Putting aside whether you need to do a full field or individual cells or nucleus vs cytoplasm, this seems to globally work.
open("C:/Users/cammem01/Downloads/Sample image_Dipanjana (1).png");
selectImage("Sample image_Dipanjana (1).png");
run("Split Channels");
/* Ideally, the raw data would be composite with each channel separate */
imageCalculator("Subtract create", "Sample image_Dipanjana (1)-1.png
(red)","Sample image_Dipanjana (1)-1.png (green)");
/*With real data, the red channel would have no components of other channels in
it and the subtraction would not be necessary. */
selectImage("Result of Sample image_Dipanjana (1)-1.png (red)");
rename("red-green");
run("Duplicate...", " ");
run("Gaussian Blur...", "sigma=1");
run("Find Maxima...", "prominence=10 output=[Point Selection]");
run("Set Measurements...", "mean centroid redirect=None decimal=2");
roiManager("Add"); // could use restore selection instead
selectImage("red-green");
run("Clear Results");
roiManager("Select", 0); // could use restore selection instead
run("Measure");
// or clear results, do a for loop for each centroid, make a circle with a 3
pixel diameter, and measure intensity
selectWindow("Results");
Cheers-
Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, New York, NY 10016
[email protected]<mailto:[email protected]>
http://nyulmc.org/micros http://microscopynotes.com/
Cell voice (no text) 1-914-309-3270
Office 1-646-501-0567
________________________________
From: Dipanjana Ghosh <[email protected]>
Sent: Sunday, August 18, 2024 6:28:09 AM
To: [email protected]
Subject: Re: Object based intensity calculation using ImageJ
[EXTERNAL]
Thanks Curtis...I will try this
Dear Philippe,
Here I attached a sample image... I want to quantify the intensity obtained
from the red channel punctas...And to the best of my knowledge, this type
of calculations should be done after filtering out 'very low intensity
producing' and 'very tiny sized' punctas.
Kindly suggest further if any...
Thanks & Regards,
Dipanjana
On Sat, Aug 17, 2024 at 9:00 PM Curtis Rueden <[email protected]>
wrote:
> Hi Dipanjana,
>
> Here is an example Jython script that segments and measures puncta in 3D:
>
> https://ops.scijava.org/en/1.1.0/examples/volume_labeling.html
>
> The steps involved are spelled out in the tutorial narrative as well as
> source code comments, so hopefully you can figure out how to adapt it to
> your specific use case. The docs (https://imagej.net/scripting), Image.sc
> Forum (https://forum.image.sc/), this mailing list, and LLMs like
> https://bioimage.io/chat and ChatGPT can all help your learn more.
>
> Regards,
> Curtis
>
>
> On Sat, Aug 17, 2024, 01:07 Dipanjana Ghosh <[email protected]> wrote:
>
> > Dear all,
> >
> > We want to calculate the intensities of a channel where objects (puncta)
> > are detected. The intensities from the puntas are to be calculated
> applying
> > some threshold for size and intensities.
> > Can someone kindly explain which tool of imageJ can be used for this and
> > how?
> >
> > Thanking you in advance
> >
> > Regards,
> > Dipanjana
> >
> > --
> > Dr. Dipanjana Ghosh
> > DST INSPIRE Faculty
> > School of Biomolecular Engineering & Biotechnology
> > RGPV, Bhopal
> > ORCID: https://orcid.org/0000-0003-0887-6798
> > Prev: DST WOS-A, IISERB
> > Post doctoral Research Fellow
> > Department of Biological Sciences
> > National University of Singapore
> > Singapore
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
--
Dr. Dipanjana Ghosh
DST INSPIRE Faculty
School of Biomolecular Engineering & Biotechnology
RGPV, Bhopal
ORCID: https://orcid.org/0000-0003-0887-6798
Prev: DST WOS-A, IISERB
Post doctoral Research Fellow
Department of Biological Sciences
National University of Singapore
Singapore
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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