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

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

Manubens-Gil, Linus
•
Zhou, Zhi
•
Chen, Hanbo
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April 17, 2023
Nature Methods

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 image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings. This resource describes a collection of neurons from a variety of light microscopy-based datasets, which can serve as a gold standard for testing automated tracing algorithms, as shown by comparison of the performance of 35 algorithms.

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Type
research article
DOI
10.1038/s41592-023-01848-5
Web of Science ID

WOS:000973675500002

Author(s)
Manubens-Gil, Linus
Zhou, Zhi
Chen, Hanbo
Ramanathan, Arvind
Liu, Xiaoxiao
Liu, Yufeng
Bria, Alessandro
Gillette, Todd
Ruan, Zongcai
Yang, Jian
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Date Issued

2023-04-17

Published in
Nature Methods
Volume

20

Issue

6

Start page

824

End page

835

Subjects

Biochemical Research Methods

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Biochemistry & Molecular Biology

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brain

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reconstruction

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morphology

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cortex

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cells

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tools

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visualization

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diversity

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diadem

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system

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computational neuroscience

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computational platforms and environments

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light microscopy

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neuron tracing

Note

Sean L. Hill is one of the senior authors on this article. His affiliation as Co-Director on EPFL's Blue Brain Project was omitted in error and he has requested a correction to add it.

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
BBP-CORE  
RelationURL/DOI

Cites

https://infoscience.epfl.ch/record/117849

Cites

https://infoscience.epfl.ch/record/218765

Cites

https://infoscience.epfl.ch/record/189283
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Available on Infoscience
June 5, 2023
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/198121
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