Voxel-based colocalisation
Pixel-based colocalization
Pixel-based co-localisation
Manders coefficient

SODA suite


Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions

Icy SODA logo



Computer-assisted Evaluation of Myelin formation (CEM) is a collection designed to automate myelin quantification. It requires use input to choose the best threshold values. The myelin is calculated as an overlap between neuronal signal and oligodendrocyte signal. Results are given as pixel counts and percents.

CEM runs as an imageJ plugin with an optional Matlab extension to remove cell bodies. More details are published at Kerman et al. 2015 Development. Supplemental Material includes a detailed user manual and the download link.




This ImageJ plug-in is a compilation of co-localization tools. It allows:

-Calculating a set of commonly used co-localization indicators:

Pearson's coefficient Overlap coefficient k1 & k2 coefficients Manders' coefficient Generating commonly used visualizations:


Having access to more recently published methods:

-Costes' automatic threshold

Li's ICA Costes' randomization Objects based methods (2 methods: distances between centres and centre-particle coincidence)

example of partial colocalisation from reference publication

Coloc 2



Coloc 2 is Fiji's plugin for colocalization analysis. It implements and performs the pixel intensity correlation over space methods of PearsonMandersCostesLi and more, for scatterplots, analysis, automatic thresholding and statistical significance testing.

Coloc 2 does NOT perform object based colocalization measurements, where objects are first segmented from the image, then their spatial relationships like overlap etc. are measured. This complementary approach is implemented in many ways elsewhere.


ICY Colocalization Scatter Plot


ICY Plugin, creates a colocalization scatter plot based on 2 channels. This plugin can take 1 ROI as input, and provides the data to build the bubble excel graph.

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