Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh
| Autor: | Axel Niemann, Pietro Incardona, Maysam Mansouri, Ivo F. Sbalzarini, Aurélien Rizk, Gregory Paul, Philipp Berger, Milica Bugarski, Urs Ziegler |
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| Rok vydání: | 2014 |
| Předmět: |
Fluorescence-lifetime imaging microscopy
Microscope Computer science business.industry Colocalization Pattern recognition Image processing Subpixel rendering General Biochemistry Genetics and Molecular Biology law.invention Microscopy Fluorescence law Microscopy Image Processing Computer-Assisted Fluorescence microscope Segmentation Artificial intelligence business Software Subcellular Fractions |
| Zdroj: | Nature Protocols. 9:586-596 |
| ISSN: | 1750-2799 1754-2189 |
| Popis: | 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 |
| Databáze: | OpenAIRE |
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