Neuron tracing from light microscopy images: automation, deep learning and bench testing

Y Liu, G Wang, GA Ascoli, J Zhou, L Liu - Bioinformatics, 2022 - academic.oup.com
Motivation Large-scale neuronal morphologies are essential to neuronal ty**, connectivity
characterization and brain modeling. It is widely accepted that automation is critical to the …

Digital reconstructions of neuronal morphology: three decades of research trends

M Halavi, KA Hamilton, R Parekh… - Frontiers in …, 2012 - frontiersin.org
The importance of neuronal morphology has been recognized from the early days of
neuroscience. Elucidating the functional roles of axonal and dendritic arbors in synaptic …

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

L Manubens-Gil, Z Zhou, H Chen, A Ramanathan… - Nature …, 2023 - nature.com
BigNeuron is an open community bench-testing platform with the goal of setting open
standards for accurate and fast automatic neuron tracing. We gathered a diverse set of …

Nonlinear dendritic integration of sensory and motor input during an active sensing task

N Xu, MT Harnett, SR Williams, D Huber, DH O'Connor… - Nature, 2012 - nature.com
Active dendrites provide neurons with powerful processing capabilities. However, little is
known about the role of neuronal dendrites in behaviourally related circuit computations …

neuTube 1.0: a new design for efficient neuron reconstruction software based on the SWC format

L Feng, T Zhao, J Kim - eneuro, 2015 - eneuro.org
Brain circuit map** requires digital reconstruction of neuronal morphologies in
complicated networks. Despite recent advances in automatic algorithms, reconstruction of …

mGRASP enables map** mammalian synaptic connectivity with light microscopy

J Kim, T Zhao, RS Petralia, Y Yu, H Peng, E Myers… - Nature …, 2012 - nature.com
The GFP reconstitution across synaptic partners (GRASP) technique, based on functional
complementation between two nonfluorescent GFP fragments, can be used to detect the …

APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree

H **ao, H Peng - Bioinformatics, 2013 - academic.oup.com
Motivation: Tracing of neuron morphology is an essential technique in computational
neuroscience. However, despite a number of existing methods, few open-source techniques …

NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites

T Quan, H Zhou, J Li, S Li, A Li, Y Li, X Lv, Q Luo… - Nature …, 2016 - nature.com
The reconstruction of neuronal populations, a key step in understanding neural circuits,
remains a challenge in the presence of densely packed neurites. Here we achieved …

Neuromantic–from semi-manual to semi-automatic reconstruction of neuron morphology

DR Myatt, T Hadlington, GA Ascoli… - Frontiers in …, 2012 - frontiersin.org
The ability to create accurate geometric models of neuronal morphology is important for
understanding the role of shape in information processing. Despite a significant amount of …

Automatic 3D neuron tracing using all-path pruning

H Peng, F Long, G Myers - Bioinformatics, 2011 - academic.oup.com
Motivation: Digital reconstruction, or tracing, of 3D neuron structures is critical toward
reverse engineering the wiring and functions of a brain. However, despite a number of …