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)

  • https://imagej.net/Colocalization_Analysis

• Commercial software and support

  • https://www.colocalizer.com

• Colocalization Benchmark Source

  • https://www.colocalization-benchmark.com

  • https://en.wikipedia.org/wiki/Colocalization_Benchmark_Source

• Wiki page(s)

  • https://en.wikipedia.org/wiki/Colocalization

• Quantitative Imaging for Colocalization Analysis

  • https://www.biodip.de/w/images/f/fa/QuantitativeColocAnalysis-10-2011.pdf

• Slides from NEUBIAS 2019, by Dominic Waithe

  • https://drive.google.com/file/d/1MiL-RXIb9R9T1qh6hl8dk_Ss0vXMdlnR/view

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

    • https://imagej.net/Coloc_2

    • Intensity based

  • JACoP2 (just another co-localisation plugin)

    • http://imagejdocu.tudor.lu/doku.php?id=plugin%3Aanalysis%3Ajacop_2.0%3Ajust_another_colocalization_plugin%3Astart

    • “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

    • ICY: http://icy.bioimageanalysis.org/plugin/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

    • http://biii.eu/search?search_api_fulltext=colocalization

Papers

• Spatially Adaptive Colocalization Analysis in Dual-Color Fluorescence Microscopy

  • https://arxiv.org/abs/1711.00069

  • 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

  • http://dx.doi.org/10.1038/s41467-018-03053-x

  • 2018 paper

  • Object based spatial statistics

• Statistical Analysis of Molecule Colocalization in Bioimaging

  • http://doi.wiley.com/10.1002/cyto.a.22629

  • 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

  • https://ieeexplore.ieee.org/abstract/document/8070393

  • 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

  • http://www.biomedcentral.com/1471-2105/11/372

  • 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

  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074624/

  • 2011 paper

  • Guide/review with links to existing tools

  • Intensity based: Pearson’s, Manders, and their statistical significance