ArticlePLoS computational biology2016
Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- ThebioRxiv : the preprint server for biology · 2026Article
- Developing a Robust Multiround HCR-FISH Method Modified for Caenorhabditis elegans.Genes to cells : devoted to molecular & cellular mechanisms · 2026Article
- Layer-specific cellular composition of mouse primary somatosensory and human temporal cortex: a direct 3D confocal counting approach.Frontiers in neuroanatomy · 2026Article
- Enhanced whole-brain calcium imaging and cell identification inJournal of biosciences · 2025Article
- Aberrant Positions of the Chemosensory Neurons in the Neurotransmitter-Release MutantInternational journal of molecular sciences · 2024Article
- Intricate response dynamics enhances stimulus discrimination in the resource-limited C. elegans chemosensory system.BMC 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
- See Elegans: Simple-to-use, accurate, and automatic 3D detection of neural activity from densely packed neurons.PloS one · 2024Article
- Deep Learning-Based Cell Tracking in Deforming Organs and Moving Animals.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation.Nature methods · 2024Article
- Statistically unbiased prediction enables accurate denoising of voltage imaging data.Nature methods · 2023Article
- Article
- A comprehensive review of computational and image analysis techniques for quantitative evaluation of striated muscle tissue architecture.Biophysics reviews · 2022Review
- Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans.PLoS computational biology · 2022Article
- Fast, efficient, and accurate neuro-imaging denoising via supervised deep learning.Nature communications · 2022Article
- Efficient automatic 3D segmentation of cell nuclei for high-content screening.BMC bioinformatics · 2022Article
- A novel jamming phase diagram links tumor invasion to non-equilibrium phase separation.iScience · 2021Article
- Article
- 3DeeCellTracker, a deep learning-based pipeline for segmenting and tracking cells in 3D time lapse images.eLife · 2021Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To measure the activity of neurons using whole-brain activity imaging, precise detection of each neuron or its nucleus is required. In the head region of the nematode C. elegans, the neuronal cell bodies are distributed densely in three-dimensional (3D) space. However, no existing computational methods of image analysis can separate them with sufficient accuracy. Here we propose a highly accurate segmentation method based on the curvatures of the iso-intensity surfaces. To obtain accurate positions of nuclei, we also developed a new procedure for least squares fitting with a Gaussian mixture model. Combining these methods enables accurate detection of densely distributed cell nuclei in a 3D space. The proposed method was implemented as a graphical user interface program that allows visualization and correction of the results of automatic detection. Additionally, the proposed method was applied to time-lapse 3D calcium imaging data, and most of the nuclei in the images were successfully tracked and measured.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.