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

2021 ◽  
Author(s):  
Peter Hawley Li ◽  
Larry F. Lindsey ◽  
Michał Januszewski ◽  
Zhihao Zheng ◽  
Alexander Shakeel Bates ◽  
...  
Keyword(s):  
Serial Section ◽  
Local Realignment

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

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.

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.

Normal Synaptonemal Complex and Abnormal Recombination Nodules in Two Alleles of the Drosophila Meiotic Mutant mei-W68

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1337-1356 ◽  
Author(s):  
Adelaide T C Carpenter
Keyword(s):  
Electron Microscopy ◽  
Synaptonemal Complex ◽  
High Frequency ◽  
Serial Section ◽  
The Other ◽  
Wild Type ◽  
Recombination Nodules ◽  
Section Electron ◽  
Serial Section Electron Microscopy ◽  
Section Electron Microscopy

Abstract The meiotic phenotypes of two mutant alleles of the mei-W68 gene, 1 and L1, were studied by genetics and by serial-section electron microscopy. Despite no or reduced exchange, both mutant alleles have normal synaptonemal complex. However, neither has any early recombination nodules; instead, both exhibit high numbers of very long (up to 2 μm) structures here named “noodles.” These are hypothesized to be formed by the unchecked extension of identical but much shorter structures ephemerally seen in wild type, which may be precursors of early recombination nodules. Although the mei-W68L1 allele is identical to the mei-W681 allele in both the absence of early recombination nodules and a high frequency of noodles (i.e., it is amorphic for the noodle phene), it is hypomorphic in its effects on exchange and late recombination nodules. The differential effects of this allele on early and late recombination nodules are consistent with the hypothesis that Drosophila females have two separate recombination pathways—one for simple gene conversion, the other for exchange.

scholarly journals Semi‐automatic stitching of filamentous structures in image stacks from serial‐section electron tomography

2021 ◽  
Author(s):  
Norbert Lindow ◽  
Florian N. Brünig ◽  
Vincent J. Dercksen ◽  
Gunar Fabig ◽  
Robert Kiewisz ◽  
...  
Keyword(s):  
Serial Section ◽  
Electron Tomography ◽  
Section Electron

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.

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