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Dear Curtis<br>
<br>
Thanks a lot for your reply. <br>
I just uploaded the zip folder "lif file problem" containing the
four files on the specified website.<br>
<br>
I am curious what the problem is.<br>
<br>
Best regards<br>
<br>
Pascal<br>
<br>
<div class="moz-cite-prefix">Am 21.11.2013 10:18, schrieb Curtis
Rueden:<br>
</div>
<blockquote
cite="mid:CADN69ym-C4UtDfgCWx=62H7LSiV+y7eV=SqmAuEwTa6Xt-yo+g@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Pascal,
<div><br>
</div>
<div>
<div>> I also tried with Fiji. I updated Fiji through the
menu and also</div>
<div>> manually updated the loci plugin there. I am not
sure if it takes the</div>
<div>> trunk build in that case. </div>
</div>
<div><br>
</div>
<div>Fiji ships with the 4.4.9 release of Bio-Formats. If you
want to enable 4.4.x or 5.x development builds, you can use
the "Bio-Formats 4" or "Bio-Formats 5" update sites. For more
details, please see the instructions at:</div>
<div><br>
</div>
<div> <a moz-do-not-send="true"
href="http://fiji.sc/Bio-Formats#Daily_builds">http://fiji.sc/Bio-Formats#Daily_builds</a><br>
</div>
<div><br>
</div>
<div>With Fiji, it should not be necessary to download
loci_tools.jar manually, nor to ever run the "Update LOCI
Plugins" command (that command is disabled in Fiji anyway).</div>
<div><br>
</div>
<div>
<div>> Anyway it is always the same. We see the change in
intensity in every</div>
<div>> second time frame.</div>
</div>
<div><br>
</div>
<div>Indeed, it sounds like a bug.</div>
<div><br>
</div>
<div>
<div>
> I can provide you with 4 files but I need an ftp access</div>
<div><br>
</div>
</div>
<div>Thanks. If you ZIP up the four files, you can upload them
using this link:</div>
<div><br>
</div>
<div> <a moz-do-not-send="true"
href="http://qa.openmicroscopy.org.uk/qa/upload/">http://qa.openmicroscopy.org.uk/qa/upload/</a><br>
</div>
<div><br>
</div>
<div>Unless your archive is >500MB? In which case, let us
know and we will provide alternative upload instructions
off-list.</div>
<div><br>
</div>
<div>Regards,<br>
</div>
<div>Curtis</div>
</div>
<div class="gmail_extra">
<br>
<br>
<div class="gmail_quote">On Thu, Nov 21, 2013 at 2:38 AM, Pascal
Lorentz <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Lorentz.Pascal@gmail.com" target="_blank">Lorentz.Pascal@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p class="MsoNormal"><span lang="EN-US">Dear Bio Formats
team</span></p>
<p class="MsoNormal"><span lang="EN-US">First of all I
would like to thank you for your impressive work. This
plugin is really great.</span></p>
<p class="MsoNormal"><span lang="EN-US">We came across a
problem yesterday.<br>
We have a lif file that has been acquired with a Leica
confocal SP5 with the LAS AF Software Version 2.7.3.
It is a timelaps dataset with 12 timepoints in 2
channels. If we look at these cells in the Leica
software the intensity over time stays in the same
range. <br>
If we open this dataset as a hyperstack with the bio
formats importer we see an increase in intensity in
every second time frame. It is not just a display
effect since we can really measure the intensity
change. <br>
As a work around we exported single tifs from the lif
file out of the Leica software. So we end up with 24
images for the 12 timepoints for the two channels. If
we then import these images as an image sequence and
if we measure the exact same area, the intensity stays
in a similar range over the whole timelaps. </span></p>
<p class="MsoNormal"><span lang="EN-US">I can provide you
with 4 files but I need an ftp access to upload them:<br>
1. The original lif file “Series 7.lif”<br>
2. The image sequence after exporting from the Leica
Software and importing as sequence in ImageJ saved as
tiff “image_sequence.tif”<br>
3. The results table of the intensity measurement of
an area of the lif dataset opened with the loci
importer “Results_loci_import.xls.<br>
4. The results table of the intensity measurement of
the same area as in point 3 after importing the single
tifs as an image sequence.</span></p>
<p class="MsoNormal"><span lang="EN-US">My user saw that
problem on a Mac with Fiji but we also saw it on my PC
as well.<br>
I downloaded the latest stable release from </span><a
moz-do-not-send="true"
href="http://downloads.openmicroscopy.org/bio-formats/4.4.9/#tools"
target="_blank"><span lang="EN-US">http://downloads.openmicroscopy.org/bio-formats/4.4.9/#tools</span></a><span
lang="EN-US"><br>
I also tried to update the plugin to the trunk build
with Plugins -> Loci -> Update loci plugins but
it always fails with the message “an error occurred
while downloading the plugins”<br>
I did all that that with ImageJ 1.48g<br>
I also tried with Fiji. I updated Fiji through the
menu and also manually updated the loci plugin there.
I am not sure if it takes the trunk build in that
case. <br>
Anyway it is always the same. We see the change in
intensity in every second time frame.<br>
I also tried an older version of the loci plugin from
2010 but it shows the same effect. <br>
<br>
We never so that problem with any lif files before.
But our acquisition software has been updated a few
weeks ago and I am not sure if Leica changed something
on the file format.</span></p>
<p class="MsoNormal"><span lang="EN-US">So I was using
ImageJ 1.48g with the loci plugin 4.4.9 on a windows 7
64bit machine with Java Version 7 Update 45 (build
1.7.0_45-b18).</span></p>
<p class="MsoNormal"><span lang="EN-US">We would be more
than happy if you can have a look at our problem. If
you need more information just let me know.</span></p>
<br>
<p class="MsoNormal"><span lang="EN-US">Many thanks and
best regards<span class="HOEnZb"></span></span></p>
<span class="HOEnZb"><font color="#888888"> <span
lang="EN-US">Pascal</span> </font></span></div>
<br>
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</blockquote>
</div>
<br>
</div>
</blockquote>
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