ArticleBMC biology2020
Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans.
Article in BMC biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 52 citations in OpenAlex.
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- Developing a Robust Multiround HCR-FISH Method Modified for Caenorhabditis elegans.Genes to cells : devoted to molecular & cellular mechanisms · 2026Article
- Deep neural networks to register and annotate cells in moving and deforming nervous systems.eLife · 2026Article
- LITE-1 Photoreceptor Mediates Light-Induced Reversal of Ivermectin Paralysis inmicroPublication biology · 2026Article
- Guide frames improve centerline estimation of complex postures in WormTracer.microPublication biology · 2026Article
- Unifying community whole-brain imaging datasets enables robust neuron identification and reveals determinants of neuron position in C. elegans.Cell reports methods · 2025Article
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- Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning inbioRxiv : the preprint server for biology · 2024Article
- Automated segmentation and recognition of C. elegans whole-body cells.Bioinformatics (Oxford, England) · 2024Article
- Ensemble dynamics and information flow deduction from whole-brain imaging data.PLoS computational biology · 2024Article
- Unraveling the hierarchical structure of posture and muscle activity changes during mating ofPNAS nexus · 2024Article
- See Elegans: Simple-to-use, accurate, and automatic 3D detection of neural activity from densely packed neurons.PloS one · 2024Article
- A cGAL-UAS bipartite expression toolkit forProceedings of the National Academy of Sciences of the United States of America · 2023Article
- WormTensor: a clustering method for time-series whole-brain activity data from C. elegans.BMC bioinformatics · 2023Article
- Article
- Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans.PLoS computational biology · 2022Article
- Article
- Toward a more accurate 3D atlas of C. elegans neurons.BMC bioinformatics · 2022Article
- Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAnnotation of cell identity is an essential process in neuroscience that allows comparison of cells, including that of neural activities across different animals. In Caenorhabditis elegans, although unique identities have been assigned to all neurons, the number of annotatable neurons in an intact animal has been limited due to the lack of quantitative information on the location and identity of neurons.
resultsHere, we present a dataset that facilitates the annotation of neuronal identities, and demonstrate its application in a comprehensive analysis of whole-brain imaging. We systematically identified neurons in the head region of 311 adult worms using 35 cell-specific promoters and created a dataset of the expression patterns and the positions of the neurons. We found large positional variations that illustrated the difficulty of the annotation task. We investigated multiple combinations of cell-specific promoters driving distinct fluorescence and generated optimal strains for the annotation of most head neurons in an animal. We also developed an automatic annotation method with human interaction functionality that facilitates annotations needed for whole-brain imaging.
conclusionOur neuron ID dataset and optimal fluorescent strains enable the annotation of most neurons in the head region of adult C. elegans, both in full-automated fashion and a semi-automated version that includes human interaction functionalities. Our method can potentially be applied to model species used in research other than C. elegans, where the number of available cell-type-specific promoters and their variety will be an important consideration.
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