Fast Marching Spanning Tree: An Automatic Neuron Reconstruction Method

2016 ◽  
pp. 52-60
Author(s):  
Ming Hao ◽  
Jian Yang ◽  
Xiaoyang Liu ◽  
Zhijiang Wan ◽  
Ning Zhong
Keyword(s):  
Spanning Tree ◽  
Reconstruction Method ◽  
Fast Marching ◽  
Neuron Reconstruction

FMST: an Automatic Neuron Tracing Method Based on Fast Marching and Minimum Spanning Tree

2018 ◽  
Vol 17 (2) ◽  
pp. 185-196 ◽  
Author(s):  
Jian Yang ◽  
Ming Hao ◽  
Xiaoyang Liu ◽  
Zhijiang Wan ◽  
Ning Zhong ◽  
...  
Keyword(s):  
Spanning Tree ◽  
Minimum Spanning Tree ◽  
Fast Marching ◽  
Neuron Tracing ◽  
Tracing Method

Hidden Markov Modeling for Maximum Probability Neuron Reconstruction

2021 ◽  
Author(s):  
Thomas Athey ◽  
Daniel Tward ◽  
Ulrich Mueller ◽  
Joshua Vogelstein ◽  
Michael Miller
Keyword(s):  
Hidden Markov ◽  
Estimation Method ◽  
Appearance Model ◽  
Reconstruction Method ◽  
Markov Modeling ◽  
Reconstruction Algorithms ◽  
Maximum Probability ◽  
Neuron Reconstruction ◽  
State Process ◽  
Neuronal Processes

Abstract Recent advances in brain clearing and imaging have made it possible to image entire mammalian brains at sub-micron resolution. These images offer the potential to assemble brain-wide atlases of neuron morphology, but manual neuron reconstruction remains a bottleneck. Several automatic reconstruction algorithms exist, but most focus on single neuron images. In this paper, we present a probabilistic reconstruction method, ViterBrain, which combines a hidden Markov state process that encodes neuron geometry with a random field appearance model of neuron flourescence. Our method utilizes dynamic programming to compute the global maximizers of what we call the ``most probable'' neuron path. Our most probable estimation method models the task of reconstructing neuronal processes in the presence of other neurons, and thus is applicable in images with several neurons. Our method operates on image segmentations in order to leverage cutting edge computer vision technology. We applied our algorithm to imperfect image segmentations where false negatives severed neuronal processes, and showed that it can follow axons in the presence of noise or nearby neurons. Additionally, it creates a framework where users can intervene to, for example, fit start and endpoints. The code used in this work is available in our open-source Python package brainlit.

Three-dimensional reconstruction of the 40S ribosomal subunit from rabbit reticulocytes

1987 ◽  
Vol 45 ◽  
pp. 936-937
Author(s):  
Neng-Yu Zhang ◽  
Terence Wagenknecht ◽  
Michael Radermacher ◽  
Tom Obrig ◽  
Joachim Frank
Keyword(s):  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Uranyl Acetate ◽  
Reconstruction Method ◽  
Single Exposure ◽  
Electron Dose ◽  
Ribosomal Subunits ◽  
40S Ribosomal Subunit ◽  
Dimensional Reconstruction ◽  
Rabbit Reticulocytes

We have reconstructed the 40S ribosomal subunit at a resolution of 4 nm using the single-exposure pseudo-conical reconstruction method of Radermacher et al.Small (40S) ribosomal subunits were Isolated from rabbit reticulocytes, applied to grids and negatively stained (0.5% uranyl acetate) in a manner that “sandwiches” the specimen between two layers of carbon. Regions of the grid exhibiting uniform and thick staining were identified and photographed twice (magnification 49,000X). The first micrograph was always taken with the specimen tilted by 50° and the second was of the Identical area untilted (Fig. 1). For each of the micrographs the specimen was subjected to an electron dose of 2000-3000 el/nm2.Three hundred thirty particles appearing in the L view (defined in [4]) were selected from both tilted- and untilted-specimen micrographs. The untilted particles were aligned and their rotational alignment produced the azimuthal angles of the tilted particles in the conical tilt series.

Development of Waveform Reconstruction Method with Current Transformer Saturation

2009 ◽  
Vol 129 (1) ◽  
pp. 15-21 ◽  
Author(s):  
Shoichi Urano ◽  
Takeshi Yamada ◽  
Yoshifumi Ooura ◽  
Youheng Xu ◽  
Yasutaka Yamaguchi ◽  
...  
Keyword(s):  
Current Transformer ◽  
Reconstruction Method

Self-Protected Spanning Tree Based Recovery Scheme to Protect against Single Failure

2009 ◽  
Vol E92-B (3) ◽  
pp. 909-921
Author(s):  
Depeng JIN ◽  
Wentao CHEN ◽  
Li SU ◽  
Yong LI ◽  
Lieguang ZENG
Keyword(s):  
Spanning Tree ◽  
Recovery Scheme

3D Scene Reconstruction Method in Relative Coordinates with Two Images from Non-Calibrated Video Cameras

2020 ◽  
Vol 25 (3) ◽  
pp. 265-276
Author(s):  
K.M. Shepilova ◽  
◽  
A.V. Sotnikov ◽  
A.V. Shipatov ◽  
Yu.V. Savchenko ◽  
...  
Keyword(s):  
Scene Reconstruction ◽  
Reconstruction Method ◽  
Video Cameras ◽  
Relative Coordinates ◽  
3D Scene ◽  
3D Scene Reconstruction
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