Posted by
Alexander Stephan on
Mar 23, 2016; 7:43am
URL: http://imagej.273.s1.nabble.com/Conversion-OIB-into-TIFF-bug-tp5015973p5015984.html
Hi Curtis,
Thanks for the help! It partially explains my problem. However, i also have the same problem when I use a macro that converts OIB files to TIFF files and adjusts the colours. The macro is as follows:
dir1 = getDirectory("Choose Source Directory ");
dir2 = getDirectory("Choose Destination Directory ");
list = getFileList(dir1);
setBatchMode(true);
for (i=0; i<list.length; i++) {
showProgress(i+1, list.length);
name=dir1+list[i];
run("Bio-Formats Importer", "open=["+name+"] autoscale=false color_mode=Grayscale view=Hyperstack stack_order=XYCZT");
run("Split Channels");
selectWindow("C2-"+list[i]);
red=getTitle();
selectWindow("C1-"+list[i]);
yellow=getTitle();
run("Merge Channels...", "red=["+red+"] yellow["+yellow+"] create ignore");
saveAs("TIFF", dir2+list[i]);
}
Can you or anyone else help?
Best,
Alex
________________________________________
Von: ImageJ Interest Group [
[hidden email]]" im Auftrag von "Curtis Rueden [
[hidden email]]
Gesendet: Dienstag, 22. März 2016 19:26
An:
[hidden email]
Betreff: Re: Conversion OIB into TIFF: bug
Hi Alexander,
Bio-Formats will adjust the brightness/contrast if (and only if) the
"Autoscale" option is checked. Otherwise, it will use the default scaling
for your image's bit depth (which might result in an all-black-looking or
very dim image; see
http://imagej.net/Troubleshooting#The_image_I_loaded_is_displayed_all_black.21_But_it_is_not_black.21).
When you inspect the pixel values (mouse over a pixel and look at the
ImageJ main window status bar) of the original OIB file, and the converted
TIFF file, do they match?
Regards,
Curtis
--
Curtis Rueden
LOCI software architect -
http://loci.wisc.edu/softwareImageJ2 lead, Fiji maintainer -
http://imagej.net/User:RuedenDid you know ImageJ has a forum?
http://forum.imagej.net/On Tue, Mar 22, 2016 at 3:28 AM, Alexander Stephan <
[hidden email]> wrote:
> Dear ImageJ community,
>
> I have some trouble converting OIB files into TIFF files. When using the
> bio-format plugin in ImageJ or FIJI, the program adjusts brightness and/or
> contrast once I open the images. Sometimes, the problem also occurs when
> adjusting colors of individual channels via macros. The problem does not
> always occur, I just can not find out how and under what circumstances. Has
> anyone experienced similar problems?
> Thanks for the help in advance!
>
> Best,
> Alexander Stephan
>
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> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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