Posted by
Cammer, Michael on
Feb 20, 2017; 5:37pm
URL: http://imagej.273.s1.nabble.com/Background-substraction-and-LUT-inconsitent-on-a-folder-tp5018144p5018151.html
I tried opening the LUT and then saving, then reopening, and it worked fine remembering the new LUT with the overlays intact.
I'm using ImageJ 1.51j9 Java 1.6.0_20 on Win7
=*===========================================================*=
Michael Cammer, DART Microscopy Laboratory, NYU Langone Medical Center
Cell: 914-309-3270 Office: Skirball 2nd Floor main office, back right
http://ocs.med.nyu.edu/microscopy &
http://microscopynotes.com/-----Original Message-----
From: Straatman, Kees (Dr.) [mailto:
[hidden email]]
Sent: Monday, February 20, 2017 11:58 AM
To:
[hidden email]
Subject: Re: Background substraction and LUT inconsitent on a folder
I noticed that there is an overlay on your images. If I remove the overlay I can save with the new LUT or for example as 16-bit, what also does not seem to work for your images.
Not sure if this is intended behaviour...
Kees
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Eric Denarier
Sent: 20 February 2017 13:34
To:
[hidden email]
Subject: Background substraction and LUT inconsitent on a folder
Hi All,
With the following code several of the images (image size 356ko) of a folder are saved with their original color instead of beeing all orange.
Any suggestion ?
It may seem that adding a wait(100); after run ("Orange Hot"); is working
but then how to know what should be the "wait" value???
Is there an other way to fix the problem ??
enclosed two files for a test.
Thanks for your help
I used Both FIJI : image2 2.0.0-rc-56/1.51h
and ImageJ 1.51i5
on Windows7 with the same problems
Thank you
/////////// Code here //////////
inputDir = getDirectory("Choose Source Directory ");
outputDir = getDirectory("Choose Destination Directory ");
list = getFileList(inputDir);
for (k=0; k<list.length; k++) {
open(inputDir +list[k]);
run ("Subtract Background...", "rolling=100");
run( "Orange Hot", "");
saveAs("Jpeg", outputDir +list[k]);
close(); }
--
Eric Denarier
Grenoble Institut des Neurosciences
Inserm U1216
Chemin Fortuné Ferrini
38700 La Tronche
France
Tél :33 (0)4 565 205 38
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