Posted by
Krs5 on
May 16, 2017; 11:00am
URL: http://imagej.273.s1.nabble.com/Combined-surface-area-of-all-ROI-in-an-image-tp5018716p5018728.html
If you have all the ROIs in the ROI manager you could use something like below in the macro language. This assumes an 8-bit image.
----------------------------------code snippet-------------------------------------------
run("Colors...", "foreground=white background=black selection=red");
run("Set Measurements...", "area display redirect=None decimal=3");
roiManager("Deselect");
roiManager("Fill");
setAutoThreshold("Default dark");
setThreshold(255, 255);
getDimensions(width, height, channels, slices, frames);
for(i=1;i<=frames;i++){
setSlice(i);
run("Analyze Particles...", "size=25-Infinity pixel summarize");
}
------------------------------------------------------------------------------------
The results should be a summary table with the total area + area fraction for each frame.
Hope it works
Kees
Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aifImageJ workshops 1 and 2 June:
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/AIF/workshops/imagej-workshops-June-2017-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Burger Wilhelm
Sent: 16 May 2017 08:49
To:
[hidden email]
Subject: Re: Combined surface area of all ROI in an image
In a Java plugin, you could use Roi's point iterator to count the included pixels, as described here:
https://imagej.nih.gov/ij/developer/api/ij/gui/Roi.htmlThis should work for composite ROIs too.
--Wilhelm
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of mmettlen
Sent: Montag, 15. Mai 2017 15:38
To:
[hidden email]
Subject: Combined surface area of all ROI in an image
Easy - yet so difficult: How can I measure the combined total surface area of all ROI in an image? In the attached example : surface area of ROIs
125+126+127+128 = ?
I'm wondering if this can be done automatically? My timeseries has 250 images and the number of ROIs is variable from frame to frame => I'd like to get one number/slice.
<
http://imagej.1557.x6.nabble.com/file/n5018716/example.jpg>
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