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Dear David
<div><br>
</div>
<div>Thanks for sending me the file. </div>
<div>It seems that FLIMfit has a problem loading .sdt files in measurement_mode 13.</div>
<div>Thanks for picking that up.</div>
<div>I hope to have a partial fix for you tomorrow.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div><br>
</div>
<div>Ian</div>
<div><br>
</div>
<div><br>
<div>
<div>On 11 Feb 2014, at 11:54, Ian Munro <<a href="mailto:i.munro@imperial.ac.uk">i.munro@imperial.ac.uk</a>> wrote:</div>
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<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div>Dear David</div>
<div><br>
</div>
<div>I have so far failed to reproduce your problem. Do you think you could send me the file in question to try?</div>
<div><br>
</div>
<div>Sincerely </div>
<div><br>
</div>
<div>Ian</div>
<div><br>
</div>
<br>
<div>
<div>On 10 Feb 2014, at 17:45, Ian Munro <<a href="mailto:i.munro@imperial.ac.uk">i.munro@imperial.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div>Dear Julio</div>
<div><br>
</div>
<div>Thank you for the clarification. I will now check for FLIMfit problems with this server & get back to you, hopefully, tomorrow.</div>
<div><br>
</div>
<div>FLIMfit is currently being tested by us against 5.0.0-rc1 & we have found no problems as yet.</div>
<div>However, any help you can give us in testing would be very welcome.</div>
<div><br>
</div>
<div>Regards </div>
<div><br>
</div>
<div>Ian </div>
<div><br>
</div>
<br>
<div>
<div>On 10 Feb 2014, at 17:19, Julio Mateos Langerak <<a href="mailto:julio.mateos-langerak@igh.cnrs.fr">julio.mateos-langerak@igh.cnrs.fr</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
Dear all,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Best regards, Julio</div>
<div><br>
</div>
<div>
<div>
<div>On 10 Feb 2014, at 15:41, David Lleres <<a href="mailto:david.lleres@igmm.cnrs.fr">david.lleres@igmm.cnrs.fr</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Dear Ian,
<div>Good to hear from you. I'm actually using the OMERO 4.4.0-ice35-b112 and the <span style="font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 19px; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; ">FLIMfitFLIMfit
4.5.12-DEV for FLIMfit.</span></div>
<div><font class="Apple-style-span" face="'Lucida Grande', Verdana, Lucida, Helvetica, Arial, sans-serif"><span class="Apple-style-span" style="font-size: 13px; line-height: 19px;">Cheers,</span></font></div>
<div><font class="Apple-style-span" face="'Lucida Grande', Verdana, Lucida, Helvetica, Arial, sans-serif"><span class="Apple-style-span" style="font-size: 13px; line-height: 19px;">David</span></font></div>
<div><font class="Apple-style-span" face="'Lucida Grande', Verdana, Lucida, Helvetica, Arial, sans-serif"><span class="Apple-style-span" style="font-size: 13px; line-height: 19px;"><br>
</span></font></div>
<div>
<div><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px; font-size: inherit;">David
Lleres, PhD<br>
IGMM (Institute of Molecular Genetics of Montpellier)<br>
CNRS/UMR 5535<br>
1919 Route de Mende<br>
34293 Montpellier Cedex 5<br>
France<br>
Tel. (33) (0)4 34 35 96 66<br>
Fax. (33) (0)4 34 35 96 34<br>
Web site : <a href="http://www.igmm.cnrs.fr/">http://www.igmm.cnrs.fr</a></span> </div>
<br>
<div>
<div>On 10 Feb 2014, at 15:12, Munro, Ian wrote:</div>
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<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
Dear David
<div><br>
</div>
<div>Thanks for your e-mail & my apologies for the problems that you have been having.</div>
<div>Could you please tell me what version of OMERO you are currently using ?</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Ian</div>
<div><br>
</div>
<div>
<div>On 10 Feb 2014, at 14:02, David Lleres <<a href="mailto:david.lleres@igmm.cnrs.fr">david.lleres@igmm.cnrs.fr</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Dear Helen,
<div><br>
<div>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 ( <span style="font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 19px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;">MATLAB
Compiler Runtime (MCR), then FLIMfitFLIMfit 4.5.12-DEV).</span></div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>I certainly do some basic mistakes using FLIMfit module as I just start discovering it ! However, I would appreciate your help to use it.</div>
<div>Many thanks in advance,</div>
<div>Best wishes,</div>
<div>David</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><span><Screen Shot 2014-02-10 at 14.53.40.png></span></div>
<div><br>
<div apple-content-edited="true">
<div>David Lleres, PhD<br>
IGMM (Institute of Molecular Genetics of Montpellier)<br>
CNRS/UMR 5535<br>
1919 Route de Mende<br>
34293 Montpellier Cedex 5<br>
France<br>
Tel. (33) (0)4 34 35 96 66<br>
Fax. (33) (0)4 34 35 96 34<br>
Web site : <a href="http://www.igmm.cnrs.fr/">http://www.igmm.cnrs.fr</a></div>
</div>
<br>
<div>
<div>On 10 Feb 2014, at 11:59, Helen Flynn wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Dear David,
<div><br>
</div>
<div>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</div>
<div><a href="http://www.openmicroscopy.org/site/products/partner/flimfit/downloads">http://www.openmicroscopy.org/site/products/partner/flimfit/downloads</a></div>
<div>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.</div>
<div>If you still have a problem, please let us know,</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>Helen Flynn</div>
<div><br>
</div>
<div><br>
<div>
<div>On 10 Feb 2014, at 09:47, David Lleres <<a href="mailto:david.lleres@igmm.cnrs.fr">david.lleres@igmm.cnrs.fr</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Dear all,
<div><br>
</div>
<div>
<div>Not sure it is the right place to post it but anyway here it's my problem:</div>
<div><br>
</div>
<div>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:</div>
<div>
<div>Executing FlIMfit from </div>
<div>/Applications/FLIMfit 4.5.10.app/Contents/Resources</div>
<div>----</div>
<div>Checking for correct version of Matlab MCR</div>
<div><br>
</div>
<div>Found MCR !</div>
<div>----</div>
<div>Setting up environment variables</div>
<div>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</div>
<div>PATH is /usr/bin:/bin:/usr/sbin:/sbin:/Applications/FLIMfit 4.5.10.app/Contents/Resources</div>
<div>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.</div>
<div>Error using cell</div>
<div>NaN and Inf not allowed.</div>
<div><br>
</div>
<div>Error in flim_data_series.get_channels (line 71)</div>
<div><br>
</div>
<div>Error in flim_data_series/load_single (line 57)</div>
<div>Error in flim_data_series_controller/load_single (line 160)</div>
<div>Error in front_end_menu_controller/menu_file_load_single_callback (line 495)</div>
<div>Error in front_end_menu_controller/set_callbacks/@(varargin)obj.menu_file_load_single_callback(varargin{:})</div>
<div>Error using waitfor</div>
<div>Error while evaluating uimenu Callback</div>
</div>
<div><br>
</div>
<div>Could anyone tell me where is the problem ?</div>
<div>Many thanks in advance for your help.</div>
<div>Best regards,</div>
<div>David</div>
<div><br>
</div>
<div><br>
<div apple-content-edited="true">
<div>David Lleres, PhD<br>
IGMM (Institute of Molecular Genetics of Montpellier)<br>
CNRS/UMR 5535<br>
1919 Route de Mende<br>
34293 Montpellier Cedex 5<br>
France<br>
Tel. (33) (0)4 34 35 96 66<br>
Fax. (33) (0)4 34 35 96 34<br>
Web site : <a href="http://www.igmm.cnrs.fr/">http://www.igmm.cnrs.fr</a></div>
</div>
<br>
</div>
</div>
</div>
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<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana"><br class="Apple-interchange-newline">
__________________________________________</font></span></font></div>
<div><span class="Apple-style-span" style="font-size: 13px; "><b><font class="Apple-style-span" face="Verdana"><i>Julio Mateos Langerak, PhD.</i></font></b></span></div>
<div><font class="Apple-style-span" face="Verdana" size="3"><span class="Apple-style-span" style="font-size: 13px; "><i>OMX manager</i></span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana">Arnaud
de Villeneuve Campus Imaging Facility</font></span></span></span></span></span></span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana">Montpellier
RIO Imaging</font></span></span></span></span></span></span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana">Montpellier
BIOCAMPUS, UMS3426</font></span></span></span></span></span></span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana">Institut
de Génétique Humaine-CNRS</font></span></span></span></span></span></span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana">141,
rue de la Cardonille</font></span></span></span></span></span></span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana">F-34396</font></span></span></span></span></span></span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana"> Montpellier</font></span></span></span></span></span></span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-converted-space"><font class="Apple-style-span" face="Verdana"> </font></span><font class="Apple-style-span" face="Verdana">(France)</font></span></span></span></span></span></span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 12px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana">e-mail:
<a href="mailto:Julio.Mateos-Langerak@igh.cnrs.fr">Julio.Mateos-Langerak@igh.cnrs.fr</a></font></span></span></span></span></span></span></font></span><font class="Apple-style-span" face="Verdana">phone: +33.4.34.35.99.90</font></span></span></span></span></span></span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana">fax:
+33.4.34.35.99.01</font></span></span></span></span></span></span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><span class="Apple-style-span" style="font-size: 13px; "><font class="Apple-style-span" face="Verdana">URL:
<a href="http://www.mri.cnrs.fr/">http://www.mri.cnrs.fr/</a></font></span></span></span></span></span></span></font></div>
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