<div dir="ltr">Thansk for the answer Curtis !o<div><br></div><div>It's my fault because I didn't explain entirely the issue but I already knew all these behaviours. My problem is when for example I duplicate or make a z projection on an OME Tiff file under data browser, the new viewer will be hyperstack (IJ/Fiji default viewer). However if I export the file with LOCI exporter and then I re open it with LOCI importer I can still have data browser and OME metadata are here as well.</div>
<div><br></div><div>Anyway I now understand all IJ1 core limitations and I guess this problem is also due to IJ1 and so I will wait for IJ2. It really awesome if you can backport some IJ2 features to Fiji 1 since IJ2 won't be released before at least one year from what I saw...</div>
<div><br></div><div>PS: quick question to end: are you considering in a mid/long term to merge Fiji/IJ2 ? Does it make really sense to separate both ? I think it would be best for everyone (devs and users) to have only one place for download and development so you would have a better visiblity and it will be much more clear for potential contributors or bug reporters to know where they need to go... I am sure you already think about all of that, so I am sorry if my question is naive but I didn't find any informations on the web.</div>
<div><br></div><div>Best,</div></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br>Hadrien Mary<div><br></div><div>Ph.D student in Biology</div><div>Tournier-Gachet Team</div><div>CNRS - LBCMCP - UMR 5088<div>
<div><br></div><div><div>Université de Toulouse - Bât. 4R3B1</div><div>118, route de Narbonne - 31062 Toulouse</div></div></div></div></div></div>
<br><br><div class="gmail_quote">On Wed, Dec 11, 2013 at 10:26 PM, Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Hadrien,<div class="im"><div><br></div><div><div>> Is there is a way to make LOCI data browser the default viewer on IJ /</div><div>> Fiji ?</div></div><div><br></div></div><div>Sort of. The Bio-Formats Importer dialog will remember that you selected the Data Browser as your stack viewer, and hence it will be initially selected upon subsequent calls to the Importer.</div>
<div><br></div><div>However, when using the File > Open command, ImageJ only calls Bio-Formats in certain cases. The rule of thumb is: if the format is one that only Bio-Formats knows how to handle, Bio-Formats will be called. If not, ImageJ will handle it internally, or with a different plugin. This behavior is not configurable.</div>
<div><br></div><div>So, if ImageJ does not call Bio-Formats (which it won't when opening e.g. a TIFF file), you will not end up with the Data Browser viewer.</div><div class="im"><div><br></div><div><div>> Or at least use LOCI data browser when an OME Tiff file is detected ?</div>
</div><div><br></div></div><div>Unfortunately, because OME-TIFF files end with the .ome.tif (or .ome.tiff) extension, ImageJ will prefer its own internal TIFF reader to Bio-Formats, even though its own internal reader does not actually support OME-TIFF's metadata.</div>
<div><br></div><div>Your options are either: A) open the file using File > Import > Bio-Formats rather than File > Open; or B) run Plugins > LOCI > LOCI Plugins Shortcut Window and then drag-and-drop your OME-TIFF files onto that window.</div>
<div><br></div><div>Regards,</div><div>Curtis<br></div><div><br></div><div>P.S. We have solved this problem in ImageJ2, thanks to its improved plugin framework and use of the extensible SCIFIO image I/O library. We are also planning to retrofit SCIFIO into Fiji in ImageJ 1.x mode, to address this problem there, too.</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On Wed, Dec 11, 2013 at 1:29 PM, Hadrien Mary <span dir="ltr"><<a href="mailto:hadrien.mary@gmail.com" target="_blank">hadrien.mary@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Hi,<div><br></div><div>Is there is a way to make LOCI data browser the default viewer on IJ / Fiji ? Or at least use LOCI data browser when an OME Tiff file is detected ?</div>
<div><br></div><div>Best,<br clear="all">
<div><div dir="ltr"><br>--<br>Hadrien Mary<div><br></div><div>Ph.D student in Biology</div><div>Tournier-Gachet Team</div><div>CNRS - LBCMCP - UMR 5088<div><div><br></div><div><div>Université de Toulouse - Bât. 4R3B1</div>
<div>118, route de Narbonne - 31062 Toulouse</div></div></div></div></div></div>
</div></div>
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