<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Dan-<div><br></div><div><large scale tooting of own horn></div><div><br></div><div>In fact, this type of data collection is not strange at all-- we, and many others do it alot. It's really very helpful for gathering many examples in timelapse, and also for tiling. Another example is the concept of a WellSample in HCS-- multiple images in different locations of the same Well.</div><div><br></div><div>In OME this is handled explicitly (<a href="http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd">http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd</a>). Look under the Plane Element for details. </div><div><br></div><div>I understand this approach is somewhat at odds with imglib. As we move forward towards a similar concept (<a href="http://trac.openmicroscopy.org.uk/ome/ticket/3678">http://trac.openmicroscopy.org.uk/ome/ticket/3678</a>), we'll definitely keep an eye on what the Fiji/Imagejdev team is doing there.</div><div><br></div><div>Obviously, implementing this in software is technically not challenging, but it's not always clear how user wants data displayed. View 10 20 GB images at once? Toggle them? Montage? Tile? </div><div><br></div><div></large scale tooting of own horn></div><div><br></div><div>Cheers,</div><div><br></div><div>jason</div><div> <br><div><div>On 5 Apr 2011, at 08:45, Daniel James White wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi all .lsm sufferers,<br><br><br>On Apr 4, 2011, at 11:46 PM, Johannes Schindelin wrote:<br><br><blockquote type="cite">Hi Mark & other .lsm experts,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">---------- Forwarded message ----------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">[...]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=258">http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=258</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">[...]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">------- Comment #9 from <a href="mailto:johannes.schindelin@gmx.de">johannes.schindelin@gmx.de</a> 2011-04-04 23:31 -------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I pushed the changes to the 'lsm-reader-4.0g' branch, and hope to merge <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">to 'master' and to upload to the Updater soon.<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">May I ask you for a quick sanity check? It's actually very small:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=commitdiff;h=7e70bc5762abf993b729910b4c3b0414e5a97ae6">http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=commitdiff;h=7e70bc5762abf993b729910b4c3b0414e5a97ae6</a><br></blockquote><br>Hmmm, looking at the diffs... it seems that tile position is stuffed into the time dimension.<br><br>So whats gonna happen if there is a time series tile scan?<br>"There may be trouble ahead, but while there's moonlight, and music, and love and romance..."<br><br>Do we have a strategy in imageJ2 for dealing with multi stage xy position data sets<br>that also allows time series?<br><br>Imglib is the answer guess? But hoiw?<br>Does imglib have a concept for this rather strange pair of extra dimensions: x and y stage position? <br>Some kind of x and y offset (in theory also z could be "tiled" eg. when a z piezo stepper has a limited range, and you do several scans in z to cover a larger range)<br><br>???<br><br>Dan<br><br><br><blockquote type="cite"><br></blockquote><blockquote type="cite">Ciao,<br></blockquote><blockquote type="cite">Dscho<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-- <br></blockquote><blockquote type="cite">You received this message because you are subscribed to the Google Groups "Fiji-devel" group.<br></blockquote><blockquote type="cite">To post to this group, send email to <a href="mailto:fiji-devel@googlegroups.com">fiji-devel@googlegroups.com</a>.<br></blockquote><blockquote type="cite">To unsubscribe from this group, send email to <a href="mailto:fiji-devel+unsubscribe@googlegroups.com">fiji-devel+unsubscribe@googlegroups.com</a>.<br></blockquote><blockquote type="cite">For more options, visit this group at <a href="http://groups.google.com/group/fiji-devel?hl=en">http://groups.google.com/group/fiji-devel?hl=en</a>.<br></blockquote><blockquote type="cite"><br></blockquote><br>Dr. Daniel James White BSc. (Hons.) PhD<br>Senior Microscopist / Image Visualisation, Processing and Analysis<br>Light Microscopy and Image Processing Facilities <br>Max Planck Institute of Molecular Cell Biology and Genetics<br>Pfotenhauerstrasse 108<br>01307 DRESDEN<br>Germany<br><br>+49 (0)15114966933 (German Mobile)<br>+49 (0)351 210 2627 (Work phone at MPI-CBG)<br>+49 (0)351 210 1078 (Fax MPI-CBG LMF)<br><br><a href="http://www.bioimagexd.net">http://www.bioimagexd.net</a> <span class="Apple-tab-span" style="white-space:pre"> </span>BioImageXD<br><a href="http://pacific.mpi-cbg.de">http://pacific.mpi-cbg.de</a><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>Fiji - is just ImageJ (Batteries Included)<br>http://www.chalkie.org.uk<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>Dan's Homepages<br>https://ifn.mpi-cbg.de <span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>Dresden Imaging Facility Network<br>dan (at) chalkie.org.uk<br>( white (at) mpi-cbg.de )<br><br><br><br><br><br><br><br><br><br><br><br><br>_______________________________________________<br>ImageJ-devel mailing list<br>ImageJ-devel@imagejdev.org<br>http://imagejdev.org/mailman/listinfo/imagej-devel<br></div></blockquote></div><br><div apple-content-edited="true"> <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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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-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 style="font-family: Helvetica; "><br class="Apple-interchange-newline"><br class="khtml-block-placeholder"></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">Wellcome Trust Centre for Gene Regulation & Expression</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">College of Life Sciences</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">MSI/WTB/JBC Complex</font></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">University of Dundee</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dow Street</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dundee DD1 5EH</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">United Kingdom</span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">phone (01382) 385819</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Intl phone: 44 1382 385819 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">FAX (01382) 388072 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">email: <a href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a></span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Lab Page: <a href="http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html">http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html</a></span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Open Microscopy Environment: <a href="http://openmicroscopy.org">http://openmicroscopy.org</a></span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><br class="webkit-block-placeholder"></div><div style="font-family: Helvetica; "><div>The University of Dundee is a Scottish Registered Charity, No. SC015096.</div></div><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div></span> </div><br></div></body></html>