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Hi all,<br>
<br>
For the purpose of my work, I'd need to convert a sequence of JPEG
images into an OME-TIFF stack using the command line tools. Despite
the original recording being in gray levels, I thus end-up with a
sequence of RGB files. I thus wanted to use the -separate option of
bfconvert to do the job (along with -stitch and -expand) but I've
noticed the following bug (I've uploaded a test RGB tiff stack under
QA
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11043 that reproduces it):<br>
<br>
So, if I run : "./bfconvert -stitch -expand -separate RGB_test.tif
RGB.ome.tiff", I get what I would expect (i.e. a 3xN stack with
R,G&B splitted, N here being the number of planes).<br>
<br>
If I run : "./bfconvert -stitch -expand -separate -channel 0
RGB_test.tif RGB_R.ome.tiff", I also do get the N stack of only the
red channel that I would expect (or G or B if specified).<br>
<br>
However, if I run : "./bfconvert -stitch -expand -separate
RGB_test.tif RGB_%c.ome.tiff", I do not get 3 separated N stacks (as
I would have expected, at least personally), but I get 3 times the
same 3xN stack as in my first example.<br>
<br>
Finally, if I run : "./bfconvert -stitch -expand -separate
RGB_test.tif RGB_%w.ome.tiff", I end up with the exact same issue as
above (plus, personally, I would think that the channels could be
named RGB or some such, instead of 0,1,2).<br>
<br>
I've been digging in the java code for a few days but could not find
a fix yet. The only interesting point I could sort out is that it
has to come from quite a low level as writing only one of the 3
channels does produce the expected output for that channel, and the
writing of the plane data is called only the required amount of
times. So there must be some cross-writing between the various
files.<br>
<br>
I'm working on a Mac OS X 10.10.2 with the latest Bio-Formats from
the GitHub repository.<br>
<br>
Cheers,<br>
Simon Blanchoud<br>
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