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<p><span style="font-family: Tahoma; font-size: 13px;">Dear Emilie,</span></p>
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<div style="font-family: Tahoma; font-size: 13px;">Apologies for the delay replying, I'm glad you're finding FLIMfit useful!</div>
<div style="font-family: Tahoma; font-size: 13px;">Hopefully the following should help:</div>
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<div style="font-family: Tahoma; font-size: 13px;"><font color="#0000ff"><span style="font-family: Verdana, sans-serif; font-size: 10pt; text-indent: -18pt;">>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>
</font><font face="Verdana, sans-serif">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;"><font face="Verdana, sans-serif">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;"><font face="Verdana, sans-serif">From the menu, select File>Export Selected Images... and choose a root filename</font></li><li><font face="Verdana, sans-serif"><font size="2">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"> 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><span style="font-family: Verdana, sans-serif; font-size: 10pt; text-indent: -18pt;"><font color="#0000ff">> Is it possible to display the IRF shift? </font></span></div>
<span style="text-indent: -24px;"><font face="Verdana, sans-serif">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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<font color="#0000ff"><span style="font-size: 10pt; text-indent: -18pt; font-family: Verdana, sans-serif;">> Would it be possible to fix the beta values between certain values, for instance always positive?</span><br>
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<font face="Verdana, sans-serif" size="2">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;">fitting </span><span style="font-family: Verdana, sans-serif; font-size: small;">(i.e. fitting pixels independently). </span></p>
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<font face="Verdana, sans-serif" size="2">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></p>
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<font face="Verdana, sans-serif" size="2">Best Regards,</font></p>
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<font face="Verdana, sans-serif" size="2">Sean </font></p>
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<div id="divRpF75611" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> FLIMfit-users [flimfit-users-bounces@lists.openmicroscopy.org.uk] on behalf of Munro, Ian [i.munro@imperial.ac.uk]<br>
<b>Sent:</b> Wednesday, 23 December 2015 07:46<br>
<b>To:</b> Wientjes, Emilie; 'flimfit-users@lists.openmicroscopy.org.uk'<br>
<b>Subject:</b> Re: [FLIMfit-users] Exporting FLIMfit data and boundaries for beta values<br>
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Hi Emile<br>
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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>
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<br>
Kind regards<br>
<br>
Ian<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size: 11pt;"><b>From:</b> FLIMfit-users <flimfit-users-bounces@lists.openmicroscopy.org.uk> on behalf of Wientjes, Emilie <emilie.wientjes@wur.nl><br>
<b>Sent:</b> 18 December 2015 10:56:09<br>
<b>To:</b> 'flimfit-users@lists.openmicroscopy.org.uk'<br>
<b>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;">Dear All,</span></p>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;"> </span></p>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;">I am a new FLIMfit user and I like it :)</span></p>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;"> </span></p>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;">However, I have few extra wishes/questions:</span></p>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;">-<span style="font-size: 7pt; line-height: normal; font-family: 'Times New Roman';"> </span></span><span style="font-size: 10pt; font-family: Verdana, sans-serif;">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></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt 54pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;">
<span style="font-size: 10pt; font-family: Verdana, sans-serif;">-<span style="font-size: 7pt; line-height: normal; font-family: 'Times New Roman';"> </span></span><span style="font-size: 10pt; font-family: Verdana, sans-serif;">Is it possible to display
the IRF shift? </span></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt 54pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;">
<span style="font-size: 10pt; font-family: Verdana, sans-serif;">-<span style="font-size: 7pt; line-height: normal; font-family: 'Times New Roman';"> </span></span><span style="font-size: 10pt; font-family: Verdana, sans-serif;">Would it be possible to
fix the beta values between certain values, for instance always positive?</span></p>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;"> </span></p>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;">Thanks,</span></p>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;">Kind regards,</span></p>
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<span style="font-size: 10pt; font-family: Verdana, sans-serif;"> </span></p>
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Emilie Wientjes</p>
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Laboratory of Biophysics</p>
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