Thanks, eta.
It is indeed possible to reconstruct the 2D histogram plot using the xyz numbers in the
table produced when 'List' is clicked. I used this following macro to convert them back into
an image:
newImage("Histogram", "8-bit black", 255, 255, 1);
f=split(File.openAsString("d:\\data\\histogram.csv"),"\n");
for (i=0;i<f.length;i++) {
n = split(f[i],",");
setPixel(parseInt(n[0]),parseInt(n[1]),parseInt(n[2]));
}
run("Fire");
run("Log");
run("Calibration Bar...", "location=[Upper Right] fill=Black label=White number=5 decimal=0 font=12 zoom=1 overlay");
The resulting image looks the same as the one displayed in the Coloc2 dialog window, only
without the regression line. The last line in the macro adds the calibration bar that I presume
Craig wants. With a bit of additional effort, the regression line could also be superimposed.
However, I think it would be helpful if there was an option to access the plots produced by
Coloc2 *as images*, so that further tweaking can be done more easily. Having a standardized
pdf report is a very good idea, but so is the flexibility afforded by making all outputs of the
analysis accessible to users.
Judging by the figures on the documentation page (
http://fiji.sc/Coloc_2) this was previously
done. (I also note that the regression line is not included in the pdf output.)
I realize that Coloc2 is a work in progress, so would humbly request the above be taken on
board at the same time as expressing gratitude for efforts so far.
Regards,
Francis Burton
________________________________________
From: ImageJ Interest Group [
[hidden email]] on behalf of Ellen T Arena [
[hidden email]]
Sent: 12 August 2015 20:15
To:
[hidden email]
Subject: Re: Coloc2 scatterplot pseudocolour scale (Fiji)
from author/maintainer Dan White:
"It uses the ImageJ fire lookup table, with log or not log scaling according to the log checkbox
You can get the actual numbers 🔢 by clicking list."
hope this helps!
eta
> On Aug 12, 2015, at 8:57 AM, Craig Livie <
[hidden email]> wrote:
>
> Hi all,
>
> I have what seems to be a pretty basic question; however, I am useless at this sort of stuff and was hoping you could help.
>
>
> I recently used the Coloc2 pluging for Fiji and it generated a scatterplot of green vs red pixel intenstiy.
>
>
> I was wondering if there is anyway in getting the generic colour scheme relating to intensity as a key for a figure?
>
> It would be great if I could get some help with this as I cannot seem to work it out.
>
> Thanks Craig
>
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