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Quantifying colocalization: thresholding, void voxels and the H-coef
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
2014 (English)In: PLoS ONE, ISSN 1932-6203, Vol. 9, no 11, e111983- p.Article in journal (Refereed) Published
Abstract [en]

A critical step in the analysis of images is identifying the area of interest e.g. nuclei. When the nuclei are brighter than the remainder of the image an intensity can be chosen to identify the nuclei. Intensity thresholding is complicated by variations in the intensity of individual nuclei and their intensity relative to their surroundings. To compensate thresholds can be based on local rather than global intensities. By testing local thresholding methods we found that the local mean performed poorly while the Phansalkar method and a new method based on identifying the local background were superior. A new colocalization coefficient, the Hcoef, highlights a number of controversial issues. (i) Are molecular interactions measurable (ii) whether to include voxels without fluorophores in calculations, and (iii) the meaning of negative correlations. Negative correlations can arise biologically (a) because the two fluorophores are in different places or (b) when high intensities of one fluorophore coincide with low intensities of a second. The cases are distinct and we argue that it is only relevant to measure correlation using pixels that contain both fluorophores and, when the fluorophores are in different places, to just report the lack of co-occurrence and omit these uninformative negative correlation. The Hcoef could report molecular interactions in a homogenous medium. But biology is not homogenous and distributions also reflect physico-chemical properties, targeted delivery and retention. The Hcoef actually measures a mix of correlation and co-occurrence, which makes its interpretation problematic and in the absence of a convincing demonstration we advise caution, favouring separate measurements of correlation and of co-occurrence.

Place, publisher, year, edition, pages
2014. Vol. 9, no 11, e111983- p.
National Category
Cell Biology
Research subject
Biology with specialization in Molecular Cell Biology
URN: urn:nbn:se:uu:diva-235777DOI: 10.1371/journal.pone.0111983PubMedID: 25375829OAI: oai:DiVA.org:uu-235777DiVA: diva2:761963
Available from: 2014-11-10 Created: 2014-11-10 Last updated: 2014-12-25Bibliographically approved

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Adler, JeremyParmryd, Ingela
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Science for Life Laboratory, SciLifeLabDepartment of Immunology, Genetics and PathologyDepartment of Medical Cell Biology
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