How to save the image created my Analyze Particles

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I have the following image

And with the following code:

run("Set Scale...", "distance=50 known=100 pixel=1 unit=um global");
run("Gaussian Blur...", "sigma=5");
run("Find Edges");
run("Enhance Contrast...", "saturated=0.4 normalize equalize");
setAutoThreshold("Minimum dark");
setThreshold(91, 255);
run("Analyze Particles...", "size=10000-Infinity display clear include summarize add");
saveAs("Results", "/Users/pdubois/Desktop/Results.xlsx")

I can save the processed picture (mypict.jpg) which look like this:

But what I do is to save image that looks like this:

Namely, those area identified with (1) and marked (yellow border) by Analyze Particles. How can I do that?


Flatten the image and then save the flattened image:[F]



I am not a regular user of FIJI. But thanks to one expert in our lab Arnim Jenett, I manage to do almost what I wanted to do: I measure cells nuclei in a electromicrophotography that I painted in photoshop layer. I used particle analysis and have a nice image with the number of each nuclei. Now I would like to save this image with the number of the nuclei as an “overlay”. I tried almost all type of saving the image but the number are not conserved and if I flatten the number disappear also… Do you know how to flatten with the number attached. The alternative is to use a screen capture, but I am sure FIJI should have it also… somewhere. Thanks for your help time and expertise. JM Hermel


Can you post an example image what you want to archive?


Hi, Yes here is one layer from a photoshop painting of the nuclei of my cell of interest. The particle analysis tool is able to find my nuclei and make the measure I needed e.g. area, Feret diameters, perimeter… of course using the calibration of the scale bar. I ended up with a number as overlay for each nuclei and wanted to save it as a flatten image. None of the image/overly/flatten or option in the threshold worked for me, neither any of the image file extension e.g. tif, gif, jpeg, png. Finally Arnim Jennet (TEFOR core facility, Neuropsi, Gif sur Yvette) help me find “capture image” that work fine for me. Note that the images are big: e.g. 5050x5399 pixel 72 pixel/inches. The one I include in this post are smaller than the one I use because the system of this post couldn’t manage it. Here before ending this post I see the “captured image”" with the number fine not the original (for whatever reason ?). Thanks for your time, best regards. JM Hermel


There was once a bug with the flatten command (font size too small) with a workaround from @Wayne and sufficient for your problem, see:

If not sufficient it would help to replicate this with an original image (with calibration) if there is a bug and if you record and post the excact workflow - record the steps with the macro recorder, see:

And of course some OS information (MacOSX, Linux…)