[ome-users] FLIMfit software issue

Thu Feb 13 10:47:43 GMT 2014

Dear Ian,

Yes it's working. Thanks !  I can upload my .sdt files and the display is correct through FLIMfit .  I'll now work on How to fit data following the notice you wrote.
You don't mind if when I'm stuck to  ask you some help and expertise.
Many thanks.

Best regards,
David

David Lleres, PhD
IGMM (Institute of Molecular Genetics of Montpellier)
CNRS/UMR 5535
1919 Route de Mende
34293 Montpellier Cedex 5
France
Tel. (33) (0)4 34 35 96 66
Fax. (33) (0)4 34 35 96 34
Web site : http://www.igmm.cnrs.fr

On 12 Feb 2014, at 19:01, Munro, Ian wrote:

> Dear David
> 
> Sorry something seems to have failed there. 
> Can you access
> http://ci.openmicroscopy.org/view/Consortium/job/FLIMFit-4.4-build/lastSuccessfulBuild/artifact/ ?
> 
> Ian
> 
> 
> 
> On 12 Feb 2014, at 17:23, David Lleres <david.lleres at igmm.cnrs.fr> wrote:
> 
>> Dear Ian,
>> 
>> Thanks a lot for your email. However, so far I can not download the today’s build of FLIMfit from the http://www.openmicroscopy.org/site/products/partner/flimfit/downloads.
>> It seems that the link is disconnected.
>> All the best,
>> David 
>> 
>> David Lleres, PhD
>> IGMM (Institute of Molecular Genetics of Montpellier)
>> CNRS/UMR 5535
>> 1919 Route de Mende
>> 34293 Montpellier Cedex 5
>> France
>> Tel. (33) (0)4 34 35 96 66
>> Fax. (33) (0)4 34 35 96 34
>> Web site : http://www.igmm.cnrs.fr
>> 
>> On 12 Feb 2014, at 13:10, Munro, Ian wrote:
>> 
>>> Good afternoon David
>>> 
>>> If you download today’s build of FLIMfit (as before) you should now be able to open your files directly from disk 
>>> using the File menu -> Load FLIm Data (or Load FLIM Dataset for multiple files.
>>> 
>>> I would appreciate it if you could try this & see if it’s ok with your data.
>>> Sadly this won’t fix the problems loading from OMERO 
>>> but if it  looks good to you I can start work on this.
>>> 
>>> All the best.
>>> 
>>> Ian
>>> 
>>> 
>>> On 11 Feb 2014, at 16:11, Ian Munro <i.munro at imperial.ac.uk> wrote:
>>> 
>>>> Dear David
>>>> 
>>>> Thanks for sending me the file. 
>>>> It seems that FLIMfit has a problem loading .sdt files in measurement_mode 13.
>>>> Thanks for picking that up.
>>>> I hope to  have a partial fix for you tomorrow.
>>>> 
>>>> Regards
>>>> 
>>>> 
>>>> Ian
>>>> 
>>>> 
>>>> On 11 Feb 2014, at 11:54, Ian Munro <i.munro at imperial.ac.uk> wrote:
>>>> 
>>>>> Dear David
>>>>> 
>>>>> I have so far failed to reproduce your problem. Do you think you could send me the file in question to try?
>>>>> 
>>>>> Sincerely 
>>>>> 
>>>>> Ian
>>>>> 
>>>>> 
>>>>> On 10 Feb 2014, at 17:45, Ian Munro <i.munro at imperial.ac.uk> wrote:
>>>>> 
>>>>>> Dear Julio
>>>>>> 
>>>>>> Thank you for the clarification. I will now check for FLIMfit  problems with this server & get back to you, hopefully, tomorrow.
>>>>>> 
>>>>>> FLIMfit is currently being tested by us against 5.0.0-rc1 & we have found no problems as yet.
>>>>>> However, any help you can give us in testing would be very welcome.
>>>>>> 
>>>>>> Regards 
>>>>>> 
>>>>>> Ian 
>>>>>> 
>>>>>> 
>>>>>> On 10 Feb 2014, at 17:19, Julio Mateos Langerak <julio.mateos-langerak at igh.cnrs.fr> wrote:
>>>>>> 
>>>>>>> Dear all,
>>>>>>> 
>>>>>>> Maybe there is a bit of my mistake here in updating people. The OMERO server we are using in Montpellier is OMERO 4.4.8p1. This is the one David is using I suppose.
>>>>>>> 
>>>>>>> Something else by the way… We are planning an upgrade to OMERO 5 as soon as it comes out. Did you try FLIMfit with OMERO 5-RC. I could try it otherwise on a virtual machine.
>>>>>>> 
>>>>>>> Best regards, Julio
>>>>>>> 
>>>>>>> On 10 Feb 2014, at 15:41, David Lleres <david.lleres at igmm.cnrs.fr> wrote:
>>>>>>> 
>>>>>>>> Dear Ian, 
>>>>>>>> Good to hear from you. I'm actually using the OMERO 4.4.0-ice35-b112 and the FLIMfitFLIMfit 4.5.12-DEV for FLIMfit.
>>>>>>>> Cheers,
>>>>>>>> David
>>>>>>>> 
>>>>>>>> David Lleres, PhD
>>>>>>>> IGMM (Institute of Molecular Genetics of Montpellier)
>>>>>>>> CNRS/UMR 5535
>>>>>>>> 1919 Route de Mende
>>>>>>>> 34293 Montpellier Cedex 5
>>>>>>>> France
>>>>>>>> Tel. (33) (0)4 34 35 96 66
>>>>>>>> Fax. (33) (0)4 34 35 96 34
>>>>>>>> Web site : http://www.igmm.cnrs.fr
>>>>>>>> 
>>>>>>>> On 10 Feb 2014, at 15:12, Munro, Ian wrote:
>>>>>>>> 
>>>>>>>>> Dear David
>>>>>>>>> 
>>>>>>>>> Thanks for your e-mail & my apologies for the problems that you have been having.
>>>>>>>>> Could you please tell me what version of OMERO you are currently using ?
>>>>>>>>> 
>>>>>>>>> Regards
>>>>>>>>> 
>>>>>>>>> Ian
>>>>>>>>> 
>>>>>>>>> On 10 Feb 2014, at 14:02, David Lleres <david.lleres at igmm.cnrs.fr> wrote:
>>>>>>>>> 
>>>>>>>>>> Dear Helen,
>>>>>>>>>> 
>>>>>>>>>> Thanks for your previous email. I did what you told me and I've followed the instructions for downloading now the latest  FLIMfit version on Mac ( MATLAB Compiler Runtime (MCR), then FLIMfitFLIMfit 4.5.12-DEV).
>>>>>>>>>> However now I've got another issue using it. I've cc this email to FLIMfit team at Imperial so they can give me advice as well.
>>>>>>>>>> 
>>>>>>>>>> From FLIMfit software menu, I do  OMERO/Load FLIM data Single FOV, then the image displayed do not represent my 256x256 orginal file but instead seems to show a part of the acquisition ( 32x32). Also the decay seems not correct, and the value tau from fitting is  out of range. I've attached a screen shot.
>>>>>>>>>> 
>>>>>>>>>> I certainly do some basic mistakes using FLIMfit module as I just start discovering it ! However, I would appreciate your help to use it.
>>>>>>>>>> Many thanks in advance,
>>>>>>>>>> Best wishes,
>>>>>>>>>> David
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> <Screen Shot 2014-02-10 at 14.53.40.png>
>>>>>>>>>> 
>>>>>>>>>> David Lleres, PhD
>>>>>>>>>> IGMM (Institute of Molecular Genetics of Montpellier)
>>>>>>>>>> CNRS/UMR 5535
>>>>>>>>>> 1919 Route de Mende
>>>>>>>>>> 34293 Montpellier Cedex 5
>>>>>>>>>> France
>>>>>>>>>> Tel. (33) (0)4 34 35 96 66
>>>>>>>>>> Fax. (33) (0)4 34 35 96 34
>>>>>>>>>> Web site : http://www.igmm.cnrs.fr
>>>>>>>>>> 
>>>>>>>>>> On 10 Feb 2014, at 11:59, Helen Flynn wrote:
>>>>>>>>>> 
>>>>>>>>>>> Dear David,
>>>>>>>>>>> 
>>>>>>>>>>> I'm afraid the version of FLIMfit you have downloaded is out of date. Many apologies for that, I've now updated the downloads page
>>>>>>>>>>> http://www.openmicroscopy.org/site/products/partner/flimfit/downloads
>>>>>>>>>>> to provide the latest stable daily build version which goes through our continuous integration testing system. Please download and install the new version and it will hopefully solve your issue.
>>>>>>>>>>> If you still have a problem, please let us know,
>>>>>>>>>>> 
>>>>>>>>>>> Regards,
>>>>>>>>>>> 
>>>>>>>>>>> Helen Flynn
>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>>>> On 10 Feb 2014, at 09:47, David Lleres <david.lleres at igmm.cnrs.fr> wrote:
>>>>>>>>>>> 
>>>>>>>>>>>> Dear all,
>>>>>>>>>>>> 
>>>>>>>>>>>> Not sure it is the right place to post it but anyway here it's my problem:
>>>>>>>>>>>> 
>>>>>>>>>>>> I'm trying to load a FLIM data (.sdt from B&H) through FLIMfit_MACI64 but I don't succeed. Nothing is uploaded. I've got the following error message:
>>>>>>>>>>>> Executing FlIMfit from 
>>>>>>>>>>>> /Applications/FLIMfit 4.5.10.app/Contents/Resources
>>>>>>>>>>>> ----
>>>>>>>>>>>> Checking for correct version of Matlab MCR
>>>>>>>>>>>> 
>>>>>>>>>>>> Found MCR !
>>>>>>>>>>>> ----
>>>>>>>>>>>> Setting up environment variables
>>>>>>>>>>>> DYLD_LIBRARY_PATH is :/Applications/MATLAB/MATLAB_Compiler_Runtime/v81/runtime/maci64:/Applications/MATLAB/MATLAB_Compiler_Runtime/v81/bin/maci64:/Applications/MATLAB/MATLAB_Compiler_Runtime/v81/sys/os/maci64:/Applications/FLIMfit 4.5.10.app/Contents/Resources
>>>>>>>>>>>> PATH is /usr/bin:/bin:/usr/sbin:/sbin:/Applications/FLIMfit 4.5.10.app/Contents/Resources
>>>>>>>>>>>> objc[3295]: Class bootstrap is implemented in both /Applications/MATLAB/MATLAB_Compiler_Runtime/v81/bin/maci64/libmwlaunchermain.dylib and /Applications/FLIMfit 4.5.10.app/Contents/Resources/FLIMfit_MACI64.app/Contents/MacOS/FLIMfit_MACI64. One of the two will be used. Which one is undefined.
>>>>>>>>>>>> Error using cell
>>>>>>>>>>>> NaN and Inf not allowed.
>>>>>>>>>>>> 
>>>>>>>>>>>> Error in flim_data_series.get_channels (line 71)
>>>>>>>>>>>> 
>>>>>>>>>>>> Error in flim_data_series/load_single (line 57)
>>>>>>>>>>>> Error in flim_data_series_controller/load_single (line 160)
>>>>>>>>>>>> Error in front_end_menu_controller/menu_file_load_single_callback (line 495)
>>>>>>>>>>>> Error in front_end_menu_controller/set_callbacks/@(varargin)obj.menu_file_load_single_callback(varargin{:})
>>>>>>>>>>>> Error using waitfor
>>>>>>>>>>>> Error while evaluating uimenu Callback
>>>>>>>>>>>> 
>>>>>>>>>>>> Could anyone tell me where is the problem ?
>>>>>>>>>>>> Many thanks in advance for your help.
>>>>>>>>>>>> Best regards,
>>>>>>>>>>>> David
>>>>>>>>>>>> 
>>>>>>>>>>>> 
>>>>>>>>>>>> David Lleres, PhD
>>>>>>>>>>>> IGMM (Institute of Molecular Genetics of Montpellier)
>>>>>>>>>>>> CNRS/UMR 5535
>>>>>>>>>>>> 1919 Route de Mende
>>>>>>>>>>>> 34293 Montpellier Cedex 5
>>>>>>>>>>>> France
>>>>>>>>>>>> Tel. (33) (0)4 34 35 96 66
>>>>>>>>>>>> Fax. (33) (0)4 34 35 96 34
>>>>>>>>>>>> Web site : http://www.igmm.cnrs.fr
>>>>>>>>>>>> 
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> ome-users mailing list
>>>>>>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> _______________________________________________
>>>>>>>>> ome-users mailing list
>>>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>> 
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>>>>>>> 
>>>>>>> 
>>>>>>> __________________________________________
>>>>>>> Julio Mateos Langerak, PhD.
>>>>>>> OMX manager
>>>>>>> Arnaud de Villeneuve Campus Imaging Facility
>>>>>>> Montpellier RIO Imaging
>>>>>>> Montpellier BIOCAMPUS, UMS3426
>>>>>>> Institut de Génétique Humaine-CNRS
>>>>>>> 141, rue de la Cardonille
>>>>>>> F-34396 Montpellier (France)
>>>>>>> e-mail: Julio.Mateos-Langerak at igh.cnrs.frphone: +33.4.34.35.99.90
>>>>>>> fax: +33.4.34.35.99.01
>>>>>>> URL: http://www.mri.cnrs.fr/
>>>>>>> __________________________________________
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 

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