NeuronID: An automatic toolkit for identifying neurons in two-photon calcium imaging data.
Overview
- School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
Abstract
Two-photon calcium imaging has emerged as a powerful technique for monitoring neuronal activity in neuroscience; however, its data processing remains challenging. Here, we introduce NeuronID, an automatic toolkit designed to process two-photon calcium imaging data. The NeuronID toolkit features a modular architecture that includes motion correction, noise reduction, segmentation of neuronal components, and extraction of neuronal signals. Notably, the NeuronID toolkit offers an optimized strategy for segmenting neuronal components, which systematically integrates morphological boundary identification, cross-correlation analysis between pixels, and evaluation of neuronal signal quality. Compared to existing tools or manual annotation by experts, the NeuronID toolkit reduces the likelihood of over-segmentation while achieving near-human accuracy. Overall, this study provides an effective solution to the segmentation of neuronal components, offering a standardized analytical tool for processing two-photon calcium imaging data.
Reproduced under the paper's license (CC BY), from the paper cited above.
Code
The paper links to its data, not to its authors' code: see the Data section.
The paper's code and data availability statement is in the Data section.
Tracing map
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Data
Datasets cited
- figshare:30918077, at figshare; found in “Data Availability”
Data Availability
The NeuronID toolkit is available on GitHub (https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
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Version 1, 30 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 9 MeSH terms, 5 funders, 29 references.
Cite
This paper
Peng, J., & Xu, T. (2026). NeuronID: An automatic toolkit for identifying neurons in two-photon calcium imaging data. PloS one, 21(3), e0343516. https://
BibTeX
@article{peng2026neuroni
author = {Peng, Jikan and Xu, Tian},
title = {{NeuronID: An automatic toolkit for identifying neurons in two-photon calcium imaging data}},
journal = {PloS one},
year = {2026},
month = mar,
volume = {21},
number = {3},
pages = {e0343516},
publisher = {PLOS},
issn = {1932-6203},
doi = {10.1371/
url = {https://
pmid = {41801931},
pmcid = {PMC12970857}
}
RIS
TY - JOUR
AU - Peng, Jikan
AU - Xu, Tian
TI - NeuronID: An automatic toolkit for identifying neurons in two-photon calcium imaging data
T2 - PloS one
J2 - PLoS One
PY - 2026
DA - 2026/
VL - 21
IS - 3
SP - e0343516
SN - 1932-6203
PB - PLOS
DO - 10.1371/
UR - https://
LA - en
ER -
CSL-JSON
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