<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Curtis,<div class=""><br class=""></div><div class="">thanks for your answer.</div><div class="">In fact, I’m not sure whether it’s more a scifio issue or a fiji one. My point is that in the fiji interface, open parses all positions although it opens a single file. </div><div class=""><br class=""></div><div class="">Does scifio aim at handling entire datasets? then I understands that it has the ability to parse entire datasets, but the way it’s called by fiji could probably be significantly more efficient. or at least open a bioformat-like dialog offering to open all positions.</div><div class="">If scifio is designed with single images, then its code could probably be stripped down to parse metadata more efficiently…</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Thomas</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 12 Aug 2015, at 00:14, Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" class="">ctrueden@wisc.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class="">Hi Thomas,<div class=""><br class=""></div><div class="">Thanks for the report. I filed an issue in the SCIFIO issue tracker with these details:</div><div class=""><br class=""></div><div class=""><a href="https://github.com/scifio/scifio/issues/279" class="">https://github.com/scifio/scifio/issues/279</a><br class=""></div><div class=""><br class=""></div><div class="">Things are crazy busy until the ImageJ conference this September, but we will try to respond more thoroughly later this fall.</div><div class=""><br class=""></div><div class="">In the meantime, in case you didn't already know, the relevant source code is here:</div><div class=""><a href="https://github.com/scifio/scifio/blob/scifio-0.24.0/src/main/java/io/scif/formats/MicromanagerFormat.java" class="">https://github.com/scifio/scifio/blob/scifio-0.24.0/src/main/java/io/scif/formats/MicromanagerFormat.java</a></div><div class=""><br class=""></div><div class="">Be warned that SCIFIO is undergoing a substantial refactoring at the moment, to move away from plane-centric API toward a block-based one.</div><div class=""><br class=""></div><div class="">Regards,</div><div class="">Curtis</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, Aug 7, 2015 at 3:34 AM, Thomas Julou <span dir="ltr" class=""><<a href="mailto:thomas.julou@normalesup.org" target="_blank" class="">thomas.julou@normalesup.org</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hello,<div class=""><br class=""></div><div class="">In line with earlier posts on ome-users mailing list [1], I’m trying to find a convenient way to open large Micro-Manager stacks in Fiji (in particular, such stacks are split in several 4.2gb tif files because MM doesn’t handle bigtiff). My problem so far has been that Bio-formats is parsing all positions in a dataset even when opening a single one. Mark Tsuchida (MM’s developer) suggested that using SCIFIO might be a workaround [2].</div><div class=""><br class=""></div><div class="">I tried the following:</div><div class="">- File > Import > SCIFIO</div><div class="">This raises an exception and open an error dialog… You might want to fix this, unless it’s a fiji specific issue…</div><div class="">- File > Open after selecting “Use SCIFIO” in Options > ImageJ2</div><div class="">This successfully opens the file but it’s slower than the File > Import > BioFormats! Moreover it parses metadata for all positions in the dataset (even when they are saved to different files). I can’t understand this behaviour since there is no way to choose to open all related positions… In my opinion the appropriate behaviour would be: if the MM dataset is saved with all positions in the same stack (i.e. no “_Posxx.ome.tif” in the file name; possibly split in several .tif files) then open each position in a separate window, if the MM dataset is saved with positions in separate files (i.e. “_Posxx.ome.tif” found in the file name; again possibly split in several .tif files if a given position is larger than 4.2gb) then **<b class="">parse only**</b> and open only the selected position… This would really speed things up for stacks acquired in datasets with many positions (of a few large ones).</div><div class=""><br class=""></div><div class="">I hope that this makes sense and that the issue can be addressed.</div><div class="">Thanks for your help. Best,</div><div class=""><br class=""></div><div class="">Thomas</div><div class=""><br class=""></div><div class="">[1] <a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-March/005101.html" target="_blank" class="">http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-March/005101.html</a></div><div class="">[2] <a href="http://micro-manager.3463995.n2.nabble.com/BigTiff-support-tt7580735.html#a7585743" target="_blank" class="">http://micro-manager.3463995.n2.nabble.com/BigTiff-support-tt7580735.html#a7585743</a></div></div><br class="">_______________________________________________<br class="">
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