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PMID: 18461488 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Review

Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls.

Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology ·Vol. 16 ·No. 3 ·2008-00-00 ·Pages 523-62

Ronneberger O, Baddeley D, Scheipl F, Verveer PJ, Burkhardt H, Cremer C, Fahrmeir L, Cremer T, Joffe B

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.

MeSH Terms
Cell Nucleus/genetics,metabolism,ultrastructure Fluorescent Dyes Humans Image Processing, Computer-Assisted Laser Scanning Cytometry/methods Microscopy, Confocal/methods,statistics & numerical data Microscopy, Fluorescence/methods Microscopy, Fluorescence, Multiphoton/methods Principal Component Analysis
Chemicals
Fluorescent Dyes
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Ronneberger O
Department of Pattern Recognition and Image Processing, University of Freiburg, 79110, Freiburg, Germany.
Baddeley D
Scheipl F
Verveer P J
Burkhardt H
Cremer C
Fahrmeir L
Cremer T
Joffe B
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Article Info
Journal
Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology
Abbr.
Chromosome Res
ISSN
0967-3849
DOI
10.1007/s10577-008-1236-4
Published
2008-00-00
Pages
523-62
Language
English
Region
Netherlands
NLM ID
9313452
Subset
IM
External Links
PubMed source DOI: 10.1007/s10577-008-1236-4 View journal details
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