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Hi Paul
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<div>1) You can use a ‘perfect’ or delta-function irf, in fact this is the default if you don’t import an irf explicitly.</div>
<div>This is placed by default at the first data point (with a perfect detector you will see no light, except background before the excitation).</div>
<div>As you have guessed you therefore need to exclude points before the peak to get this to work.</div>
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<div>2) You can do this using the 'Time Min' control on the Data tab. </div>
<div>You can also move the irf in time using the 'IRF shift ‘ control on the IRF tab.</div>
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<div>3) Re ROIs : Top left Just under ‘File’ are three shapes. You can use these to draw an ROI on the intensity image & fit this region </div>
<div>as a single summed decay.</div>
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<div>You can also use the ‘Integrated Min’ control on the data tab to threshold dim pixels out of the fit. Recommended!</div>
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<div>4) If you fit only the tail after the peak (as described) My guess is that you will get a v. similar answer to other software</div>
<div>as it’s a fairly simple task. Once you add in irfs & multi-exponentials we’re in 40 page thesis territory I’m afraid.</div>
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<div>Please note that although, currently, FLIMfit can’t open .msr files directly from disc you can open these images from an OMERO 5.0.0 server.</div>
<div>In addition we hope to release a version with this capability (via bio-formats) very shortly.</div>
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<div>Regards</div>
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<div>ian</div>
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<div>On 6 Mar 2014, at 17:17, Paul Thomas (SCI) <<a href="mailto:P.Thomas@uea.ac.uk">P.Thomas@uea.ac.uk</a>> wrote:</div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">Hi Ian,<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);"> </span></font></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">I’ve messed around with FLIMfit a little this afternoon, and can import data files (*.ome.tif) and my IRF data. I
was able to “shift” the IRF and use the program to generate lifetimes, but what I would like to do to start with is to compare ImSpectorPro with FLIMfit, and then to see the effect of the IRF. So, I have some basic questions on FLIMfit:<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);"> </span></font></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">1) Can I fit data without the IRF? – I’ve tried this but I’m obviously not doing it correctly; probably related to
my second question.<o:p></o:p></span></font></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">2) Can I set limits on the data so that I make a fit from the “peak” to the end of the recording (see example from
ImSpectorPro attached)?<o:p></o:p></span></font></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">3) Is it possible to choose an ROI to fit (again, see example from ImSpectorPro attached) rather than a point?<o:p></o:p></span></font></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">4) I’m afraid I don’t know exactly how ImSpector fits the curve (I can probably find out), but I’d like to use as
similar conditions as I can with FLIMfit to get a reasonable comparison. I’m not sure there’s a simple answer to this one, but some guidelines as to what options to choose (or avoid) might help? – This may require a tutorial!<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">Thanks,<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">Paul.<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">____________________<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Dr. Paul Thomas, Manager,<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">The Henry Wellcome Laboratory for Cell Imaging,<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Faculty of Science,<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">University of East Anglia,<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Norwich Research Park,<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Norwich,<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">NR4 7TJ,<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">United Kingdom.<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">e-mail:<span class="Apple-converted-space"> </span><a href="mailto:p.thomas@uea.ac.uk" style="color: purple; text-decoration: underline;">p.thomas@uea.ac.uk</a><o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Tel: +44-1603-592196<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Fax: +44-1603-592250<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Imaging web-site:<span class="Apple-converted-space"> </span><a href="https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab" style="color: purple; text-decoration: underline;">https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab</a><o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Personal web-page:<span class="Apple-converted-space"> </span><a href="https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people" style="color: purple; text-decoration: underline;">https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people</a><o:p></o:p></span></font></div>
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<b><font size="2" face="Tahoma"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; font-weight: bold;">From:</span></font></b><font size="2" face="Tahoma"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif;"><span class="Apple-converted-space"> </span>Munro,
Ian [<a href="mailto:i.munro@imperial.ac.uk">mailto:i.munro@imperial.ac.uk</a>]<span class="Apple-converted-space"> </span><br>
<b><span style="font-weight: bold;">Sent:</span></b><span class="Apple-converted-space"> </span>06 March 2014 13:47<br>
<b><span style="font-weight: bold;">To:</span></b><span class="Apple-converted-space"> </span>Paul Thomas (SCI)<br>
<b><span style="font-weight: bold;">Subject:</span></b><span class="Apple-converted-space"> </span>Re: [ome-users] CZI dimension<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">Hi Paul<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">You’re already aware of FLIMfit then. Good!<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> Feel free to ask if you need help with using it. We are aware that we need to get some user guides out.<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">FLIMfit is capable of using an image as an irf i.e. if you take a picture of something with a known lifetime (or an extremely short one like a scatterer)<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">you can then import that image as a irf.<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">Regards<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">Ian<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">On 6 Mar 2014, at 13:39, Paul Thomas (SCI) <<a href="mailto:P.Thomas@uea.ac.uk" style="color: purple; text-decoration: underline;">P.Thomas@uea.ac.uk</a>> wrote:<o:p></o:p></span></font></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">Hi Ian,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);"> </span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">Yes, I have a TCSPC detector from LaVision, and do generate FLIM files. I can do some analysis with ImSpectorPro,
but have had trouble correcting for the IRF (not available in ImSpectorPro). I’ve never been able to analyse my data with the plug-in in Fiji, but have downloaded FLIMfit – although I haven’t learned how to use it properly, yet.</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);"> </span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">Regards,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">Paul.</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">____________________</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Dr. Paul Thomas, Manager,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">The Henry Wellcome Laboratory for Cell Imaging,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Faculty of Science,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">University of East Anglia,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Norwich Research Park,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Norwich,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">NR4 7TJ,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">United Kingdom.</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">e-mail:<span class="apple-converted-space"> </span><a href="mailto:p.thomas@uea.ac.uk" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">p.thomas@uea.ac.uk</span></font></a></span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Tel: +44-1603-592196</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Fax: +44-1603-592250</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Imaging web-site:<span class="apple-converted-space"> </span><a href="https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab</span></font></a></span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Personal web-page:<span class="apple-converted-space"> </span><a href="https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people</span></font></a></span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);"> </span></font><o:p></o:p></div>
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<b><font size="2" face="Tahoma"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; font-weight: bold;">From:</span></font></b><span class="apple-converted-space"><font size="2" face="Tahoma"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif;"> </span></font></span><font size="2" face="Tahoma"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif;">Munro,
Ian [<a href="mailto:i.munro@imperial.ac.uk" style="color: purple; text-decoration: underline;">mailto:i.munro@imperial.ac.uk</a>]<span class="apple-converted-space"> </span><br>
<b><span style="font-weight: bold;">Sent:</span></b><span class="apple-converted-space"> </span>06 March 2014 13:05<br>
<b><span style="font-weight: bold;">To:</span></b><span class="apple-converted-space"> </span>Paul Thomas (SCI)<br>
<b><span style="font-weight: bold;">Subject:</span></b><span class="apple-converted-space"> </span>Re: [ome-users] CZI dimension</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> <o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">Dear Paul<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> <o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">Given your interest in .msr files cam I ask if you are interested in FLIM ?<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> <o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">Ian<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> <o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> <o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;">On 6 Mar 2014, at 08:56, Paul Thomas (SCI) <<a href="mailto:P.Thomas@uea.ac.uk" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">P.Thomas@uea.ac.uk</span></font></a>>
wrote:<o:p></o:p></span></font></div>
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<font size="3" face="Times New Roman"><span style="font-size: 12pt;"><br>
<br>
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<o:p></o:p></span></font></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">Hi Curtis,</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);"> </span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">Thanks. In addition, I should also thank the team for including support for ImSpectorPro (*.msr) files. I’ve had no
problems (yet!) opening these files since upgrading to Bioformats 5.</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);"> </span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);">Paul.</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">____________________</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Dr. Paul Thomas, Manager,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">The Henry Wellcome Laboratory for Cell Imaging,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Faculty of Science,</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">University of East Anglia,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Norwich Research Park,</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Norwich,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">NR4 7TJ,</span></font><o:p></o:p></div>
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<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">United Kingdom.</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">e-mail:<span class="apple-converted-space"> </span><a href="mailto:p.thomas@uea.ac.uk" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">p.thomas@uea.ac.uk</span></font></a></span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Tel: +44-1603-592196</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Fax: +44-1603-592250</span></font><o:p></o:p></div>
</div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Imaging web-site:<span class="apple-converted-space"> </span><a href="https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab</span></font></a></span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Calibri"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Personal web-page:<span class="apple-converted-space"> </span><a href="https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people</span></font></a></span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" color="#1f497d" face="Book Antiqua"><span style="font-size: 11pt; font-family: 'Book Antiqua', serif; color: rgb(31, 73, 125);"> </span></font><o:p></o:p></div>
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<b><font size="2" face="Tahoma"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; font-weight: bold;">From:</span></font></b><span class="apple-converted-space"><font size="2" face="Tahoma"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif;"> </span></font></span><font size="2" face="Tahoma"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif;"><a href="mailto:ctrueden.wisc@gmail.com" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">ctrueden.wisc@gmail.com</span></font></a><span class="apple-converted-space"> </span>[<a href="mailto:ctrueden.wisc@gmail.com" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">mailto:ctrueden.wisc@gmail.com</span></font></a>]<span class="apple-converted-space"> </span><b><span style="font-weight: bold;">On
Behalf Of<span class="apple-converted-space"> </span></span></b>Curtis Rueden<br>
<b><span style="font-weight: bold;">Sent:</span></b><span class="apple-converted-space"> </span>05 March 2014 20:08<br>
<b><span style="font-weight: bold;">To:</span></b><span class="apple-converted-space"> </span>Paul Thomas (SCI)<br>
<b><span style="font-weight: bold;">Cc:</span></b><span class="apple-converted-space"> </span><a href="mailto:melissa@glencoesoftware.com" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">melissa@glencoesoftware.com</span></font></a>;
vbindokas;<span class="apple-converted-space"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">ome-users@lists.openmicroscopy.org.uk</span></font></a><br>
<b><span style="font-weight: bold;">Subject:</span></b><span class="apple-converted-space"> </span>Re: [ome-users] CZI dimension</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> <o:p></o:p></span></font></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Times New Roman"><span style="font-size: 12pt;">Hi Paul,<o:p></o:p></span></font></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> <o:p></o:p></span></font></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Times New Roman"><span style="font-size: 12pt;">> </span></font><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial, sans-serif;">I had to do a complete reinstallation of Fiji to update Bioformats to version 5.</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> <o:p></o:p></span></font></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial, sans-serif;">I completed the update of Fiji to use Bio-Formats 5 earlier today. Simply updating Fiji should now give you a working Bio-Formats 5.0.0. And enabling the Bio-Formats
update site (</span></font><font face="Arial"><span style="font-family: Arial, sans-serif;"><a href="http://fiji.sc/Bio-Formats#Daily_builds" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">http://fiji.sc/Bio-Formats#Daily_builds</span></font></a>)
should give you the latest development builds.</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> <o:p></o:p></span></font></div>
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<font size="3" face="Arial"><span style="font-size: 12pt; font-family: Arial, sans-serif;">Regards,</span></font><o:p></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Arial"><span style="font-size: 12pt; font-family: Arial, sans-serif;">Curtis</span></font><o:p></o:p></div>
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<p class="MsoNormal" style="margin: 0cm 0cm 12pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Times New Roman"><span style="font-size: 12pt;"> <o:p></o:p></span></font></p>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Times New Roman"><span style="font-size: 12pt;">On Thu, Feb 27, 2014 at 10:11 AM, Paul Thomas (SCI) <<a href="mailto:P.Thomas@uea.ac.uk" target="_blank" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">P.Thomas@uea.ac.uk</span></font></a>>
wrote:<o:p></o:p></span></font></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">
<font size="3" face="Times New Roman"><span style="font-size: 12pt;">This didn't work for me, I had to do a complete reinstallation of Fiji to update Bioformats to version 5.<br>
Paul.<br>
<br>
____________________<br>
Dr. Paul Thomas, Manager,<br>
The Henry Wellcome Laboratory for Cell Imaging,<br>
Faculty of Science,<br>
University of East Anglia,<br>
Norwich Research Park,<br>
Norwich,<br>
NR4 7TJ,<br>
United Kingdom.<br>
<br>
e-mail:<span class="apple-converted-space"> </span><a href="mailto:p.thomas@uea.ac.uk" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">p.thomas@uea.ac.uk</span></font></a><br>
Tel:<span class="apple-converted-space"> </span><a href="tel:%2B44-1603-592196" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">+44-1603-592196</span></font></a><br>
Fax:<span class="apple-converted-space"> </span><a href="tel:%2B44-1603-592250" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">+44-1603-592250</span></font></a><br>
Imaging web-site:<span class="apple-converted-space"> </span><a href="https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab" target="_blank" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab</span></font></a><br>
Personal web-page:<span class="apple-converted-space"> </span><a href="https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people" target="_blank" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people</span></font></a><o:p></o:p></span></font></div>
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> -----Original Message-----<br>
> From:<span class="apple-converted-space"> </span><a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">ome-users-bounces@lists.openmicroscopy.org.uk</span></font></a><span class="apple-converted-space"> </span>[mailto:<a href="mailto:ome-users-" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">ome-users-</span></font></a><br>
><span class="apple-converted-space"> </span><a href="mailto:bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">bounces@lists.openmicroscopy.org.uk</span></font></a>] On
Behalf Of Melissa Linkert<br>
> Sent: 27 February 2014 01:23<br>
> To: vbindokas<br>
> Cc:<span class="apple-converted-space"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">ome-users@lists.openmicroscopy.org.uk</span></font></a><br>
> Subject: Re: [ome-users] CZI dimension<br>
><br>
> Hi Vytas,<br>
><br>
> > Might there be instructions on how to install the rc? I did the<br>
> > drag/drop in FIJI with bio-formats and/or loci_plugins jars [one at a<br>
> > time], but when i ask help/about Loci, it still reports vers<br>
> > 4.4.10-DEV. I take it I'm not running 5.0.<br>
> > I've deleted all bio-formats and loci jars I found in fiji, except<br>
> for<br>
> > the installed rc.<br>
> > What am I doing wrong?<br>
><br>
> The best way to use 5.0.0 with Fiji is by following the instructions<br>
> here:<br>
><br>
><span class="apple-converted-space"> </span><a href="http://fiji.sc/Bio-Formats#Daily_builds" target="_blank" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">http://fiji.sc/Bio-Formats#Daily_builds</span></font></a><br>
><br>
> Downloading the files by hand and copying them into the plugins folder<br>
> is not recommended when using Fiji, as it is very easy to accidentally<br>
> have an older version of the plugin still installed.<br>
><br>
> If "Help > About Plugins > ..." shows something other than 5.0.0 after<br>
> following those instructions, please let us know.<br>
><br>
> Regards,<br>
> -Melissa<br>
><br>
> On Tue, Feb 25, 2014 at 09:27:04AM -0600, vbindokas wrote:<br>
> > Dear Melissa,<br>
> > Thanks for the response.<br>
> > Might there be instructions on how to install the rc? I did the<br>
> > drag/drop in FIJI with bio-formats and/or loci_plugins jars [one at a<br>
> > time], but when i ask help/about Loci, it still reports vers<br>
> > 4.4.10-DEV. I take it I'm not running 5.0.<br>
> > I've deleted all bio-formats and loci jars I found in fiji, except<br>
> for<br>
> > the installed rc.<br>
> > What am I doing wrong?<br>
> > thanks!<br>
> ><br>
> > On 2/24/2014 6:45 PM, Melissa Linkert wrote:<br>
> > >Hi Vytas,<br>
> > ><br>
> > >>>It appears bioformats importer does not recognize the CZI fields<br>
> > >>>created by the recent Lightsheet microscope system. The<br>
> lightsheet<br>
> > >>>stored angular rotation "views" within the structure in addition<br>
> to<br>
> > >>>CH, T, Z. The importer does open the first 'view', but not beyond<br>
> that.<br>
> > >>>Can I request that tag/data be read for CZI?<br>
> > >Which version of Bio-Formats are you currently using? If you<br>
> haven't<br>
> > >already, I would suggest updating to 5.0.0-rc1:<br>
> > ><br>
> > ><a href="http://downloads.openmicroscopy.org/bio-formats/5.0.0-rc1" target="_blank" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">http://downloads.openmicroscopy.org/bio-formats/5.0.0-rc1</span></font></a><br>
> > ><br>
> > >and/or the very, very soon-to-be-released 5.0.0. 5.0.0-rc1 contains<br>
> > >many improvements to .czi support, and I would expect it to open all<br>
> > >rotations in a lightsheet dataset.<br>
> > ><br>
> > >>>The Zeiss software export is not very friendly [outputs views in<br>
> > >>>stacks per Z and time], meaning that output must be then split and<br>
> > >>>resorted to get data suitable for openSPIM processing.<br>
> > >>>These are hugely big.<br>
> > >>>If the czi could be opened as a virtual stack and then written out<br>
> > >>>with the usual sequential tif naming, then it at least saves one<br>
> > >>>step and much time/space.<br>
> > >>>[I can try to upload a smaller czi file (5GBs), if that helps]<br>
> > >A sample dataset would be very helpful if you find that there are<br>
> > >still problems with 5.0.0-rc1/<a href="http://5.0.0./" target="_blank" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">5.0.0.</span></font></a><span class="apple-converted-space"> </span> If you are
interested in<br>
> > >uploading a file, please let me know and I will send the current FTP<br>
> > >server information off-list.<br>
> > ><br>
> > >Regards,<br>
> > >-Melissa<br>
> > ><br>
> > >On Fri, Feb 21, 2014 at 10:23:43AM -0600, Curtis Rueden wrote:<br>
> > >>Hi Vytas,<br>
> > >><br>
> > >>>It appears bioformats importer does not recognize the CZI fields<br>
> > >>>created by the recent Lightsheet microscope system.<br>
> > >>I am replying with the OME-users mailing list in CC, which is the<br>
> > >>best place to report Bio-Formats issues.<br>
> > >><br>
> > >>Regards,<br>
> > >>Curtis<br>
> > >><br>
> > >><br>
> > >>On Wed, Feb 19, 2014 at 8:45 AM, vbindokas<br>
> <<a href="mailto:vbindoka@bsd.uchicago.edu" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">vbindoka@bsd.uchicago.edu</span></font></a>>wrote:<br>
> > >><br>
> > >>>Dear Curtis,<br>
> > >>>It appears bioformats importer does not recognize the CZI fields<br>
> > >>>created by the recent Lightsheet microscope system. The<br>
> lightsheet<br>
> > >>>stored angular rotation "views" within the structure in addition<br>
> to<br>
> > >>>CH, T, Z. The importer does open the first 'view', but not beyond<br>
> that.<br>
> > >>>Can I request that tag/data be read for CZI?<br>
> > >>>The Zeiss software export is not very friendly [outputs views in<br>
> > >>>stacks per Z and time], meaning that output must be then split and<br>
> > >>>resorted to get data suitable for openSPIM processing.<br>
> > >>>These are hugely big.<br>
> > >>>If the czi could be opened as a virtual stack and then written out<br>
> > >>>with the usual sequential tif naming, then it at least saves one<br>
> > >>>step and much time/space.<br>
> > >>>[I can try to upload a smaller czi file (5GBs), if that helps]<br>
> best<br>
> > >>>regards,<br>
> > >>><br>
> > >>>--<br>
> > >>>__<br>
> > >>><br>
> > >>>Vytas Bindokas, Ph.D.<br>
> > >>>Research Assoc. / Assoc. Prof.,<br>
> > >>>Director, BSD Light Microscopy Core Facility<br>
> > >>>phone:<span class="apple-converted-space"> </span><a href="tel:773-702-4875" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">773-702-4875</span></font></a><br>
> > >>><br>
> > >>> [address for letters ONLY (see shipping addr below):] Dept<br>
> > >>>Pharmacol Physiol Sci MC0926<br>
> > >>>947 E 58th Street<br>
> > >>>The University of Chicago<br>
> > >>>Chicago IL 60637<br>
> > >>>Room Abbott 129<br>
> > >>><br>
> > >>><br>
> > >>>shipping address (main KCBD site):<br>
> > >>>V. Bindokas<br>
> > >>>900 E 57th Street<br>
> > >>>KCBD room 1250, Microscopy Core<br>
> > >>>The University of Chicago<br>
> > >>>Chicago IL 60637<br>
> > >>><br>
> > >>><br>
> > >>>email<span class="apple-converted-space"> </span><a href="mailto:vbindoka@bsd.uchicago.edu" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">vbindoka@bsd.uchicago.edu</span></font></a><br>
> > >>>web site for LMCF:<br>
> > >>><a href="http://digital.uchicago.edu/index.html" target="_blank" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">http://digital.uchicago.edu/index.html</span></font></a><br>
> > >>><br>
> > >>><br>
> > >>_______________________________________________<br>
> > >>ome-users mailing list<br>
> > >><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">ome-users@lists.openmicroscopy.org.uk</span></font></a><br>
> > >><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</span></font></a><br>
> ><br>
> > --<br>
> > __<br>
> ><br>
> > Vytas Bindokas, Ph.D.<br>
> > Research Assoc. / Assoc. Prof.,<br>
> > Director, BSD Light Microscopy Core Facility<br>
> > phone:<span class="apple-converted-space"> </span><a href="tel:773-702-4875" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">773-702-4875</span></font></a><br>
> ><br>
> > [address for letters ONLY (see shipping addr below):] Dept<br>
> > Pharmacol Physiol Sci MC0926<br>
> > 947 E 58th Street<br>
> > The University of Chicago<br>
> > Chicago IL 60637<br>
> > Room Abbott 129<br>
> ><br>
> ><br>
> > shipping address (main KCBD site):<br>
> > V. Bindokas<br>
> > 900 E 57th Street<br>
> > KCBD room 1250, Microscopy Core<br>
> > The University of Chicago<br>
> > Chicago IL 60637<br>
> ><br>
> ><br>
> > email<span class="apple-converted-space"> </span><a href="mailto:vbindoka@bsd.uchicago.edu" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">vbindoka@bsd.uchicago.edu</span></font></a><br>
> > web site for LMCF:<br>
> ><span class="apple-converted-space"> </span><a href="http://digital.uchicago.edu/index.html" target="_blank" style="color: purple; text-decoration: underline;"><font color="purple"><span style="color: purple;">http://digital.uchicago.edu/index.html</span></font></a><br>
> ><br>
> _______________________________________________<br>
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<span><ImSpectorPro fit.pdf></span></div>
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