Colocalization Analyzer

With colocalization analysis for fluorescence microscopy you can obtain quantitative information about the amount of spatial overlap between structures in different channels for 3D images and 3D-time series.

As the spatial overlap can be defined in many ways, the Huygens Colocalization Analyzer gives you eleven different colocalization coefficients most commonly used in literature that are part of the following major groups:
  • Pearson
  • Spearman
  • Overlap
  • The coefficients due to Manders M1,2 and K1,2
  • intersection coefficients
  • Li's ICQ
  • van Steensel's CCF

For more information about the mathematics behind the coefficients see Colocalization Theory. For a thorough explanation on colocalization and how the coefficients are influenced by imaging artifacts, see Colocalization Basics. Colocalization analysis is available in Huygens Essential and Huygens Professional as a very intuitive and interactive option. Colocalization analysis in Huygens Core via it's web-interface Huygens Remote Manager (HRM) is optimally suited for high-content and high-throughput analysis.

Colocalization analysis with Huygens Essential and Professional

Colocalization analysis has been available in Huygens from version 3.0 onwards. Since version 18.10, the Colocalization Analyzer option includes three different modes namely Wizard, Advanced, and Compact.


With any of these modes, you can:
  • select your channels,
  • select a specific time frame or calculate the coefficients for all time frames at once,
  • set the thresholds using one of the "Estimation Methods" or the 2D-histogram or the histogram per colorchannel, using the togglebutton,
  • look at the 2D histogram more closely using the magnifier, by clicking on the histogram,
  • save the 2D histogram with or without the background sliders and intensity-bars,
  • select an optional region of interest (ROI) to calculate the coefficients for a specific image area,
  • choose your __coefficient,
  • and of course the final calculation of the colocalization coefficients, by pressing Compute.

Upon starting each of the Colocalization Analyzer modes, a colocalization map is calculated from the (by default selected) Pearson coefficient and visualized with 3D iso-surface rendering. The coefficent for calculating the colocalization map can be changed within all modes. Mouse buttons allow you to tilt, twist, and zoom the view of the scene (see below).


You can:
  • set the threshold of the surface renderer to see which voxels contribute at least that much to the colocalization coefficient,
  • twist and tilt the scene for a better perspective,
  • turn the MIP renderer on or off per channel or both at the same time, to see the whole data in comparison with the colocalized region,
  • and finally by clicking on an object in the scene, analyze this colocalized region.

Use the Object Statistics tab to view the table with the Object colocalization statistics.


You can:
  • look at the statistics of the object you clicked on in the Surface-Renderer-tab,
  • and quickly analyze all objects.

This object analysis tab allows you to quickly determine the properties of the different colocalization regions in your data. This is realized by visualizing the colocalization map as iso-colocalization surfaces.
In all Colocalization Analyzer modes, these surfaces are computed at the same time as the coefficients.

The surface objects show regions in which the degree of colocalization exceeds a certain value. By clicking on the objects local colocalization parameters are computed and reported. To relate the iso-colocalization objects to the original data the surface objects can be blended with a Red-Green MIP projection of the colocalizing channels, or with a colored MIP of another reference channel. The color range in which these objects will be displayed can be modified using a Hue Selector.

Object level analysis

Notice that the Object Analyzer in the Huygens Software also provides colocalization measurements at the object level. The Colocalization Analyzer works more at the level of the whole image, so that local statistics of the colocalizing regions can be easily retrieved.

Both analyzers work, in a sense, in complementary ways.

The Object Analyzer allows you to define objects and see how much they overlap, in volume or intensity. Objects defined like this can overlap with other objects, or not.

The Colocalization Analyzer explores the whole image to search for colocalizing regions based on the usual colocalization coefficients. These regions are then segmented and treated as objects to analyze. These objects are therefore always volumes of intersection.

How to use it

Download the manual of Essential or Professional for the Colocalization Analyzer chapter.
For a tutorial video on how to use the Colocalization Analyzer see here.

More information

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