SNAP: a structure-based neuron morphology reconstruction automatic pruning pipeline

Article Biochemical Research Methods

Tracing weak neuron fibers

Yufeng Liu et al.

Summary: In this study, a method called NeuMiner was proposed for tracing weak fibers by combining online sample mining strategy and modified gamma transformation. NeuMiner significantly improved the recall of weak signals, especially for axons.

BIOINFORMATICS (2023)

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Article Computer Science, Information Systems

Minimizing Probability Graph Connectivity Cost for Discontinuous Filamentary Structures Tracing in Neuron Image

Qing Huang et al.

Summary: In this paper, a graph connectivity theoretical method for precise filamentary structure tracing in neuron image is proposed. The method uses CNN technique and linear programming function to trace broken traces from noisy background, and it achieves good results in experiments.

IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS (2022)

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Article Biochemical Research Methods

Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons

Shuxia Guo et al.

Summary: The study addresses the major bottleneck in neuroscience of digitally reconstructing 3D neuron morphologies by proposing a pipeline to enhance neuron signal and suppress background, achieving high contrast and image uniformity. The performance of the method was quantitatively verified and shown to significantly improve image quality and neuron reconstruction, with a five-fold increase in compression rate in enhanced images.

BIOINFORMATICS (2022)

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Article Neurosciences

Single-neuron projectome of mouse prefrontal cortex

Le Gao et al.

Summary: This study reveals the organization principles of axon projections within and outside the prefrontal cortex (PFC) using single-neuron reconstruction. It identifies different subtypes of PFC projection neurons and uncovers topographic rules and target selection patterns. The study also provides a hierarchical map within PFC and identifies three functionally related PFC modules. The findings highlight the importance of neuronal connectivity in understanding diverse PFC functions.

NATURE NEUROSCIENCE (2022)

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Article Computer Science, Interdisciplinary Applications

GTree: an Open-source Tool for Dense Reconstruction of Brain-wide Neuronal Population

Hang Zhou et al.

Summary: A new open-source software called GTree has been developed to address the time-consuming process of neuron digital reconstruction from large datasets. GTree features an error-screening system for fast error localization in neuron branches and achieves high automation. The study shows that GTree is five times faster than widely used commercial software and applicable to large datasets.

NEUROINFORMATICS (2021)

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Article Multidisciplinary Sciences

Morphological diversity of single neurons in molecularly defined cell types

Hanchuan Peng et al.

Summary: The study systematically examined the complete single-neuron morphologies on a brain-wide scale and identified 11 major projection neuron types with distinct features. The research found extensive projectional diversity within each major type, following generalizable principles governing long-range axonal projections including molecular correspondence, divergent or convergent projection, axon termination pattern, and regional specificity. This study highlights the crucial need for quantitative description of complete single-cell anatomy in cell-type classification.

NATURE (2021)

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Article Engineering, Electrical & Electronic

Crossover Structure Separation With Application to Neuron Tracing in Volumetric Images

Changhao Guo et al.

Summary: An automatic algorithm is proposed in this article to detect and separate crossover structures for improving neuron reconstruction results. Experimental results demonstrate that the proposed method can effectively enhance the performance of neuron tracing in volumetric images.

IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT (2021)

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Article Engineering, Electrical & Electronic

Automatic Repair of 3-D Neuron Reconstruction Based on Topological Feature Points and an MOST-Based Repairer

Fuhao Yu et al.

Summary: This study proposed a proof-editing algorithm for automatically detecting and repairing false negative branches in neuron reconstructions, utilizing a multiscale upgraded ray-shooting model and a MOST-based repairer. Experimental results demonstrated a reduction of up to 20% in the false-negative rate, confirming the effectiveness of the proposed method in generating faithful reconstructions.

IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT (2021)

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Article Multidisciplinary Sciences