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

[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>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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> ome-users at lists.openmicroscopy.org.uk
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>
>
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