[ome-users] FLIMfit software issue

Mon Feb 10 14:41:21 GMT 2014

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 I'm afraid the version of FLIMfit you have downloaded is out of date.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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