[ome-users] Increase in intensity in every second frame in Leica lif files
Pascal Lorentz
Lorentz.Pascal at gmail.com
Wed Feb 5 09:20:09 GMT 2014
Dear Melissa
>> 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.
This is exactly what I did. Thanks a lot for clarifying.
Best regards
Pascal
>
> 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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>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>> <mailto:ome-users at lists.openmicroscopy.org.uk>
>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>
>>>>>>>
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