[ome-users] FLIMfit software issue

Melissa Linkert melissa at glencoesoftware.com
Wed Feb 12 08:41:22 GMT 2014 

Hi 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.

With respect to Ian's comment about viewing these files in OMERO, there is
now a ticket for the problem on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/11983

You have been CC'd on the ticket, and so will be automatically notified
of our progress.  If you prefer not to receive updates, please let us
know.

Regards,
-Melissa

On Wed, Feb 12, 2014 at 12:10:38PM +0000, 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<mailto: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<mailto: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<mailto: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<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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