ArticleNeuroinformatics2019
FMST: an Automatic Neuron Tracing Method Based on Fast Marching and Minimum Spanning Tree.
Article in Neuroinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Modeling 3D mesoscaled neuronal complexity through learning-based dynamic morphometric convolution.Brain informatics · 2026Article
- BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.Nature methods · 2023Article
- Tracing weak neuron fibers.Bioinformatics (Oxford, England) · 2023Article
- Neuron tracing from light microscopy images: automation, deep learning and bench testing.Bioinformatics (Oxford, England) · 2022Review
- NeuroConstruct: 3D Reconstruction and Visualization of Neurites in Optical Microscopy Brain Images.IEEE transactions on visualization and computer graphics · 2022Article
- Smart imaging to empower brain-wide neuroscience at single-cell levels.Brain informatics · 2022Review
- Hidden Markov modeling for maximum probability neuron reconstruction.Communications biology · 2022Article
- Classifying the tracing difficulty of 3D neuron image blocks based on deep learning.Brain informatics · 2021Article
- Exploring highly reliable substructures in auto-reconstructions of a neuron.Brain informatics · 2021Article
- Neuron tracing and quantitative analyses of dendritic architecture reveal symmetrical three-way-junctions and phenotypes of git-1 in C. elegans.PLoS computational biology · 2021Article
- Improving the Usability of Virtual Reality Neuron Tracing with Topological Elements.IEEE transactions on visualization and computer graphics · 2021Article
- Automated Neuron Tracing Using Content-Aware Adaptive Voxel Scooping on CNN Predicted Probability Map.Frontiers in neuroanatomy · 2021Article
- Extrafollicular B cell responses correlate with neutralizing antibodies and morbidity in COVID-19.Nature immunology · 2020Article
- Retrieving similar substructures on 3D neuron reconstructions.Brain informatics · 2020Article
- Skeleton optimization of neuronal morphology based on three-dimensional shape restrictions.BMC bioinformatics · 2020Article
- Brain-Wide Shape Reconstruction of a Traced Neuron Using the Convex Image Segmentation Method.Neuroinformatics · 2020Article
- Weakly Supervised Learning of 3D Deep Network for Neuron Reconstruction.Frontiers in neuroanatomy · 2020Article
- The diversity of GABAergic neurons and neural communication elements.Nature reviews. Neuroscience · 2019Review
- Optimization of Traced Neuron Skeleton Using Lasso-Based Model.Frontiers in neuroanatomy · 2019Article
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Authors and funding
6 authors.
Funding
Abstract
Neuron reconstruction is an important technique in computational neuroscience. Although there are many reconstruction algorithms, few can generate robust results. In this paper, we propose a reconstruction algorithm called fast marching spanning tree (FMST). FMST is based on a minimum spanning tree method (MST) and improve its performance in two aspects: faster implementation and no loss of small branches. The contributions of the proposed method are as follows. Firstly, the Euclidean distance weight of edges in MST is improved to be a more reasonable value, which is related to the probability of the existence of an edge. Secondly, a strategy of pruning nodes is presented, which is based on the radius of a node's inscribed ball. Thirdly, separate branches of broken neuron reconstructions can be merged into a single tree. FMST and many other state of the art reconstruction methods were implemented on two datasets: 120 Drosophila neurons and 163 neurons with gold standard reconstructions. Qualitative and quantitative analysis on experimental results demonstrates that the performance of FMST is good compared with many existing methods. Especially, on the 91 fruitfly neurons with gold standard and evaluated by five metrics, FMST is one of two methods with best performance among all 27 state of the art reconstruction methods. FMST is a good and practicable neuron reconstruction algorithm, and can be implemented in Vaa3D platform as a neuron tracing plugin.
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