[ome-users] FLIMfit software issue

Mon Feb 10 17:45:25 GMT 2014

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<mailto: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<mailto: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<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<mailto: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<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<mailto: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<http://www.igmm.cnrs.fr/>

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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.fr<mailto:Julio.Mateos-Langerak at igh.cnrs.fr>phone: +33.4.34.35.99.90
fax: +33.4.34.35.99.01
URL: http://www.mri.cnrs.fr/
__________________________________________

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