http://imagej.273.s1.nabble.com/JACop-batch-processing-tp5009015p5009144.html
Hello,
This is the macro that I have been working on: Basically, it is supposed to open my directory that contains all the images I want to apply batch processing to. From these images I want to select cells (by creating a rectangle), crop the cell, split channels,
convert to 8-bit format and then apply JaCop. The problem once again, is that y macro is specific for one image that I used to record the macro (ex. you will notice C2-practivComposite in the code).
Thanks again for your help,
Kamaldeep
dir=getDirectory("image");
close();
list=getFileList(dir);
for (i=0;i<list.length;i++){
path = dir+list[i];
if (!endsWith(path,"/")) open(path);
runMacro("Macro2.ijm");
}
makeRectangle(173, 282, 48, 46);
run("Crop");
run("Split Channels");
title = getTitle();
"red=[Edges of " + title + "] green=[" + title + "] blue=[" + title + "] gray=*None*");
selectWindow("C2-practivComposite.tif");
selectWindow("C1-practivComposite.tif");
run("8-bit");
selectWindow("C2-practivComposite.tif");
run("8-bit");
run("JACoP ");
selectWindow("C2-practivComposite.tif");
selectWindow("C1-practivComposite.tif");
selectWindow("C2-practivComposite.tif");
run("JACoP ", "imga=C1-practivComposite.tif imgb=C2-practivComposite.tif thra=43 thrb=24 pearson mm costesthr ccf=20 cytofluo ica costesrand=1-16-100-0.0010-0-false-true-true");
selectWindow("Costes' threshold C1-practivComposite.tif and C2-practivComposite.tif");
selectWindow("Costes' mask");
selectWindow("Van Steensel's CCF between C1-practivComposite.tif and C2-practivComposite.tif");
selectWindow("Cytofluorogram between C1-practivComposite.tif and C2-practivComposite.tif");
selectWindow("ICA A (C1-practivComposite.tif)");
selectWindow("ICA B (C2-practivComposite.tif)");
selectWindow("Randomized images of C2-practivComposite.tif");
selectWindow("Costes' method (C1-practivComposite.tif & C2-practivComposite.tif)");
selectWindow("Costes' threshold C1-practivComposite.tif and C2-practivComposite.tif");
selectWindow("Costes' mask");
selectWindow("C1-practivComposite.tif");
selectWindow("C2-practivComposite.tif");
selectWindow("Van Steensel's CCF between C1-practivComposite.tif and C2-practivComposite.tif");
selectWindow("Cytofluorogram between C1-practivComposite.tif and C2-practivComposite.tif");
selectWindow("ICA A (C1-practivComposite.tif)");
selectWindow("ICA B (C2-practivComposite.tif)");
selectWindow("Randomized images of C2-practivComposite.tif");
selectWindow("C1-practivComposite.tif");
selectWindow("C2-practivComposite.tif");
selectWindow("Costes' method (C1-practivComposite.tif & C2-practivComposite.tif)");
run("Close All");
From: Jasvinder S Ahuja [via ImageJ] [ml-node+[hidden email]]
Sent: Monday, August 11, 2014 8:06 PM
To: Jawanda, Kamaldeep Kaur
Subject: Re: JACop batch processing
Hi Kamaldeep,
I have recently learnt how a bit of code can make life so much easier! To
begin I suggest you visit -
http://adm.mri.cnrs.fr/datas/fichiers/articles/60/184.pdf
http://www.sussex.ac.uk/gdsc/intranet/pdfs/ImageJBatchProcessing.pdf
These are nice resources to get you started with batches of images.
Jasvinder
On Mon, Aug 11, 2014 at 11:38 AM, Interleukin-10 <
[hidden email]> wrote:
> Hi Pariksheet,
>
> Thank you for your response. I have figured out how to record the macros,
> but the problem I am having now is that my macro is specific for one image.
> How can I apply the macro to all my images? I get an error message saying
> my image name is different than the one in the macro (since it is specific
> for the image that I used to record the macro).
>
> I hope this makes sense.
>
> Anyways, any help would be greatly appreciated.
>
> Thanks again,
> Kamaldeep
> ________________________________
> From: Pariksheet Nanda [via ImageJ] [
[hidden email]
> ]
> Sent: Sunday, August 10, 2014 3:50 PM
> To: Jawanda, Kamaldeep Kaur
> Subject: Re: JACop batch processing
>
> Hi Kamal,
>
> On Fri, Aug 1, 2014 at 7:00 PM, Interleukin-10
> <[hidden email]<UrlBlockedError.aspx>> wrote:
>
> >
> > I have a collection of several dozen images and I would like to do a
> > colocalisation analysis using JaCoP. Normally I do this manually
> > image-by-image but I believe there must be a way to record the macro for
> it;
> > I need to open each image, split it into the red and green channel, open
> > JACoP and choose the object-based analysis for the two channels, setting
> the
> > pixel size and threshold (which remain the same for all the images) and
> > running the analysis.
> >
> > What do you suggest? I would be very grateful for any comments.
>
> Open your image, then launch the macro recorder using:
>
> Plugins > Macros > Record...
>
> Then as you perform your usual image processing steps, the
> corresponding ImageJ macro commands will be recorded. When you are
> done, in the Recorder window, hit the "Create" button to save the
> macro. You can run it the next time with:
>
> Plugins > Macros > Run...
>
> Further reading:
>
http://imagej.nih.gov/ij/docs/guide/146-31.html#toc-Subsection-31.1
>
http://imagej.nih.gov/ij/developer/macro/macros.html
>
>
> Pariksheet
>
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