Drosophila Brain

Three-Dimensional Reconstruction Using Stereo Pairs from Serial Thick Sections

1977 ◽  
Vol 35 ◽  
pp. 562-563
Author(s):  
Robert Glaeser ◽  
Thomas Bauer ◽  
David Grano
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Serial Sections ◽  
Thin Sections ◽  
3 Dimensional ◽  
Transmission Electron ◽  
Freeze Dried ◽  
Dimensional Reconstruction ◽  
Stereo Imagery ◽  
Whole Mounts

In transmission electron microscopy, the 3-dimensional structure of an object is usually obtained in one of two ways. For objects which can be included in one specimen, as for example with elements included in freeze- dried whole mounts and examined with a high voltage microscope, stereo pairs can be obtained which exhibit the 3-D structure of the element. For objects which can not be included in one specimen, the 3-D shape is obtained by reconstruction from serial sections. However, without stereo imagery, only detail which remains constant within the thickness of the section can be used in the reconstruction; consequently, the choice is between a low resolution reconstruction using a few thick sections and a better resolution reconstruction using many thin sections, generally a tedious chore. This paper describes an approach to 3-D reconstruction which uses stereo images of serial thick sections to reconstruct an object including detail which changes within the depth of an individual thick section.

Cell morphology, volume, and surface area determinations from multilevel contouring within HVEM micrographs of serial sections and whole-cell mounts

1987 ◽  
Vol 45 ◽  
pp. 588-589
Author(s):  
M. Marko ◽  
A. Leith ◽  
D. Parsons
Keyword(s):  
Surface Area ◽  
Electron Micrographs ◽  
Cell Morphology ◽  
Individual Variation ◽  
Serial Section ◽  
Stereo Pair ◽  
Complex Structures ◽  
Serial Sections ◽  
Surface Areas ◽  
Computer Based

The use of serial sections and computer-based 3-D reconstruction techniques affords an opportunity not only to visualize the shape and distribution of the structures being studied, but also to determine their volumes and surface areas. Up until now, this has been done using serial ultrathin sections.The serial-section approach differs from the stereo logical methods of Weibel in that it is based on the Information from a set of single, complete cells (or organelles) rather than on a random 2-dimensional sampling of a population of cells. Because of this, it can more easily provide absolute values of volume and surface area, especially for highly-complex structures. It also allows study of individual variation among the cells, and study of structures which occur only infrequently.We have developed a system for 3-D reconstruction of objects from stereo-pair electron micrographs of thick specimens.

TEM investigation of defect reduction and etch pit formation in GaN

2003 ◽  
Vol 798 ◽  
Author(s):  
Angelika Vennemann ◽  
Jens Dennemarck ◽  
Roland Kröger ◽  
Tim Böttcher ◽  
Detlef Hommel ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Dislocation Density ◽  
Line Tension ◽  
Threading Dislocations ◽  
Dislocation Loops ◽  
Etch Pits ◽  
Defect Reduction ◽  
Transmission Electron ◽  
Order Of Magnitude ◽  
Edge Dislocations

ABSTRACTGaN samples of this study were chemically wet etched to gain easier access to the dislocation sturcture. The scanning electron microscopy and transmission electron microscopy investigations revealed four different types of etch pits. After brief etching, several dislocations with screw component showed large etch pits, which may be correlated with the core of the screw dislocation. By means of SiNx micromasking the dislocation density could be reduced by more than one order of magnitude. The reduction of threading dislocations in the SiNx region in GaN grown on 〈0001〉 sapphire is due to bending of the threading dislocations into the {0001} plane, such that they form dislocation loops if they meet dislocations with opposite Burgers vectors. Accordingly, the achievable reduction of the dislocation density is limited by the probability that these dislocations interact. Edge dislocations bend more easily on account of their low line tension. This results in a preferential bending and reduction of dislocations with edge character.

scholarly journals EXTIRPATION OF THE THYMUS IN THE GUINEA PIG

1917 ◽  
Vol 25 (1) ◽  
pp. 129-152 ◽  
Author(s):  
Edwards A. Park
Keyword(s):  
Guinea Pig ◽  
Serial Section ◽  
Guinea Pigs ◽  
Close Association ◽  
Main Lobe ◽  
Technical Error ◽  
Serial Sections ◽  
Pharyngeal Pouch ◽  
The Third ◽  
Third Pharyngeal Pouch

1. Accessory lobes of thymus, derived from the third pharyngeal pouch, occurring in close association with the parathyroids from the third pouch, were found in serial section of the cervical tissues of eleven out of fourteen guinea pigs, and probably would have been found in all fourteen but for a technical error. 2. It is probable, therefore, that accessory lobes of thymus having this situation and origin are usually, if not always, present in the guinea pig. 3. Additional accessory lobes of thymus belonging to, but at some distance from the main lobe were also present in several of the animals. 4. The discovery of these accessory lobes makes it certain that the guinea pig is unsuitable material for complete thymectomy, and probably complete extirpation of the thymus in this animal is rarely, if ever accomplished. 5. The extirpation experiments of previous investigators in the guinea pig must now be regarded as partial extirpations, and their results interpreted in that light. 6. Extirpation of the thymus in the guinea pig produced no changes in the writer's experiments. 7. The study of the serial sections of the cervical tissues of the guinea pig indicates that Ruben's statements regarding the parathyroid derived from the fourth pharyngeal pouch in the guinea pig are correct,—that it is much smaller than parathyroid III, may be rudimentary, and is sometimes absent at least on one side. 8. No accessory lobe of thymus was found accompanying the parathyroid from the fourth pouch, a finding also bearing out Ruben's statement that no thymus anlarge springs from the fourth pouch in the guinea pig.

Fine structure of the kinetochores in six species of the Coleoptera

Genome ◽  
1997 ◽  
Vol 40 (3) ◽  
pp. 379-385
Author(s):  
Klaus Werner Wolf
Keyword(s):  
Direct Contact ◽  
Karyotype Evolution ◽  
Coccinella Septempunctata ◽  
Cell Types ◽  
Male Meiosis ◽  
Serial Sections ◽  
Cell Type ◽  
Present Survey ◽  
Transmission Electron ◽  
Size Variability

Kinetochore structure was examined in a total of 6 species from 5 different families of the Coleoptera using transmission electron microscopy of ultrathin serial sections. Metaphase spermatogonia and primary and secondary spermatocytes were studied in Tenebrio molitor (Tenebrionidae) to determine whether kinetochore structure varies depending on the cell type. In all three cell types, the kinetochore microtubules (MTs) were in direct contact with the chromosomal surface, and kinetochore plates were not detectable. In the other species, only metaphase I spermatocytes were examined. As in T. molitor, distinct kinetochore plates were also absent in Adelocera murina (Elateridae), Agapanthia villosoviridescens (Cerambycidae), and Coccinella septempunctata (Coccinellidae). However, bivalents in male meiosis of two representatives of the Chrysomelidae, Agelastica alni and Chrysolina graminis, showed roughly spherical kinetochores at their poleward surfaces. Microtubules were in contact with this material. Thus, although the present survey covers only a small number of species, it is clear that at least two kinetochore types occur in the Coleoptera. The cytological findings are discussed in the context of chromosome number and genome size variability in the Coleopteran families studied. It is suggested that properties of the kinetochores could play a role in karyotype evolution in the Coleoptera.Key words: bivalent, microtubule, meiosis, metaphase, spermatocyte.

Critical current density and microstructure variations in YBa2Cu3O7−x + BaSnO3 films with different concentrations of BaSnO3

2008 ◽  
Vol 23 (12) ◽  
pp. 3363-3369 ◽  
Author(s):  
C.V. Varanasi ◽  
J. Burke ◽  
L. Brunke ◽  
H. Wang ◽  
J.H. Lee ◽  
...  
Keyword(s):  
Critical Current Density ◽  
Critical Current ◽  
Current Density ◽  
Gradual Increase ◽  
Critical Transition ◽  
Critical Transition Temperature ◽  
Transmission Electron ◽  
Order Of Magnitude ◽  
High Fields ◽  
Magnitude Increase

Previous work on YBa2Cu3O7−x (YBCO) + BaSnO3 (BSO) films with a single composition showed significant critical current density (Jc) improvements at higher fields but lowered Jc in low fields. A detailed study on BSO concentrations provided here demonstrates that significant Jc enhancement can occur even up to 20 mol% BSO inclusion, where typical particulate inclusions in these concentrations degrade the YBCO performance. YBCO + BSO films were processed on (100) LaAlO3 substrates using premixed targets of YBa2Cu3O7-x (YBCO) with additions of 2, 4, 10, and 20 mol% BSO. The critical transition temperature Tc of the films remained high (>87 K), even with large amounts (20 mol%) of BSO. YBCO + BSO films showed a gradual increase in Jc at high fields as the amount of BSO was increased. More than an order of magnitude increase in Jc was measured in YBCO + BSO samples as compared to regular YBCO at 4 T. YBCO + 10 mol% BSO films showed overall improvement at all the field ranges while YBCO + 20 mol% BSO was better only at high fields. Transmission electron microscopy revealed the presence of ∼7–8-nm-diameter BSO nanocolumns, the density of which increased with increasing BSO content correlating well with the observed improvements in Jc.

High Quality AlN Layer Grown on Patterned Sapphire Substrates by Hydride Vapor-Phase Epitaxy: A Route for Cost Efficient AlN Templates for Deep Ultraviolet Light Devices

2021 ◽  
Vol 21 (9) ◽  
pp. 4881-4885
Author(s):  
Seung-Jae Lee ◽  
Seong-Ran Jeon ◽  
Young Ho Song ◽  
Young-Jun Choi ◽  
Hae-Gon Oh ◽  
...  
Keyword(s):  
Vapor Phase ◽  
Vapor Phase Epitaxy ◽  
Hydride Vapor Phase Epitaxy ◽  
Threading Dislocation ◽  
Sapphire Substrates ◽  
Transmission Electron ◽  
Dislocation Densities ◽  
Order Of Magnitude ◽  
Cost Efficient ◽  
Patterned Sapphire Substrates

We report the characteristics of AlN epilayers grown directly on cylindrical-patterned sapphire substrates (CPSS) by hydride vapor-phase epitaxy (HVPE). To evaluate the effect of CPSS, we analyzed the threading dislocation densities (TDDs) of AlN films grown simultaneously on CPSS and flat sapphire substrate (FSS) by transmission electron microscopy (TEM). The corresponding TDD is measured to be 5.69 x 108 cm−2 for the AlN sample grown on the CPSS that is almost an order of magnitude lower than the value of 3.43 × 109 cm−2 on the FSS. The CPSS contributes to reduce the TDs originated from the AlN/sapphire interface via bending the TDs by lateral growth during the coalescence process. In addition, the reduction of direct interface area between AlN and sapphire by CPSS reduce the generation of TDs.

Elevated Temperature Implantation of GaAs with Si Ions.

1996 ◽  
Vol 438 ◽  
Author(s):  
R. A. Brown ◽  
J. S. Williams
Keyword(s):  
Elevated Temperatures ◽  
Amorphous Layer ◽  
Ion Flux ◽  
Implantation Temperature ◽  
Transmission Electron ◽  
Order Of Magnitude ◽  
Residual Damage ◽  
Radiation Induced ◽  
Small Clusters ◽  
Induced Defects

AbstractThe formation of amorphous layers in GaAs during ion bombardment at elevated temperatures, where dynamic annealing of radiation-induced defects is substantial, is shown to be extremely sensitive to the ion flux, fluence, and implantation temperature. For example, with increasing fluence, damage can first build up extremely slowly, then suddenly collapse to the amorphous phase. Alternatively, for a constant ion fluence, a change in flux by one order of magnitude can change the critical temperature for amorphisation by 27°C, and at constant flux and fluence, a change of only 6°C can alter the residual damage from small clusters barely visible by conventional transmission electron microscopy and Rutherford backscattering to a thick amorphous layer. The temperature at which this occurs is strongly dependent upon the ion flux and fluence.

A method of precise misorientation determination

2003 ◽  
Vol 36 (6) ◽  
pp. 1319-1323 ◽  
Author(s):  
A. Morawiec
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Spatial Resolution ◽  
Standard Procedure ◽  
Good Spatial Resolution ◽  
Transmission Electron ◽  
Order Of Magnitude ◽  
Achievable Accuracy ◽  
Better Than

A method that improves the accuracy of misorientations determined from Kikuchi patterns is described. It is based on the fact that some parameters of a misorientation calculated from two orientations are more accurate than other parameters. A procedure which eliminates inaccurate elements is devised. It requires at least two foil inclinations. The quality of the approach relies on the possibility to set large sample-to-detector distances and the availability of good spatial resolution of transmission electron microscopy. Achievable accuracy is one order of magnitude better than the accuracy of the standard procedure.

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