Posted by
Krs5 on
URL: http://imagej.273.s1.nabble.com/ROIManager-tp5022037p5022043.html
Dear Glen,
Before you copy the ROI to the new Image you have to tell where you want to add the ROI otherwise it will be in the centre of your image. So add
roiManager("select", i);
before run("Paste");
and I think it will work
Best wishes
Kees
Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility
ImageJ workshops 15 and 16 July, Leicester, UK. For registration visit
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-----Original Message-----
From: Glen MacDonald <
[hidden email]>
Sent: 10 April 2019 02:36
To:
[hidden email]
Subject: ROIManager
A user drew ovals around nuclei and saved the rois in ROIManager.
I want to automate copying the nuclear profiles from the original 3-channel 16-bit image into a blank channel in a new 3-channel 16-bit image stack.
Problem:
The following bare bones macro works to a point. somewhere, the macro loses control of the coordinates and begins pasting the nuclear profiles in the center of the target slice.
//assumes the roiManager list is open
origid=getImageID();//original stack
basename=File.nameWithoutExtension;
run("Select All”);
run("Duplicate...","title=["+basename+"] duplicate");//make target stack, select all required dupid=getImageID(); setBackgroundColor(0,0,0); run("Select All"); run("Clear","stack");//clear target roiManager("Show All");//avoid prevent double counting roic=roiManager("count"); for (i = 0; i < roic; i++) {
selectImage(origid);
Stack.setActiveChannels("100");
roiManager("select", i);
run("Copy");
selectImage(dupid);
Stack.setActiveChannels("100");
run("Paste");
}
any suggestion appreciated. MacBookPro, OS10.14.3. IJ 1.52n, Java 1.8.0_162.
thanks,
Glen
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