ArticleBMC bioinformatics2019
LimeSeg: a coarse-grained lipid membrane simulation for 3D image segmentation.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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
38 citing papers in PubMed.
- Reviewing reproducibility and replicability in 'Deconstructing gastrulation at single-cell resolution' by Stern et al. (2022).Journal of microscopy · 2026Review
- Nuclear size and physical properties of the nucleoplasm are determined by colloid osmotic pressure at the nuclear envelope.bioRxiv : the preprint server for biology · 2026Article
- Cells Dynamically Adapt Their Nuclear Volumes and Proliferation Rates During Single to Multicellular Transitions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Permeability-driven pressure and cell proliferation control lumen morphogenesis in pancreatic organoids.Nature cell biology · 2026Article
- From Shallow to Full Wrapping: Geometry and Deformability Dictate Lipid Vesicle Internalization.Nano letters · 2025Article
- Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells.Nature cell biology · 2025Article
- Timely neurogenesis drives the transition from nematic to crystalline nuclear packing during retinal morphogenesis.Science advances · 2025Article
- Synthetic photoresponsive hydrogels enableAdvanced functional materials · 2025Article
- Article
- Emerin deficiency drives MCF7 cells to an invasive phenotype.bioRxiv : the preprint server for biology · 2024Article
- Plasma membrane nanodeformations promote actin polymerization through CIP4/CDC42 recruitment and regulate type II IFN signaling.Science advances · 2023Article
- Quantifying turgor pressure in budding and fission yeasts based upon osmotic properties.Molecular biology of the cell · 2023Article
- CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia.Cell reports methods · 2023Article
- Article
- Quantifying turgor pressure in budding and fission yeasts based upon osmotic properties.bioRxiv : the preprint server for biology · 2023Article
- From cells to form: A roadmap to study shape emergence in vivo.Biophysical journal · 2023Review
- Active mesh and neural network pipeline for cell aggregate segmentation.Biophysical journal · 2023Article
- UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape.Membranes · 2023Article
- Ultrastructure of COPII vesicle formation in yeast characterized by correlative light and electron microscopy.Molecular biology of the cell · 2022Article
- Cellular shape reinforces niche to stem cell signaling in the small intestine.Science advances · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
background3D segmentation is often a prerequisite for 3D object display and quantitative measurements. Yet existing voxel-based methods do not directly give information on the object surface or topology. As for spatially continuous approaches such as level-set, active contours and meshes, although providing surfaces and concise shape description, they are generally not suitable for multiple object segmentation and/or for objects with an irregular shape, which can hamper their adoption by bioimage analysts.
resultsWe developed LimeSeg, a computationally efficient and spatially continuous 3D segmentation method. LimeSeg is easy-to-use and can process many and/or highly convoluted objects. Based on the concept of SURFace ELements ("Surfels"), LimeSeg resembles a highly coarse-grained simulation of a lipid membrane in which a set of particles, analogous to lipid molecules, are attracted to local image maxima. The particles are self-generating and self-destructing thus providing the ability for the membrane to evolve towards the contour of the objects of interest. The capabilities of LimeSeg: simultaneous segmentation of numerous non overlapping objects, segmentation of highly convoluted objects and robustness for big datasets are demonstrated on experimental use cases (epithelial cells, brain MRI and FIB-SEM dataset of cellular membrane system respectively).
conclusionIn conclusion, we implemented a new and efficient 3D surface reconstruction plugin adapted for various sources of images, which is deployed in the user-friendly and well-known ImageJ environment.
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.