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Updated: May 5, 2026
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Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging
Published on: April 30, 2019
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Segmentation and quantitative analysis of individual cells in developmental tissues
Kaustav Nandy1, Jusub Kim, Dean P McCullough
1Optical Microscopy and Analysis Laboratory, SAIC, Frederick National Lab of Cancer Research, NCI, NIH, Frederick, MD, USA.
Methods in Molecular Biology (Clifton, N.J.)
|December 10, 2013
Summary
This chapter details image segmentation techniques for biological research. It explains using free software like ImageJ, MIPAV, and VisSeg for accurate object delineation in 2D and 3D images.
Area of Science:
- Biological imaging
- Developmental biology
- Quantitative image analysis
Background:
- Image analysis is crucial for extracting quantitative data from biological images.
- Segmentation, the delineation of objects, is the first step in image analysis.
- This process is widely applied in fields like developmental biology.
Purpose of the Study:
- To focus on the critical image segmentation task.
- To explain the utilization of three freely available software packages for segmentation.
- To highlight the capabilities of ImageJ, MIPAV, and VisSeg.
Main Methods:
- Explaining the use of ImageJ for versatile image segmentation.
- Detailing the application of MIPAV (Medical Image Processing, Analysis, and Visualization) for image analysis.
- Demonstrating VisSeg for specialized and accurate 2D and 3D object segmentation.
Main Results:
- ImageJ and MIPAV offer versatility for diverse segmentation applications.
- VisSeg provides highly accurate and reliable segmentation of cells and cell nuclei.
- All discussed software packages are freely available for use.
Conclusions:
- Effective image segmentation is essential for biological research.
- Freely available tools like ImageJ, MIPAV, and VisSeg facilitate accurate image analysis.
- The choice of software depends on the specific segmentation requirements, with VisSeg offering specialized accuracy.
