[ome-users] Increase in intensity in every second frame in Leica lif files
Melissa Linkert
melissa at glencoesoftware.com
Tue Feb 4 08:51:58 GMT 2014
Hi Pascal,
> Thanks that did the trick. I always thought updating Fiji would also
> automatically install the latest loci plugin.
I'm glad to hear it's working now!
> In addition I tried to update the loci plugin in ImageJ: Plugins ->
> LOCI -> Update LOCI plugins. Unfortunately I always get the message:
> "An Error occurred while downloading the LOCI plugins.
> I found a temp file in the plugins folder called loci_
> tools.jar.tmp. From the size of the file it seemed that it has been
> fully downloaded. Therefore I tried to just remove the .tmp and this
> seems to work.
> Anyway, any idea why the installation through the update menu does not work?
The "Plugins > LOCI > Update LOCI Plugins" option is not intended to be
used in Fiji - in fact, current versions should not attempt to download
a new loci_tools.jar at all if you are using Fiji.
In regular ImageJ installations, that message often means that the download may
have been successful, but the existing loci_tools.jar could not be overwritten
due to insufficient permissions. In that case, closing ImageJ, renaming
loci_tools.jar.tmp to loci_tools.jar, and restarting ImageJ should
finish the upgrade procedure.
Regards,
-Melissa
On Tue, Feb 04, 2014 at 09:27:21AM +0100, Pascal Lorentz wrote:
> Dear Melissa
>
> Thanks that did the trick. I always thought updating Fiji would also
> automatically install the latest loci plugin.
>
> In addition I tried to update the loci plugin in ImageJ: Plugins ->
> LOCI -> Update LOCI plugins. Unfortunately I always get the message:
> "An Error occurred while downloading the LOCI plugins.
> I found a temp file in the plugins folder called loci_
> tools.jar.tmp. From the size of the file it seemed that it has been
> fully downloaded. Therefore I tried to just remove the .tmp and this
> seems to work.
> Anyway, any idea why the installation through the update menu does not work?
>
> At least the problem is solved and I am very grateful.
>
> Best regards
>
> Pascal
>
>
> Am 03.02.2014 19:30, schrieb Melissa Linkert:
> >Hi Pascal,
> >
> >>We still have problems with the intensity changes in every second
> >>frame after opening the mentioned lif files. I used the latest Fiji.
> >>I can again send you the file if you need it.
> >>
> >>I think the problem that has been solved under the following link
> >>was something different.
> >>
> >>https://github.com/openmicroscopy/bioformats/pull/804
> >>
> >>
> >>Could you please have a look at the problem again.
> >Have you followed the instructions for updating Fiji to Bio-Formats 5 from
> >http://fiji.sc/Bio-Formats#Daily_builds? Could you please verify that
> >"Help > About Plugins > LOCI Plugins" shows a recent date (within the
> >last couple of days) and a version number similar to 5.0.0-DEV?
> >
> >Regards,
> >-Melissa
> >
> >On Fri, Jan 31, 2014 at 11:16:09AM +0100, Pascal Lorentz wrote:
> >>Dear Melissa
> >>
> >>We still have problems with the intensity changes in every second
> >>frame after opening the mentioned lif files. I used the latest Fiji.
> >>I can again send you the file if you need it.
> >>
> >>I think the problem that has been solved under the following link
> >>was something different.
> >>
> >>https://github.com/openmicroscopy/bioformats/pull/804
> >>
> >>
> >>Could you please have a look at the problem again.
> >>
> >>Thanks a lot and best regards
> >>
> >>Pascal
> >>
> >>
> >>
> >>
> >>
> >>Am 22.11.2013 03:27, schrieb Melissa Linkert:
> >>>Hi Pascal,
> >>>
> >>>>I just uploaded the zip folder "lif file problem" containing the
> >>>>four files on the specified website.
> >>>>
> >>>>I am curious what the problem is.
> >>>Thank you for uploading an example dataset.
> >>>
> >>>The problem is that the reported order of channels and timepoints does
> >>>not match the actual order. We are reviewing a fix for the problem
> >>>here:
> >>>
> >>>https://github.com/openmicroscopy/bioformats/pull/804
> >>>
> >>>Once that shows as being closed, enabling the "Bio-Formats 5" update
> >>>site (in Fiji) or downloading the latest trunk build (in ImageJ) from:
> >>>
> >>>http://downloads.openmicroscopy.org/bio-formats/5.0.0-beta1/
> >>>
> >>>should solve the problem.
> >>>
> >>>Regards,
> >>>-Melissa
> >>>
> >>>On Thu, Nov 21, 2013 at 03:33:34PM +0100, Pascal Lorentz wrote:
> >>>>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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> >>>>> <mailto:ome-users at lists.openmicroscopy.org.uk>
> >>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >>>>>
> >>>>>
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