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Related Concept Videos

Membrane Lipids01:32

Membrane Lipids

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Lipids are an essential component of all biological membranes. The average lipid content in mammalian membranes is 50%, though it can be as low as 20% in the inner mitochondrial membrane or as high as 80% in the myelin sheath present around the nerve cells.
Phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin are the most common phospholipids present in mammalian membranes. At physiological pH, phosphatidylserine is negatively charged, while the other three...
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Shape and Texture of Coarse Aggregate01:25

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Aggregate shape is classified based on the relative sharpness or roundness of the edges and corners. This classification includes categories like rounded, angular, elongated, and flaky, each with specific characteristics. Rounded aggregates, fully shaped by attrition, are typical of river or seashore gravel, while angular aggregates, such as crushed rock, have well-defined edges. Aggregates that are elongated and flaky are less desirable, as they can reduce the workability and strength of...
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What are Lipids?01:38

What are Lipids?

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Overview
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What are Lipids?01:31

What are Lipids?

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Lipids function as structural components of cellular membranes, in addition to acting as energy reservoirs and signaling molecules. They are thus crucial to all living organisms.  The three biologically important classes of lipids are triglycerides, phospholipids, and steroids.
Non-Polar and Hydrophobic Characteristics of Lipids
Lipids are a structurally and functionally diverse group of hydrocarbons—compounds consisting of carbon and hydrogen atoms. The carbon-carbon and...
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Structure of Lipids03:38

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Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon-carbon or carbon-hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic...
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Lipid Digestion01:06

Lipid Digestion

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Lipids are large molecules that are generally not water-soluble. Since most of the digestive enzymes in the human body are water-based, there are specific steps the body must take to break down lipids and make them available for use.
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Related Experiment Video

Updated: Jan 31, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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LimeSeg: a coarse-grained lipid membrane simulation for 3D image segmentation.

Sarah Machado1, Vincent Mercier2, Nicolas Chiaruttini3

  • 1Marcos González Gaitán lab, University of Geneva, Department of Biochemistry, quai Ernest-Ansermet 30, Geneva, 1211, Switzerland.

BMC Bioinformatics
|January 5, 2019
PubMed
Summary

We developed LimeSeg, an efficient 3D segmentation method using SURFace ELements (Surfels) for processing complex biological images. This new tool enables simultaneous segmentation of multiple, convoluted objects, improving bioimage analysis workflows.

Keywords:
3D segmentationCell membrane segmentationCell surfaceCell volumeImageJPoint-cloudSurfel-based

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Area of Science:

  • Bioimage analysis
  • Computational imaging
  • 3D reconstruction

Background:

  • 3D segmentation is crucial for 3D object display and measurements.
  • Existing voxel-based methods lack surface and topology information.
  • Continuous methods struggle with multiple or irregular object segmentation.

Purpose of the Study:

  • To develop a computationally efficient and spatially continuous 3D segmentation method.
  • To create a user-friendly tool for segmenting numerous and/or convoluted objects.
  • To address limitations of existing 3D segmentation approaches in bioimage analysis.

Main Methods:

  • Developed LimeSeg, a novel 3D segmentation method based on SURFace ELements (Surfels).
  • LimeSeg simulates a lipid membrane with self-generating/destructing particles attracted to image maxima.
  • The method allows for dynamic evolution of the segmentation surface towards object contours.

Main Results:

  • LimeSeg enables simultaneous segmentation of numerous non-overlapping objects.
  • The method successfully segments highly convoluted objects.
  • Demonstrated robustness on large datasets including epithelial cells, brain MRI, and FIB-SEM data.

Conclusions:

  • Implemented an efficient 3D surface reconstruction plugin, LimeSeg.
  • The plugin is adapted for diverse image sources and user-friendly.
  • LimeSeg is deployed within the ImageJ environment for broad accessibility.