WatershedCounting3D: A New Method for Segmenting and Counting Punctate Structures from Confocal Image Data

Current research in cell biology frequently uses light microscopy to study intracellular organelles. To segment and count organelles, most investigators have used a global thresholding method, which relies on homogeneous background intensity values within a cell. Because this is not always the case,...

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Bibliographic Details
Published in:Traffic (Copenhagen, Denmark) Denmark), 2007-04, Vol.8 (4), p.339-346
Main Authors: Gniadek, Thomas J., Warren, Graham
Format: Article
Language:English
Subjects:
Algorithms
Animals
Cell Line
Cercopithecus aethiops
confocal
ER exit site
Golgi
Golgi Apparatus
Image Interpretation, Computer-Assisted
Microscopy, Confocal
segmentation
Software
watershed algorithm
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Summary:Current research in cell biology frequently uses light microscopy to study intracellular organelles. To segment and count organelles, most investigators have used a global thresholding method, which relies on homogeneous background intensity values within a cell. Because this is not always the case, we developed WatershedCounting3D, a program that uses a modified watershed algorithm to more accurately identify intracellular structures from confocal image data, even in the presence of an inhomogeneous background. We give examples of segmenting and counting endoplasmic reticulum exit sites and the Golgi apparatus.
ISSN:1398-9219
1600-0854
DOI:10.1111/j.1600-0854.2007.00538.x