<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 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 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 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<u></u><u></u></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.<u></u><u></u></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. <u></u><u></u></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.<u></u><u></u></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 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.<u></u><u></u></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).<u></u><u></u></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.<u></u><u></u></span></p>
<br>
<p class="MsoNormal"><span lang="EN-US">Many thanks and best regards<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></span></p><span class="HOEnZb"><font color="#888888">
<span lang="EN-US">Pascal</span>
</font></span></div>
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