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<div class="">Hello again Emilie</div>
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<div class="">Just to clarify a couple of points now that I’m back at work.</div>
<div class="">Firstly, in addition to being able to control the colour map range , as I described earlier, FLIMfit also allows you to invert the colour map used.</div>
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<div class="">If this doesnn’t give you exactly the display you need then as Sean describes you can simply export the fitted data as a .tiff and re-import into Matlab to display as you wish using File-> Export Images.</div>
<div class="">However please be aware that the exported .tiff contains NaNs in those pixels which were excluded from the fit using the “Integrated Min” Intensity threshold on the Data tab.</div>
<div class="">You may, therefore, have to replace these with a suitable value in order to get the display that you require.</div>
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<div class="">Best Regards</div>
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<div class="">Ian</div>
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<div class="">On 27 Dec 2015, at 12:23, Warren, Sean Christopher <<a href="mailto:sean.warren09@imperial.ac.uk" class="">sean.warren09@imperial.ac.uk</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Tahoma; font-size: 13px;" class="">Dear Emilie,</span></div>
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<div style="font-family: Tahoma; font-size: 13px;" class="">Apologies for the delay replying, I'm glad you're finding FLIMfit useful!</div>
<div style="font-family: Tahoma; font-size: 13px;" class="">Hopefully the following should help:</div>
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</span></div>
<div style="font-family: Tahoma; font-size: 13px;" class=""><font color="#0000ff" class=""><span style="font-family: Verdana, sans-serif; font-size: 10pt; text-indent: -18pt;" class="">>Is it possible to export FLIMfit results to matlab, such that I can make
changes to the colours and not have the lifetime range written in the image itself.</span><br class="">
</font><font face="Verdana, sans-serif" class="">Yes, the raw lifetime (or other parameter values) may be exported as floating point TIFF files using the following procedure:</font></div>
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<li style="font-size: 10pt; font-family: Verdana;" class=""><font face="Verdana, sans-serif" class="">In the images tab, select the desired parameters for export from the list on the right. Use the first tick box, not the second which displays the intensity
merged images. </font></li><li style="font-size: 10pt; font-family: Verdana;" class=""><font face="Verdana, sans-serif" class="">From the menu, select File>Export Selected Images... and choose a root filename</font></li><li class=""><font face="Verdana, sans-serif" class=""><font size="2" class="">For all the processed images, all of the selected parameters will be exported as images. There will be one </font>colour mapped<font size="2" class=""> image with the lifetime scale
and one with 'raw' in the filename which contains the true lifetime values and may be opened in MATLAB etc. </font></font></li></ul>
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<div class=""><span style="font-family: Verdana, sans-serif; font-size: 10pt; text-indent: -18pt;" class=""><font color="#0000ff" class="">> Is it possible to display the IRF shift? </font></span></div>
<span style="text-indent: -24px;" class=""><font face="Verdana, sans-serif" class="">The IRF shift is displayed as 't0' (for time zero) in the parameter tab and images when fitted.</font></span></div>
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<div style="text-indent: -24px;" class=""><span style="color: rgb(0, 0, 255); font-size: 10pt; text-indent: -18pt; font-family: Verdana, sans-serif;" class=""><span style="font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> </span></span></div>
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</span></div>
<font color="#0000ff" class=""><span style="font-size: 10pt; text-indent: -18pt; font-family: Verdana, sans-serif;" class="">> Would it be possible to fix the beta values between certain values, for instance always positive?</span><br class="">
</font>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<font face="Verdana, sans-serif" size="2" class="">For technical reasons, this is not currently possible using global analysis. However, if you set the fitting algorithm to 'Maximum Likelihood' in the Advanced fitting tab the beta values will be constrained
to positive values. This will only work for 'pixelwise' </font><span style="font-family: Verdana, sans-serif; font-size: small;" class="">fitting </span><span style="font-family: Verdana, sans-serif; font-size: small;" class="">(i.e. fitting pixels independently). </span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;" class=""><br class="">
</span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<font face="Verdana, sans-serif" size="2" class="">It's worth noting that if you're consistently observing negative beta values this is often due to a mismatch between the model and the data which is being compensated by fitting negative values. Examples of
potential problems include a difference in the IRF shift between the measured IRF (or reference) and the data, an uncompensated background component, or, in the case of FRET, a donor with a complex decay. If you'd like to discuss this further please feel free
to drop me an email. </font></div>
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<font face="Verdana, sans-serif" size="2" class="">Best Regards,</font></div>
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<font face="Verdana, sans-serif" size="2" class="">Sean </font></div>
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<div id="divRpF75611" style="direction: ltr;" class=""><font face="Tahoma" size="2" class=""><b class="">From:</b> FLIMfit-users [<a href="mailto:flimfit-users-bounces@lists.openmicroscopy.org.uk" class="">flimfit-users-bounces@lists.openmicroscopy.org.uk</a>]
on behalf of Munro, Ian [<a href="mailto:i.munro@imperial.ac.uk" class="">i.munro@imperial.ac.uk</a>]<br class="">
<b class="">Sent:</b> Wednesday, 23 December 2015 07:46<br class="">
<b class="">To:</b> Wientjes, Emilie; '<a href="mailto:flimfit-users@lists.openmicroscopy.org.uk" class="">flimfit-users@lists.openmicroscopy.org.uk</a>'<br class="">
<b class="">Subject:</b> Re: [FLIMfit-users] Exporting FLIMfit data and boundaries for beta values<br class="">
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Hi Emile<br class="">
<br class="">
Glad to hear you're finding FLIMfit useful. I'm afraid I'm away from the office now until next year and only have a phone with me so can't reply in full but p!ease note that you can manually set the range over which the colour map is stretched by unticking
the 'auto' box at top right in the images tab . I hope this helps for now.<br class="">
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Kind regards<br class="">
<br class="">
Ian<br class="">
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<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b> FLIMfit-users <<a href="mailto:flimfit-users-bounces@lists.openmicroscopy.org.uk" class="">flimfit-users-bounces@lists.openmicroscopy.org.uk</a>>
on behalf of Wientjes, Emilie <<a href="mailto:emilie.wientjes@wur.nl" class="">emilie.wientjes@wur.nl</a>><br class="">
<b class="">Sent:</b> 18 December 2015 10:56:09<br class="">
<b class="">To:</b> '<a href="mailto:flimfit-users@lists.openmicroscopy.org.uk" class="">flimfit-users@lists.openmicroscopy.org.uk</a>'<br class="">
<b class="">Subject:</b> [FLIMfit-users] Exporting FLIMfit data and boundaries for beta values</font>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">Dear All,</span></div>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class=""> </span></p>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">I am a new FLIMfit user and I like it :)</span></div>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class=""> </span></p>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">However, I have few extra wishes/questions:</span></div>
<div style="margin: 0cm 0cm 0.0001pt 54pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;" class="">
<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">-<span style="font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> </span></span><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">Is
it possible to export FLIMfit results to matlab, such that I can make changes to the colours and not have the lifetime range written in the image itself?</span></div>
<div style="margin: 0cm 0cm 0.0001pt 54pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;" class="">
<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">-<span style="font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> </span></span><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">Is
it possible to display the IRF shift? </span></div>
<div style="margin: 0cm 0cm 0.0001pt 54pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;" class="">
<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">-<span style="font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> </span></span><span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">Would
it be possible to fix the beta values between certain values, for instance always positive?</span></div>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class=""> </span></p>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">Thanks,</span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class="">Kind regards,</span></div>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;" class=""> </span></p>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Emilie Wientjes</div>
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Laboratory of Biophysics</div>
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