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Colour Deconvolution

    TODO component: {"content"=>"sc.fiji:Colour\\_Deconvolution"} Similarly to the command Image › Color › RGB split , this plugin unmixes an RGB image produced by subtractive mixing (inks, histological dyes) into separate channels corresponding to up to 3 determined colors. This is useful e.g. to do pigment separation.


    See Gabriel Landini webpage.

    This plugin implements the method described in the following paper:

    Ruifrok A.C., Johnston D.A., “Quantification of histochemical staining by color deconvolution”, Anal. Quant. Cytol. Histol. 23: 291-299 .

    Version history

    • 30/Mar/2004 released - based on macro code from A.C. Ruifrok.
    • 03/Apr/2004 resolved ROI exiting
    • 07/Apr/2004 added Methyl Green DAB vectors
    • 08/Jul/2004 shortened the code
    • 01/Aug/2005 added fast red/blue/DAB vectors
    • 02/Nov/2005 changed code to work with image stacks (DLC - dchao at fhcrc org)
    • 02/Nov/2005 changed field names so user-defined colours can be set within macros (DLC - dchao at fhcrc org)
    • 04/Feb/2007 1.3 disable popup menu when right clicking
    • 23/May/2009 added Feulgen-light green vectors
    • 14/Apr/2010 v 1.4 added Giemsa vector (Methylene blue & eosin). The images are now names “title”-(Colour_1) etc so there are not clash of names when using [ ]. The log window now prints the java code of the translation matrix to include new vectors in the plugin. Added “Hide legend” option.
    • 22/Jun/2010 v 1.5 added Masson Trichrome vector (Methyl blue & Ponceau Fuchsin only (this does not have Iron Haematoxylin vector!). Fixed bug: check for 0 components before hiding legend (otherwise there was no image shown if legend hidden)
    • 26/Mar/2011 v.1.6 added Brilliant_Blue stain.
    • 03/Aug/2011 v1.7 added progress bar (thanks to Oskari Jaaskelainen), added warning about immunostains.
    • 17/Oct/2015 v 1.8 B. Pavie refactorized the code into multiple classes and made some public method to generate the result ImageStacks without displaying them so it can be called from scripts.

    Image › Color › Colour Deconvolution