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Related Concept Videos

Cells of the Epidermis01:24

Cells of the Epidermis

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The epidermis is made of four or five layers of epithelial cells, depending on its location in the body. From deep to superficial, these layers are the stratum basale, stratum spinosum, stratum granulosum, stratum lucidum, and stratum corneum.
The cells in all these layers except the stratum basale are called keratinocytes, a type of cell that manufactures and stores the protein keratin. The keratinocytes in the stratum corneum are dead and regularly slough away, being replaced by cells from...
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Layers of the Epidermis01:21

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The epidermis, the outermost layer of the skin, is composed of several distinct layers. From deep to superficial, the layers of the epidermis are as follows:
Stratum Basale
Stratum basale, also known as the stratum germinativum, is the deepest layer of the epidermis. It is composed of a single layer of actively dividing cells called basal cells or basal keratinocytes. These cells constantly undergo cell division to replenish the upper layers of the epidermis. Additionally, melanocytes, which...
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Design Example: Joints in Concrete Pavements01:28

Design Example: Joints in Concrete Pavements

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Concrete pavement joints are essential for maintaining the structural integrity and longevity of pavement by controlling where and how the pavement cracks. These joints can be categorized based on their functions, such as contraction or control joints, construction joints, isolation joints, and expansion joints.
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Microbial Morphologies01:29

Microbial Morphologies

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Bacterial and archaeal cells exhibit remarkable diversity in shape and structure, critical in their adaptability and functionality. Among bacteria, the most commonly observed shapes include cocci and bacilli. Cocci are spherical and may exist singly or in groupings such as pairs (diplococci), chains (streptococci), clusters (staphylococci), or tetrads. Bacilli, in contrast, are rod-shaped and can also occur as single cells, in pairs, or chains, depending on their environmental and genetic...
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Plant Cells and Tissues02:01

Plant Cells and Tissues

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Plant tissues are collections of similar cells performing related functions. Different plant tissues will have their own specialized roles and can be combined with other tissues to form organs such as flowers, fruit, stem, and leaves. Two major types of plant tissue include meristematic and permanent tissue.
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Qualitative Analysis03:46

Qualitative Analysis

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For solutions containing mixtures of different cations, the identity of each cation can be determined by qualitative analysis. This technique involves a series of selective precipitations with different chemical reagents, each reaction producing a characteristic precipitate for a specific group of cations. Metal ions within a group are further separated by varying the pH, heating the mixture to redissolve a precipitate, or adding other reagents to form complex ions.
For instance, group IV...
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Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development
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Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant.

Birgit Möller1, Yvonne Poeschl1,2, Sandra Klemm3

  • 1Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.

Methods in Molecular Biology (Clifton, N.J.)
|June 1, 2019
PubMed
Summary

PaCeQuant is a new ImageJ plugin and R package for automatic cell shape analysis. It quantifies cell shape descriptors from 2D images, aiding in plant pavement cell research.

Keywords:
Confocal laser scanning microscopyEpidermisImageJ/FijiLeaf morphogenesisPaCeQuantPavement cell shapeR software

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Area of Science:

  • Plant biology
  • Computational biology
  • Image analysis

Background:

  • Accurate cell shape analysis is crucial for understanding cell characteristics.
  • Existing methods for cell segmentation and feature extraction can be complex and time-consuming.

Purpose of the Study:

  • To introduce PaCeQuant, an ImageJ plugin, and PaCeQuantAna, an R package, for automated cell shape analysis.
  • To provide a comprehensive pipeline for segmentation, feature extraction, statistical analysis, and visualization of cell shape properties.

Main Methods:

  • Development of the PaCeQuant ImageJ plugin for image segmentation.
  • Creation of the PaCeQuantAna R package for statistical analysis and visualization.
  • Implementation of automated workflows for global, contour-based, skeleton-based, and pavement cell-specific shape descriptors.

Main Results:

  • PaCeQuant enables fully automatic segmentation and feature extraction of cell shapes.
  • The software is particularly effective for analyzing jigsaw puzzle-like leaf epidermis pavement cells.
  • Quantitative assessment of diverse cell shape properties is supported.

Conclusions:

  • PaCeQuant and PaCeQuantAna offer an efficient and accessible solution for cell shape analysis.
  • This tool facilitates both qualitative and quantitative evaluation of cell morphology.
  • The pipeline supports research in plant biology and related fields requiring detailed shape characterization.