Co-localisation
Fraught term. Consider also these:
co-occurence
correlation, spatial (temporal is rarely studied)
co-variation
There are two main categories: object-based and intensity-based. Mixed versions exist.
Web-pages
General intro (read this first)
Commercial software and support
Colocalization Benchmark Source
Wiki page(s)
Quantitative Imaging for Colocalization Analysis
Slides from NEUBIAS 2019, by Dominic Waithe
Software
Tesseler?
Paper in revision in 2019-Q1
Florian Levet from NEUBIAS
Uses Mander's coefficients on scatter plots from a Voronoi diagram of images, centered on detected objects
Not to be confused with 2015 paper and software "TR-Tesseler"
Imaris
Colocalisation toolkit
Essentially Manders with Costes
Not recommended
Fiji plugins
Coloc2
Intensity based
JACoP2 (just another co-localisation plugin)
“This plug-in is a compilation of co-localization tools.”
Several intensity based methods
Two, simple, object based methods
Works in 2D and 3D
ICY
ColocalizationStudio
http://icy.bioimageanalysis.org/plugin/Colocalization_Studio
Includes possibility for simulating data
Localisation based
Can be restricted to regions of interest
GcoPS software
Wbpage: http://serpico.rennes.inria.fr/doku.php?id=software:gcops:gcops
PDF: http://serpico.rennes.inria.fr/lib/exe/fetch.php?media=software:gcops:gcops-notice.pdf
“GcoPS is non parametric and allows to quantify the colocalization between two images. Given a 2D/3D segmented image for each channel, GcoPS tests whether the Pearson correlation between the two binary images is significantly positive. This procedure is only controlled by a p-value.”
Requires binary 2D or 3D images
Search results on www.biii.eu
Papers
Spatially Adaptive Colocalization Analysis in Dual-Color Fluorescence Microscopy
2017 preprint
ImageJ plugin mentioned as coming, at some point
"quantify colocalization levels at each individual location and automatically identify pixels or regions where colocalization occurs."
Intensity based
Very mathematical
Chapter 21 - Experimenters' guide to colocalization studies: Finding a way through indicators and quantifiers, in practice
https://www.sciencedirect.com/science/article/pii/B9780124201385000215?via%3Dihub
2014 paper
Pedagogical review of existing methods, both pixel-intensity and object based
Distinguishes between indicators and quantifiers
Manders, Pearson, Costes, overlap, Spearman,
Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics
2018 paper
Object based spatial statistics
Statistical Analysis of Molecule Colocalization in Bioimaging
2015 paper
Review of object based spatial statistics and pixel-based methods
Automated and Robust Quantification of Colocalization in Dual-Color Fluorescence Microscopy: A Nonparametric Statistical Approach
2017 paper
New, non-parametric, approach to intensity based colocalisation, including tests that scramble pixel-regions
Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy image
2010 paper
Ivo Sbalzarini
A Guide to Accurate Fluorescence Microscopy Colocalization Measurements
https://www.sciencedirect.com/science/article/pii/S0006349506721737
2006 paper
Compares standard to Spatial image cross-correlation spectroscopy (ICCS)
Intensity based
A practical guide to evaluating colocalization in biological microscopy
2011 paper
Guide/review with links to existing tools
Intensity based: Pearson’s, Manders, and their statistical significance