[ome-users] Increase in intensity in every second frame in Leica lif files

[Pascal Lorentz]

Dear Curtis

Thanks a lot for your reply.
I just uploaded the zip folder "lif file problem" containing the four 
files on the specified website.

I am curious what the problem is.

Best regards

Pascal

Am 21.11.2013 10:18, schrieb Curtis Rueden:
> Hi Pascal,
>
> > 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.
>
> 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:
>
> http://fiji.sc/Bio-Formats#Daily_builds
>
> 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).
>
> > Anyway it is always the same. We see the change in intensity in every
> > second time frame.
>
> Indeed, it sounds like a bug.
>
> > I can provide you with 4 files but I need an ftp access
>
> Thanks. If you ZIP up the four files, you can upload them using this link:
>
> http://qa.openmicroscopy.org.uk/qa/upload/
>
> Unless your archive is >500MB? In which case, let us know and we will 
> provide alternative upload instructions off-list.
>
> Regards,
> Curtis
>
>
> On Thu, Nov 21, 2013 at 2:38 AM, Pascal Lorentz 
> <Lorentz.Pascal at gmail.com <mailto:Lorentz.Pascal at gmail.com>> wrote:
>
>     Dear Bio Formats team
>
>     First of all I would like to thank you for your impressive work.
>     This plugin is really great.
>
>     We came across a problem yesterday.
>     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.
>     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.
>     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.
>
>     I can provide you with 4 files but I need an ftp access to upload
>     them:
>     1. The original lif file “Series 7.lif”
>     2. The image sequence after exporting from the Leica Software and
>     importing as sequence in ImageJ saved as tiff “image_sequence.tif”
>     3. The results table of the intensity measurement of an area of
>     the lif dataset opened with the loci importer
>     “Results_loci_import.xls.
>     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.
>
>     My user saw that problem on a Mac with Fiji but we also saw it on
>     my PC as well.
>     I downloaded the latest stable release from
>     http://downloads.openmicroscopy.org/bio-formats/4.4.9/#tools
>     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”
>     I did all that that with ImageJ 1.48g
>     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.
>     Anyway it is always the same. We see the change in intensity in
>     every second time frame.
>     I also tried an older version of the loci plugin from 2010 but it
>     shows the same effect.
>
>     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.
>
>     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).
>
>     We would be more than happy if you can have a look at our problem.
>     If you need more information just let me know.
>
>
>     Many thanks and best regards
>
>     Pascal
>
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>

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