Re: Make Binary, Analyze Particles (different results on different systems)

Posted by Gabriel Landini on Aug 05, 2013; 10:17am
URL: http://imagej.273.s1.nabble.com/Make-Binary-Analyze-Particles-different-results-on-different-systems-tp5004298p5004300.html

On Monday 05 Aug 2013 10:46:28 you wrote:

> I got different results when converting a mask to binary. On one system
> it gets inverted (inverting LUT) on the other it stays the same.
>
> On one system I can run "Analyze Particles" and get one element in
> canvas middle, on the other the whole canvas is detected.
>
> I read about the "Black background" Option of the Binary menu.
> Process > Binary > Options and remembered having heard of that before.
> And since I wrote this mail to get help in the first place, I intend to
> send it right away.

Most likely you have a different setting in the 2 installed systems.

I put these 2 lines (and some other defaults) in the AutoRun macro of the
StartupMacros.txt file to make sure that I have the same in all the installs.
 
run("Colors...", "foreground=white background=black selection=yellow");
run("Options...", "iterations=1 black pad edm=Overwrite count=1");

This makes IJ to consider foreground as white (255) and background as black
(0).
Also if you start with a file that has an inverted LUT to start with, the
results might not be what you expect.

Make Binary and Convert to Mask can do different things depending on the
settings of Make Binary.

Cheers

Gabriel

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