[ome-users] FLIMfit software issue

Mon Feb 10 17:19:40 GMT 2014

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
>>> 
>> 
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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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