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Hi Mark,<div><br></div><div>Thanks very much for that.</div><div><br></div><div>Very handy!</div><div><br></div><div> Cheers,</div><div><br></div><div> Will. </div><div><br></div><div><br></div><div><br><div><div>On 20 Jul 2009, at 14:37, Woodbridge, Mark R wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Hi,<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Leica’s free<span class="Apple-converted-space"> </span><a href="ftp://ftp.llt.de/softlib/LAS_AF_Lite/1.7.0_build_1111/setup.exe" style="color: blue; text-decoration: underline; "><span style="color: windowtext; text-decoration: none; ">LAS AF Lite</span></a><span class="Apple-converted-space"> </span>software can open .lif files:<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><a href="ftp://ftp.llt.de/softlib/LAS_AF_Lite" style="color: blue; text-decoration: underline; ">ftp://ftp.llt.de/softlib/LAS_AF_Lite</a><o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">The Bio-Formats homepage links to free software for various imaging formats:<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><a href="http://www.loci.wisc.edu/ome/formats.html" style="color: blue; text-decoration: underline; "><span style="color: windowtext; text-decoration: none; ">http://www.loci.wisc.edu/ome/formats.html</span></a><o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Mark.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="border-top-style: none; border-right-style: none; border-bottom-style: none; border-width: initial; border-color: initial; border-left-style: solid; border-left-color: blue; border-left-width: 1.5pt; padding-top: 0cm; padding-right: 0cm; padding-bottom: 0cm; padding-left: 4pt; "><div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; "><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span>ome-users-bounces@lists.openmicroscopy.org.uk [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>]<span class="Apple-converted-space"> </span><b>On Behalf Of<span class="Apple-converted-space"> </span></b>Will Moore<br><b>Sent:</b><span class="Apple-converted-space"> </span>20 July 2009 11:37<br><b>To:</b><span class="Apple-converted-space"> </span><a href="mailto:mallouh@igbmc.fr">mallouh@igbmc.fr</a><br><b>Cc:</b><span class="Apple-converted-space"> </span>ome-users@lists.openmicroscopy.org.uk<br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] LIF format - metadata<o:p></o:p></span></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Hi Veronique,<o:p></o:p></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">We would like to be able to import all this metadata if possible.<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">However, it is quite tricky to map the data in the LIF file to our OME data model. <o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">For example, in a sample LIF file I'm looking at (with ImageJ and BioFormats plugin), there appears to be only 1 pin-hole size, whereas our model requires a pin-hole size for each channel. <o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">One problem we have is that we don't know how the LIF files are read and displayed by the Leica software. <o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">(Do you know of any LIF viewing software that is available to download?)<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">You could help us a lot by sending us any sample LIF files you have, together with a list of all the metadata you want to view from the files. <o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Alternatively, if you could also take a screen-shot of what the files look like, and what metadata is displayed in the Leica software, that would allow us to work out how to read this metadata from the file. <o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">If you want details of how to upload sample files to our image repository, please e-mail melissa <a href="mailto:melissa@glencoesoftware.com" style="color: blue; text-decoration: underline; ">melissa@glencoesoftware.com</a><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> Many thanks,<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "> Will. <o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">On 20 Jul 2009, at 08:36, V. Mallouh wrote:<o:p></o:p></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><br><br><o:p></o:p></div><p class="MsoNormal" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 12pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Hello,<br><br>We are importing LIF files in Omero 4.0.3 : it would be very useful to have original metadata (Laser wavelength, Pinhole, PMT, SP Mirror Channel, ...) available in Insight.<span class="Apple-converted-space"> </span><br>Is it planned to import these informations in Omero?<br><br>Best regards,<br><br><span style="color: rgb(102, 102, 102); ">Véronique Mallouh<br>IGBMC<br>1 Rue Laurent Fries<br>67404 Illkirch Cedex<br>France<br><a href="mailto:mallouh@igbmc.u-strasbg.fr" style="color: blue; text-decoration: underline; ">mallouh@igbmc.fr</a><br><br></span><o:p></o:p></p><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">_______________________________________________<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">ome-users mailing list<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: blue; text-decoration: underline; ">ome-users@lists.openmicroscopy.org.uk</a><o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: blue; text-decoration: underline; ">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">William Moore<o:p></o:p></span></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">Division of Gene Regulation and Expression<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">College of Life Sciences<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">University of Dundee<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">Scotland<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">DD1 5PH<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; "><o:p> </o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">Tel 01382 386364<o:p></o:p></span></div></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div></div></div></span></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div>William Moore</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Division of Gene Regulation and Expression</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">College of Life Sciences</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">University of Dundee</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Scotland</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">DD1 5PH</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Tel 01382 386364</div></div></span> </div><br></div></body></html>