Hi everyone,
I’m interested in capturing pixel values within a fixed ROI that is rectangular. I’m able to use the Pixel Inspection Tool to accomplish this in a square matrix. Is anyone aware of a way to alter the matrix or use an alternative tool that will recruit all pixel values within the ROI and allow for copy/export?
Thanks,
Mark
Hi @mprage,
not sure if ImageJ/Fiji have this functionality per default. But with CLIJ2 you can get pixel intensities of a custom rectangle into the results table by using a custom macro:
run("Blobs (25K)");
makeRectangle(78, 109, 10, 9);
// init GPU
run("CLIJ2 Macro Extensions", "cl_device=");
// push current selection to GPU memory
image = getTitle();
Ext.CLIJ2_pushCurrentSelection(image);
// pull image back to the results table
run("Clear Results");
Ext.CLIJ2_pullToResultsTable(image);
May I ask what you would do next with this table of numbers?
Cheers,
Robert
In between the lines it reads as if you are after an irregular ROI, but in both cases, doesn’t Roi.getContainedPoints combined with a for loop over x and over y do what you want?
The even simpler solution to a rectangular region is this:
run("AuPbSn 40 (56K)");
makeRectangle(188, 43, 26, 21);
run("Duplicate...", "title=AuPbSn40-1.txt");
saveAs("Text Image",getDirectory("temp")+"AuPbSn40-1.txt");
Many thanks for the solutions!
The purpose is to count the number of pixels within a range +/- std dev and estimate the thickness of an object of known thickness between two contrast interfaces.