title: WatershedCounting3D: a new method for segmenting and counting punctate structures from confocal image data.
abstract: 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.
authors.affiliation: Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, PO Box 208002, New Haven, CT 06520-8002, USA. thomas.gniadek@yale.edu
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Gniadek
authors.forename: Graham
authors.initials: G
authors.lastname: Warren
mesh_terms: D000465:Algorithms; D000818:Animals; D002460:Cell Line; D002522:Chlorocebus aethiops; D006056:Golgi Apparatus; D007090:Image Interpretation, Computer-Assisted; D018613:Microscopy, Confocal; D012984:Software