Colocalization Highligter



Dear all,

I can’t find Colocalization Highligter plug-in for imageJ. I’m trying to use a macro that requires this plug-in .Has anyone used this before?


Thank you!



I do not know that plugin… but perhaps you can alter your macro to use Coloc 2 (which is macro-recordable) or the new colocalization ops that are available. For the former… here is a helpful script to get coloc measures from Coloc 2.
For the latter - there is an example code snippet here.

Just let us know what you need for your analysis… and perhaps post the macro code you are trying to use? That will help us help you better.

eta :slightly_smiling_face:


Thank you for your response.
The macro that I try to use is published on a paper with the title: Quantification of Mitochondrial Morphology in Neurites of Dopaminergic Neurons using Multiple Parameters.
For that I need the WCIF version of ImageJ which I cannot find.
The code is:

macro "Close All Windows [F11] " //F11 used as a shortcut to close all active windows
while (nImages>0) {
macro "Open Images for colocalization [F8] " //F8 used as shortcut
open(); //select red image
run("8-bit"); //makes image 8-bit
open(); //select green image
run("8-bit"); //makes images 8-bit
run("Colocalization Highligter", "ratio=50 threshold_channel_1=52 threshold_channel_2=52 display=255 colocalized"); //Colocalization Highlighter is a tool from the WCIF version of
//ImageJ, adjust threshold here if necessary
//user may wish to use this image for making figures
setTool(3); //activates freehand selection tool for drawing around region of interest
selectWindow("Colocalized points (8-bit) "); //selects image containing only colocalized
setThreshold(15, 255); //threshold setting not important here
macro "Measure Morphometrics [F10] " //F10 used as shortcut
run("Clear Results");
run("Set Measurements… ", "area perimeter circularity redirect=None decimal=2");
run("Analyze Particles… ", "minimum=5 maximum=500 bins=100 show=Outlines display summarize"); //set size range of particles here
for (i=0; i<nResults; i++){
MP += getResult('Perim.',i);
MA +=getResult('Area', i);
MC +=abs(getResult('Circ.', i)); //old version of ImageJ reports circularities of -1 if the
//calculated circularity > 1, so absolute value needed here
}//loop to assign variables from results
AMP= (MP/i); //calculates mean perimeter
Wiemerslage and Lee Page 13
J Neurosci Methods. Author manuscript; available in PMC 2017 March 15.
Author Manuscript Author Manuscript Author Manuscript Author Manuscript
AMA= (MA/i); //calculates mean area
AMC= (MC/i); //calculates mean circularity
Rmorph= (AMA/AMP); //measures the area perimeter ratio, a.k.a. interconnectivity
print("Count:" +i);
print("Total Area:" +MA);
print("Avg. Perimeter:" +AMP);
print ("Avg. Area:" + AMA);
print ("Avg. Circularity:"+ AMC);
print ("Area/Perim:"+ Rmorph);




This is stated right in the macro. This WCIF version of ImageJ - something they created for this publication - is possible provided via link in the paper itself:

They reference this plugin from this publication.

I would read both publications - the original and the one I just linked above - and investigate there. Or contact the WCIF folks directly.



Apparently they don’t ship their own ImageJ distribution anymore (and therefore no “Colocalization Highligter” plugin), but link to the official Fiji download instead…

You might want to contact Dr. Kevin Conway, the facility manager, to get the original plugin. FWIW, I just invited him to this forum topic.

At least, the very specific typo in the plugin name makes it easy to specifically search for this plugin and not show up any other colocalization highlighters :smiley:


I contacted Dr.Kevin Conway and it seems that the version they cite on this paper is just the FIJI version of the imageJ and the Colocalization Highligter its a plug-in of the MBF Plugin Collection.

Thank you for your assistance!



Maybe it is already clear from the MBF Plugin Collection page, but just to state it directly here in this topic: the distribution first known as WCIF ImageJ later became MBF ImageJ when Tony Collins moved from WCIF to MBF. Unfortunately, the existing WCIF ImageJ web page was not able to be updated to point to the newer MBF ImageJ version of the manual.

In a nutshell: “WCIF ImageJ” and “MBF ImageJ” are really the same thing.

After the MBF ImageJ web site went offline, we mirrored it to just to keep the information online. (But note that we pulled it out of the Wayback Machine, so the content there may not be the most complete and latest version of the site that ever existed.)

We also created the Fiji Cookbook, a manual with corresponding ImageJ update site inspired by, and shipping many of the same plugins as, the MBF plugin collection. The Cookbook does not include all the plugins of MBF ImageJ—and indeed the Colocalization Highlighter plugin is not one of the ones included—but we could certainly add it to the Cookbook update site if this would be helpful to users. Contributions welcome: the code behind the cookbook can be found here.