ArticleNature methods2025
Nellie: automated organelle segmentation, tracking and hierarchical feature extraction in 2D/3D live-cell microscopy.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- GPU-accelerated MitoGraph for high-throughput three-dimensional mitochondrial morphology analysis.BMC bioinformatics · 2026Article
- Metformin Redirects Autophagy from Bulk Turnover to Mitochondrial Clearance.bioRxiv : the preprint server for biology · 2026Article
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- RoundMi: A quantitative method to analyze mitochondrial morphology in mitotic cells.FEBS open bio · 2026Article
- Enhancing biomedical optical volumetric imaging via self-supervised orthogonal learning.Science advances · 2026Article
- Potassium ion homeostasis modulates mitochondrial function.The Journal of cell biology · 2026Article
- 3D Mitochondria Shape Library for Optical Microscopy (3DMSL): A multimodal dataset for deep learning based mitochondrial analysis.Data in brief · 2026Article
- Integrating Human Intestinal Organoids into FDA's New Approach Methodologies for Drug Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- A foundation model for multi-task cross-distribution restoration of fluorescence microscopy images.Nature communications · 2026Article
- Machine Learning-Assisted Quantification of Organelle Abundance.Bio-protocol · 2026Article
- Review
- Targeting organelle function in T cells for cancer immunotherapy.Nature reviews. Immunology · 2026Review
- Cooperative Architecture of Mitochondrial Proteome Homeostasis.medRxiv : the preprint server for health sciences · 2026Article
- Systematic evaluation of computational methods for cell segmentation.Briefings in bioinformatics · 2026Article
- Mitochondrial fission and fusion in inflammatory diseases: mechanisms and therapeutic implications.Journal of translational medicine · 2025Review
- Controlling lipid droplet dynamics via tether condensates.Nature chemical biology · 2025Article
- Article
- RHOA-dependent regulation of mitochondrial remodeling and cell motility in hypoxia-exposed gastric epithelial cells.Journal of cell science · 2025Article
- Article
- MitoLandscape, a semi-automated pipeline for subcellular localization and quantification of mitochondria.Frontiers in cell and developmental biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cellular organelles undergo constant morphological changes and dynamic interactions that are fundamental to cell homeostasis, stress responses and disease progression. Despite their importance, quantifying organelle morphology and motility remains challenging due to their complex architectures, rapid movements and the technical limitations of existing analysis tools. Here we introduce Nellie, an automated and unbiased pipeline for segmentation, tracking and feature extraction of diverse intracellular structures. Nellie adapts to image metadata and employs hierarchical segmentation to resolve sub-organellar regions, while its radius-adaptive pattern matching enables precise motion tracking. Through a user-friendly Napari-based interface, Nellie enables comprehensive organelle analysis without coding expertise. We demonstrate Nellie's versatility by unmixing multiple organelles from single-channel data, quantifying mitochondrial responses to ionomycin via graph autoencoders and characterizing endoplasmic reticulum networks across cell types and time points. This tool addresses a critical need in cell biology by providing accessible, automated analysis of organelle dynamics.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.