I think I fixed the problem. At least practically, although I wonder if there
is still a bug.
Even though the image shows that every pixel falls under the threshold, I
thought that maybe median filtering it would help.
I added a run("Median...", "radius=2"); following the 8 bit conversion and now
it seems to work.
Cheers-
Michael
-----Original Message-----
From: Cammer, Michael <[email protected]>
Sent: Thursday, July 3, 2025 9:48 AM
To: [email protected]
Subject: help with wand tool
[EXTERNAL]
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
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