Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls.
Document Type
Article
Publication Date
2008
Keywords
Fluorescent-Dyes, Humans, Image-Processing-Computer-Assisted, Laser-Scanning-Cytometry, Microscopy-Confocal, Microscopy-Fluorescence, Microscopy-Fluorescence-Multiphoton, Principal-Component-Analysis
First Page
523
Last Page
562
JAX Source
Chromosome Res 2008; 16(3):523-62.
Abstract
The vast majority of microscopic data in biology of the cell nucleus is currently collected using fluorescence microscopy, and most of these data are subsequently subjected to quantitative analysis. The analysis process unites a number of steps, from image acquisition to statistics, and at each of these steps decisions must be made that may crucially affect the conclusions of the whole study. This often presents a really serious problem because the researcher is typically a biologist, while the decisions to be taken require expertise in the fields of physics, computer image analysis, and statistics. The researcher has to choose between multiple options for data collection, numerous programs for preprocessing and processing of images, and a number of statistical approaches. Written for biologists, this article discusses some of the typical problems and errors that should be avoided. The article was prepared by a team uniting expertise in biology, microscopy, image analysis, and statistics. It considers the options a researcher has at the stages of data acquisition (choice of the microscope and acquisition settings), preprocessing (filtering, intensity normalization, deconvolution), image processing (radial distribution, clustering, co-localization, shape and orientation of objects), and statistical analysis.
Recommended Citation
Ronneberger O,
Baddeley D,
Scheipl F,
Verveer PJ,
Burkhardt H,
Cremer C,
Fahrmeir L,
Cremer T,
Joffe B.
Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls. Chromosome Res 2008; 16(3):523-62.