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Which Elements to Build Co-localization Workflows? From Metrology to Analysis

  • Patrice Mascalchi
  • Fabrice P. CordelièresEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2040)

Abstract

Co-localization analysis is one of the main interests of users entering a facility with slides in hands and nice analysis perspectives in mind. While being available through most, if not all, analysis software, co-localization tools are mainly perceived as black boxes, fed with images, that will, hopefully, return (the expected) numbers.

In this chapter, we will aim at deconstructing existing generic co-localization workflows, extracting elementary tools that may be reused and recombined to generate new workflows. By differentiating work cases, identifying co-localization reporters and the metrics others have been using, we aim at providing the audience with the elementary bricks and methods to build their really own co-localization workflows. A special emphasis is given on the preparatory phase where the acquisition system is assessed, using basic metrological tests.

Key words

Co-localization Co-expression Co-occurrence Correlation Co-distribution Elements Workflow Image processing Image analysis 

Notes

Acknowledgment

The Bordeaux Imaging Center is a service unit of the CNRS-INSERM and Bordeaux University, member of the national infrastructure France BioImaging supported by the French National Research Agency (ANR-10-INBS-04). FPC is a member of NEUBIAS (Network for European Bioimage Analysts), COST Action CA15124. Figures have been assembled using ImageJ’s FigureJ plugin [78].

Supplementary material

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Bordeaux Imaging CenterUMS 3420 CNRS—Université de Bordeaux—US4 INSERM, Pôle d’imagerie photonique, Centre Broca Nouvelle-AquitaineBordeauxFrance

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