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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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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creator Gniadek, Thomas J.
Warren, Graham
description 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.
doi_str_mv 10.1111/j.1600-0854.2007.00538.x
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source Wiley-Blackwell Read & Publish Collection
subjects Algorithms
Animals
Cell Line
Cercopithecus aethiops
confocal
ER exit site
Golgi
Golgi Apparatus
Image Interpretation, Computer-Assisted
Microscopy, Confocal
segmentation
Software
watershed algorithm
title WatershedCounting3D: A New Method for Segmenting and Counting Punctate Structures from Confocal Image Data
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