http://imagej.273.s1.nabble.com/Re-Colocalization-Finder-tp5022772p5022773.html
Thanks for reporting this issue. I added a warning note to the plugin's
Le mar. 10 déc. 2019 à 12:32, Jeremy Adler <
> The Colocalization Finder plugin allows for selection part of scatterplot
> for subsequent measurement of correlations.
> This means that we are using a display that shows correlation to select
> which pixels to use in a correlation measurement - somewhat self
> referential.
> To test the plugin I generated two uncorrelated images
> newImage("Untitled", "8-bit noise", 256, 256, 2);// Gaussian
> distributions
> and the split them, before running the plugin.
> 1) Using the whole image produces a sensible Pearson correlation - around
> zero.
> 2) Adjusting the ROI to select the upper right quadrant produces a
> correlation near 1.00 -
> A near perfect positive correlation.
> 3) Selecting the lower right quadrant also produces a near perfect
> positive correlation
>
> 2) and 3) cannot be correct, a perfect positive correlation in a
> scatterplot should appear as a diagonal line going thru the origin.
>
> is the Pearson's_Rr shown in the results table the normal Pearson
> correlation ?
>
> presumably I am missing something important, but what ?
>
> Jeremy Adler
> BioVis
> Uppsala U
>
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>
> -----Original Message-----
> From: ImageJ Interest Group <
[hidden email]> On Behalf Of CARL
> Philippe (LBP)
> Sent: den 6 december 2019 18:09
> To:
[hidden email]
> Subject: Re: Colocalization with Coloc2
>
> Dear David,
> I would rather recommend you to use the Colocalization Finder plugin:
>
https://imagejdocu.tudor.lu/plugin/analysis/colocalizationfinder/start> for which I took over the maintenance.
> The plugin can be applied for whatever bit depth picture (i.e. 8, 16 or 32
> Bit picture) and able you to define "on the fly" an analysis ROI (i.e.
> within the scatterPlot picture) as well as within the composite picture.
> The calculations are generated (inside a results window) when you click
> inside a ROI (i.e. within the scatterPlot or composite picture) and you can
> as well set a ROI selection with a double click inside a ROI.
> Nevertheless, the plugin has only be written for the analysis of two
> single pictures as start conditions (i.e. not for a stack).
> But the code is very easily scriptable for stacks and you can find two
> example macros within the website link I indicted higher.
> The only drawback of the tool is maybe the lack of a good "biologist
> compatible" description (sorry I'm only a physicist) of it's features for
> which I'm waiting for some "biologist colleagues" to write it and you are
> as well welcome to do so if you wish.
> Feel free to contact me if you have any issues with this tool or ideas for
> improving it.
> My best regards,
> Philippe
>
> Philippe CARL
> Laboratoire de Bioimagerie et Pathologies UMR 7021 CNRS - Université de
> Strasbourg Faculté de Pharmacie
> 74 route du Rhin
> 67401 ILLKIRCH
> Tel : +33(0)3 68 85 41 84
>
> ----- Mail original -----
> De: "Knecht, David" <
[hidden email]>
> À: "imagej" <
[hidden email]>
> Envoyé: Vendredi 6 Décembre 2019 16:56:21
> Objet: Colocalization with Coloc2
>
> I was trying to use the Coloc2 in Fiji and the colocsample data provided
> in the cookbook. (
https://imagej.net/Colocalization_Analysis) to instruct
> my microscopy students. I have not done much of this myself so wanted to
> understand the software before teaching it.
>
> I was unable to generate any useful data. I got all kinds of warnings
> when I ran it with the stacks or a single slice from the stacks even though
> the dataset was clearly colocalized.
>
> 1. I tried to use a freehand ROI to focus on the membrane edge of the
> cell, but it did not seem to be used or make any difference. The image
> shown in the results was always the entire image and nothing seemed to
> indictate it was working with just the ROI
> 2. I tried subtracting background (around 60) from the images so only
> real data was analyzed and still got lots of warnings.
> 3. The results scatterplots seemed meaningless. In no case did it show
> the high degree of colocalization of the two probes in the sample data.
> 4. I am not sure how to generate the useful dot scatterplots of the sort
> shown in Dunn et al. from this analysis.
> 5. With the stacks, I expected a slice by slice analysis. The image
> shown in the results seemed to be only the first slice.
> 6. I was never able to see an image with the colocalized pixels found by
> the analysis highlighted.
>
> It would be really useful to someone doing this for the first time if that
> page were updated with a complete astep by step nalysis of that sample
> data. Settings, results, etc. with different inputs (ROI, noise reduction,
> stacks vs. slices etc.). so all the complexities are clarified. Is that
> available somewhere? Thanks- Dave
>
> Dr. David Knecht
> Professor, Department of Molecular and Cell Biology University of
> Connecticut
> 91 N. Eagleville Rd.
> U-3125
> Storrs, CT 06269-3125
> 860-486-2200
>
>
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