I posted images at
https://microscopynotes.com/temp/wand_tool_works.png
https://microscopynotes.com/temp/wand_tool_does_not_work.png
The following code always works when the run("Median...", "radius=2"); is run.
But looking at the image that does not work, I don’t see a single pixel near
getWidth/2, getHeight/2 which does not fall withing the threshold range.
Cheers-
Michael
run("Select None");
run("8-bit");
//run("Median...", "radius=2");
setAutoThreshold("Default no-reset");
getThreshold(min, max);
max = max * 1.25; // grab additional periphery
which may be thin and light
setThreshold(0, max, "raw");
doWand(getWidth/2, getHeight/2);
run("Set Measurements...", "area display redirect=None decimal=2");
run("Measure");
print(getTitle + "\t " + getResult("Area") + "\t pixels -- result
really should be reported as um^2");
selectWindow("Log");
-----Original Message-----
From: Gluender <[email protected]>
Sent: Thursday, July 3, 2025 9:56 AM
To: [email protected]
Subject: Re: help with wand tool
[EXTERNAL]
Greetings Michael,
do have images to test?
Best
Herbie
:::::::::::::::::::::::::::::::::::::::::::::
Am 03.07.25 um 15:48 schrieb Cammer, Michael:
> We have images where there is dark object at the center of the field that we
> want to measure. We are very puzzled because the following code works for
> some images and not for others. When we manually click using the wand tool,
> it always works, but this code only works on some images and not others.
>
> We are using ImageJ 1.54q14 with java 1.8.0_172.
>
> Help would be appreciated. Thank you!
>
> // This only reports area. Best fitting ellipse or other
> morphometrics could be reported.
> run("Select None");
> run("8-bit");
> setAutoThreshold("Default no-reset");
> getThreshold(min, max);
> max = max * 1.25;
> // grab additional periphery which may be thin and light
> setThreshold(0, max, "raw");
> doWand(getWidth/2, getHeight/2);
> run("Set Measurements...", "area display redirect=None
> decimal=2");
> run("Measure");
> print(getTitle + "\t " + getResult("Area") + "\t pixels --
> result really should be reported as um^2");
> selectWindow("Log");
>
> Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory NYU
> Langone Health, 540 First Avenue, New York, NY 10016
> Office: RB (formerly Skirball) 4-102 -- call if door is locked (phone
> near elevators)
> Office: 646-501-0567 Cell (voice only, not text): 914-309-3270
> [email protected]<mailto:[email protected]>
> https://urldefense.com/v3/__http://nyulmc.org/micros__;!!MXfaZl3l!ZXZzBOssOTsy1L_yBR01V3HlavHaYYXIQsn6k_-gmg0nJ1i0f77fj1Ji4siraz3ftIUS7LOL6rDlOCJeaXfxFlo$
>
> https://urldefense.com/v3/__http://microscopynotes.com/__;!!MXfaZl3l!ZXZzBOssOTsy1L_yBR01V3HlavHaYYXIQsn6k_-gmg0nJ1i0f77fj1Ji4siraz3ftIUS7LOL6rDlOCJeYipsd6Y$
> Scheduling the time you want is far more reliable by phone call. Why not
> provide your phone number?
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