scholarly journals NeuroRetriever: Automatic Neuron Segmentation for Connectome Assembly

2021 ◽  
Vol 15 ◽  
Author(s):  
Chi-Tin Shih ◽  
Nan-Yow Chen ◽  
Ting-Yuan Wang ◽  
Guan-Wei He ◽  
Guo-Tzau Wang ◽  
...  
Keyword(s):  
Large Scale ◽  
Dynamic Range ◽  
Large Population ◽  
Three Dimensional ◽  
High Dynamic Range ◽  
Structural Features ◽  
Single Neurons ◽  
Brain Images ◽  
Human Segmentation ◽  
The Brain

Segmenting individual neurons from a large number of noisy raw images is the first step in building a comprehensive map of neuron-to-neuron connections for predicting information flow in the brain. Thousands of fluorescence-labeled brain neurons have been imaged. However, mapping a complete connectome remains challenging because imaged neurons are often entangled and manual segmentation of a large population of single neurons is laborious and prone to bias. In this study, we report an automatic algorithm, NeuroRetriever, for unbiased large-scale segmentation of confocal fluorescence images of single neurons in the adult Drosophila brain. NeuroRetriever uses a high-dynamic-range thresholding method to segment three-dimensional morphology of single neurons based on branch-specific structural features. Applying NeuroRetriever to automatically segment single neurons in 22,037 raw brain images, we successfully retrieved 28,125 individual neurons validated by human segmentation. Thus, automated NeuroRetriever will greatly accelerate 3D reconstruction of the single neurons for constructing the complete connectomes.

Foundations of Advanced Neuroanatomy: Technical Guidelines for Specimen Preparation, Dissection, and 3D-Photodocumentation in a Surgical Anatomy Laboratory

2019 ◽  
Author(s):  
Luciano César PC Leonel ◽  
Lucas P. Carlstrom ◽  
Christopher S. Graffeo ◽  
Avital Perry ◽  
Carlos Diogenes Pinheiro-Neto ◽  
...  
Keyword(s):  
Oral Tradition ◽  
Dynamic Range ◽  
Tap Water ◽  
Three Dimensional ◽  
High Dynamic Range ◽  
Surgical Anatomy ◽  
Lessons Learned ◽  
Specimen Preparation ◽  
Technological Advances ◽  
Key Steps

Abstract Objective This study was aimed to provide a key update to the seminal works of Prof. Albert L. Rhoton Jr., MD, with particular attention to previously unpublished insights from the oral tradition of his fellows, recent technological advances including endoscopy, and high-dynamic range (HDR) photodocumentation, and, local improvements in technique, we have developed to optimize efficient neuroanatomic study. Methods Two formaldehyde-fixed cadaveric heads were injected with colored latex to demonstrate step-by-step specimen preparation for microscopic or endoscopic dissection. One formaldehyde-fixed brain was utilized to demonstrate optimal three-dimensional (3D) photodocumentation techniques. Results Key steps of specimen preparation include vessel cannulation and securing, serial tap water flushing, specimen drainage, vessel injection with optimized and color-augmented latex material, and storage in 70% ethanol. Optimizations for photodocumentation included the incorporation of dry black drop cloth and covering materials, an imaging-oriented approach to specimen positioning and illumination, and single-camera stereoscopic capture techniques, emphasizing the three-exposure-times-per-eye approach to generating images for HDR postprocessing. Recommended tools, materials, and technical nuances were emphasized throughout. Relative advantages and limitations of major 3D projection systems were comparatively assessed, with sensitivity to audience size and purpose specific recommendations. Conclusion We describe the first consolidated step-by-step approach to advanced neuroanatomy, including specimen preparation, dissection, and 3D photodocumentation, supplemented by previously unpublished insights from the Rhoton fellowship experience and lessons learned in our laboratories in the past years such that Prof. Rhoton's model can be realized, reproduced, and expanded upon in surgical neuroanatomy laboratories worldwide.

scholarly journals Ab initiostructure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

2016 ◽  
Vol 72 (2) ◽  
pp. 236-242 ◽  
Author(s):  
E. van Genderen ◽  
M. T. B. Clabbers ◽  
P. P. Das ◽  
A. Stewart ◽  
I. Nederlof ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Room Temperature ◽  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Direct Methods ◽  
Liquid Nitrogen Temperature ◽  
High Dynamic Range ◽  
Electron Diffraction Data ◽  
High Signal

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enablingab initiophasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS,SHELX) and for electron crystallography (ADT3D/PETS,SIR2014).

scholarly journals Adaptive Binocular Fringe Dynamic Projection Method for High Dynamic Range Measurement

Sensors ◽  
2019 ◽  
Vol 19 (18) ◽  
pp. 4023 ◽  
Author(s):  
Changzhi Yu ◽  
Fang Ji ◽  
Junpeng Xue ◽  
Yajun Wang
Keyword(s):  
Projection Method ◽  
Dynamic Range ◽  
Three Dimensional ◽  
High Dynamic Range ◽  
Fringe Projection ◽  
Range Measurement ◽  
Optimal Projection ◽  
Three Dimensional Measurement ◽  
High Dynamic ◽  
Adaptively Adjusting

Three-dimensional measurement with fringe projection sensor has been commonly researched. However, the measurement accuracy and efficiency of most fringe projection sensors are still seriously affected by image saturation and the non-linear effects of the projector. In order to solve the challenge, in conjunction with the advantages of stereo vision technology and fringe projection technology, an adaptive binocular fringe dynamic projection method is proposed. The proposed method can avoid image saturation by adaptively adjusting the projection intensity. Firstly, the flowchart of the proposed method is explained. Then, an adaptive optimal projection intensity method based on multi-threshold segmentation is introduced to adjust the projection illumination. Finally, the mapping relationship of binocular saturation point and projection point is established by binocular transformation and left camera–projector mapping. Experiments demonstrate that the proposed method can achieve higher accuracy for high dynamic range measurement.

scholarly journals Brownian motion of inert tracer macromolecules in polymerized and spontaneously bundled mixtures of actin and filamin.

1990 ◽  
Vol 110 (5) ◽  
pp. 1645-1654 ◽  
Author(s):  
L Hou ◽  
K Luby-Phelps ◽  
F Lanni
Keyword(s):  
Brownian Motion ◽  
Large Scale ◽  
Three Dimensional ◽  
Structural Features ◽  
Polystyrene Latex ◽  
Rabbit Muscle ◽  
Optical Cell ◽  
Structural Result ◽  
Latex Particles ◽  
Filament Bundles

By use of light microscopy and fluorescence photobleaching recovery, we have studied (a) structures that form in a system composed of copolymerized rabbit muscle actin and chicken gizzard filamin and (b) the Brownian motion of inert tracer macromolecules in this matrix. We have used as tracers size-fractionated fluorescein-labeled ficoll and submicron polystyrene latex particles. In F-actin solutions, the relative diffusion coefficient of the tracer was a decreasing function of both tracer size and actin concentration. Also, a percolation transition for latex particle mobility was found to follow a form suggested by Ogston (Ogston, A. G. 1958. Trans. Faraday Soc. 54:1754-1757) for random filament matrices. The inclusion of filamin before polymerization resulted in increased tracer mobility. Below a filamin dimer-to-actin monomer ratio of 1:140, no structural features were observed in the light microscope. At or above this ratio for all actin concentrations tested, a three-dimensional network of filament bundles was clearly discriminated. Latex particles were always excluded from the bundles. By use of a dialysis optical cell in which polymerization could be initiated with very little hydrodynamic stress, we found that filamin can spontaneously bundle F-actin. A simple physical picture explains how dynamics can affect the structural result of coassembly and provides a further hypothesis on the balance between random filament cross-linking and large-scale bundling. Control of this balance may be important in cytoplasmic motile events.

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