Short Description

This plugin contains most of existing colocalization methods in 2D and 3D fluorescence microscopy images: Pearson and Manders coefficients, Image Cross Correlation Spectroscopy (ICCS) and Object-based methods.

Team: Bio Image Alalysis
Institution: Institut Pasteur
Website: http://icy.bioimageanalysis.org/

Documentation

DEMONSTRATION VIDEO

Presentation & Litterature

Correlation & Overlap methods, and Parametric analysis (fit) of Ripley K function are described in

Lagache T, Sauvonnet N, Danglot L, Olivo-Marin JC. Statistical analysis of molecule colocalization in bioimaging. Cytometry A. 2015

SODA (object-based, non-parametric Ripley K function analysis) is described in

Lagache, T., Grassart, A., Dallongeville, S., Faklaris, O., Sauvonnet, N., Dufour, A., … & Olivo-Marin, J. C. (2018). Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics. Nature communications9(1), 698.

This plugin contains most of the existing colocalization methods. Before using it, you can find here an introduction to colocalization methods.

This plugin is decomposed into two main method classes:

1- Correlation & Overlap methods.

These methods are based either on the quantification of Pearson and cross-correlation (ICCS) between fluoresecent images or between the overlap of segmented objects (detections) through Manders, or Overlap (% of segmented objects 1 that overlap more than T% with objects 2, T is a free parameter (50% by default)) analysis

Detections for overlap analysis are output of spot detector plugin(be sure to check the “Export to Swimming-pool” box in the “Output” menu)

For each coefficient (except ICCS), a p-value and its log are provided. For Pearson correlation coefficient, we compute a closed formula based on pixel scrambling and Central Limit theorem. For overlap analysis (Manders&Overlap), we use Monte-Carlo randomizations of detections’masks are used (number of MC simulations is a free parameter (10 by default)).

These methods are also implemented as a block: ColocalizationStudio_correlation

An exemple of protocol can be found here

1- “Distance between objects”-based methods.

These methods also use 2 sequences and detections sets from spot detector plugin.

3 methods are proposed:

Distance analysis (centers of mass 1 inside masks 2): It counts the % of detections 1 whose center of mass (position) is inside a detection 2 mask. p-value and its log are computed analytically using binomial probabilities.

Parametric analysis (fit) of the Ripley’s K function (see Lagache T, Sauvonnet N, Danglot L, Olivo-Marin JC. Statistical analysis of molecule colocalization in bioimaging. Cytometry A. 2015).

Here, we compute the Ripley’s K function (Step and Maximal distance for the analysis are free parameters) and fit it (avec zero-mean and unit-variance normalization) with the expected mean curve obtained when p% of detections 2 are colocalized around detections 1, at mean distance mu. These two fitting parameters appear in % of coloc. spots 2 and Mean coloc distance in the output section Ripley’s analysis (parametric). 

The quality of the fit can be checked (Plot K function graph to check the fit box)

Non-parametric Ripley’s analysis (SODA) (see Lagache, T., Grassart, A., Dallongeville, S., Faklaris, O., Sauvonnet, N., Dufour, A., … & Olivo-Marin, J. C. (2018). Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics. Nature communications9(1), 698.)

SODA performs a non-parametric analysis of Ripley’s function (statistical thresholding) and is more robust than parametric analysis. Based on maximum of the Ripley’s function it computes analytically the p-value and its log.

These methods are also implemented as a block: ColocalizationStudio_object

An example of protocol can be found here

3 reviews on “Colocalization Studio

  1. IcyLyd
    Very nice plugin regrouping various colocalization methods. I would love to use it in batch thanks to a protocol block.
  2. Very nice to have the statistics missing from the colocalizer! I was wondering if for the object-based colocalization would be possible to also have the colocalized components, in order to display them on the original image?
  3. The new update have a problem. I can not use colocalization studio. The plug in says i have to set detection set, but it is unable to set. The previous version worked very well until now. please send me help with that

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Changelog

  • Version 0.2.0.6 • Released on: 2019-08-13 16:00:00
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    Description:

    Fixed bug with POI library update (Stephane)

  • Version 0.2.0.5 • Released on: 2018-10-15 23:24:24
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    Description:

    Allow the computation of Pearson & Cross-correlation when no detection are selected

  • Version 0.2.0.4 • Released on: 2018-08-12 21:47:38
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    Description:

    compatible with java 6

  • Version 0.2.0.3 • Released on: 2018-07-18 02:19:15
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    Description:

    Fixed bugs for ROIs manipulation in Manders computation
    Provides the mean value obtained with Monte-Carlo simulations for Manders and Overlap coefficients

  • Version 0.2.0.2 • Released on: 2018-06-29 03:39:39
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    Description:

    bug correction: ask the user to select detections when launching the plugin

  • Version 0.2.0.1 • Released on: 2018-06-28 21:00:30
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    Description:

    New methods (Overlap, distance, SODA) are implemented
    p-value & log p-value are both provided
    Detections sets are required for overlap and object analysis (simplifying and debugging the ROIs management : incompatibility between Z/T dimensions etc..)

  • Version 0.1.0.2 • Released on: 2015-06-12 14:59:41
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    Description:

    -implements a manual counting of objects at a distance< "maximal distance for the analysis" (option "manual" in the standalone plugin) -xls save is replaced by a workbook outbut in blocks (more convenient for batch analysis)

  • Version 0.1.0.1 • Released on: 2015-04-23 21:58:43
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  • Version 0.1.0.0 • Released on: 2015-02-25 21:28:32
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    Description:

    -bugs fixed
    -possibility to define ROI with detections convex hull

  • Version 0.0.1.11 • Released on: 2015-02-11 16:00:57
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    Description:

    -now support the 3D
    -includes Manders Analysis
    -external definition of the analysis area (ROIs)

  • Version 0.0.1.10 • Released on: 2015-01-27 21:44:10
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  • Version 0.0.1.9 • Released on: 2015-01-24 16:54:43
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  • Version 0.0.1.8 • Released on: 2015-01-23 13:43:56
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  • Version 0.0.1.7 • Released on: 2014-11-18 16:13:30
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  • Version 0.0.1.6 • Released on: 2014-11-10 16:38:29
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  • Version 0.0.1.5 • Released on: 2014-10-10 14:51:45
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    Description:

    Bug set

  • Version 0.0.1.4 • Released on: 2014-10-10 12:02:58
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    Description:

    Option to export colocalized detections as ROIs

  • Version 0.0.1.3 • Released on: 2014-09-14 17:14:23
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    Description:

    Set the problem with class detections

  • Version 0.0.1.2 • Released on: 2014-09-02 15:54:06
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  • Version 0.0.1.1 • Released on: 2014-09-01 12:52:45
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    Description:

    Compute the maximum of the Ripley's K function

  • Version 0.0.1.0 • Released on: 2014-08-29 12:08:02
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