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          Institute: MPI für molekulare Zellbiologie und Genetik     Collection: MPI-CBG Publications 2014 (arch)     Display Documents

ID: 705778.0, MPI für molekulare Zellbiologie und Genetik / MPI-CBG Publications 2014 (arch)
Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.
Authors:Rizk, Aurelien; Paul, Gregory; Incardona, Pietro; Bugarski, Milica; Mansouri, Maysam; Niemann, Axel; Ziegler, Urs; Berger, Philipp; Sbalzarini, Ivo F.
Date of Publication (YYYY-MM-DD):2014
Title of Journal:Nature Protocols
Issue / Number:3
Start Page:586
End Page:596
Copyright:not available
Audience:Experts Only
Intended Educational Use:No
Abstract / Description:Detection and quantification of fluorescently labeled molecules in subcellular compartments is a key step in the analysis of many cell biological processes. Pixel-wise colocalization analyses, however, are not always suitable, because they do not provide object-specific information, and they are vulnerable to noise and background fluorescence. Here we present a versatile protocol for a method named 'Squassh' (segmentation and quantification of subcellular shapes), which is used for detecting, delineating and quantifying subcellular structures in fluorescence microscopy images. The workflow is implemented in freely available, user-friendly software. It works on both 2D and 3D images, accounts for the microscope optics and for uneven image background, computes cell masks and provides subpixel accuracy. The Squassh software enables both colocalization and shape analyses. The protocol can be applied in batch, on desktop computers or computer clusters, and it usually requires <1 min and <5 min for 2D and 3D images, respectively. Basic computer-user skills and some experience with fluorescence microscopy are recommended to successfully use the protocol.
External Publication Status:published
Document Type:Article
Communicated by:thuem
Affiliations:MPI für molekulare Zellbiologie und Genetik
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