<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Curtis and Will, <div><br></div><div>I haven been using OMERO recently, but make efforts in having our OME.TIF in good shape, including SPW. This will permit us to migrate across imaging platforms.</div><div>The problem with some ome.tif (generated by scripting or by companies) is that multi-file and SPW capabilities can be missing.</div><div>The same way that OMERO has a solution for this, we though in having a file-based command-line tool. </div><div><br></div><div>I consider the ImageJ plugins and macros a temporal solution, because actually they can be slow for our throughput. </div><div>Therefore tried this with bfconvert, even when appending to existing OME.TIF is not supported yet.</div><div><br></div><div>However wIth the latest revision of bioformats 7034 when I output the bfconvert to the same file consecutively, the file is always getting bigger in size.</div><div><br></div><div>Is appending to OME.TIF a work in progress or is there a bug there?</div><div><br></div><div>Thanks for the help, best regards,</div><div><br></div><div>Rubén</div><div><br></div><div><div><div>On Sep 30, 2010, at 3:27 PM, Curtis Rueden wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Rubén,<br><br><blockquote style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote">
I believe similar functionality exists in ImageJ but don't know the details?<br></blockquote>
<br>In ImageJ, you can use the Bio-Formats Importer with the "Concatenate series when compatible" option to stitch together the 48 series, as long as they all have the same dimensional extents.<br><br>-Curtis<br>
<br><div class="gmail_quote">On Thu, Sep 30, 2010 at 5:22 AM, Will Moore <span dir="ltr"><<a href="mailto:will@lifesci.dundee.ac.uk">will@lifesci.dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Ruben,<div class="im"><br>
<br>
On 30 Sep 2010, at 10:38, Rubén Muńoz wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
I have asked the author of these images. She produced the data using a Zeiss macro that actually doesn't perform series, but many different single images, renamed independently.<br>
I have nothing to add to this thread. It is not an issue. Never mind about that dataset, I am not sure how I will convert them, but bioformats should not do it directly.<br>
<br>
However... Can one add the corresponding independent series to one OME.TIF file creating a new multiT set?<br>
<br>
</blockquote>
<br></div>
There is a script in OMERO to stitch multiple images into a single image with more dimensions (which you could then export). This would duplicate the data. See:<br>
<a href="http://cvs.openmicroscopy.org.uk/snapshots/movies/omero-4-2/mov/Scripting1.mov" target="_blank">http://cvs.openmicroscopy.org.uk/snapshots/movies/omero-4-2/mov/Scripting1.mov</a><br>
The script has evolved a bit since then to auto recognise images by name. See:<br>
<a href="http://trac.openmicroscopy.org.uk/shoola/wiki/UtilScripts#CombineImages" target="_blank">http://trac.openmicroscopy.org.uk/shoola/wiki/UtilScripts#CombineImages</a><br>
<br>
You could edit the script itself to tailor it to your requirements if necessary.<br>
<br>
I believe similar functionality exists in ImageJ but don't know the details?<br>
<br>
Cheers,<br>
<br>
Will.<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
Thanks for the discussion.<br>
<br>
Rubén<br>
<br>
<br></div><div class="im">
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
</div></blockquote>
<br>
William Moore<br>
Wellcome Trust Centre for Gene Regulation & Expression<br>
College of Life Sciences<br>
MSI/WTB/JBC Complex<br>
University of Dundee<br>
Dow Street<br>
Dundee DD1 5EH<br>
United Kingdom<br>
<br>
Phone 01382 386364<br>
<a href="http://openmicroscopy.org.uk/" target="_blank">http://openmicroscopy.org.uk</a><div><div></div><div class="h5"><br>
<br>
<br>
<br>
<br>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
</div></div></blockquote></div><br>
</blockquote></div><br></div></body></html>