Thank you for this detailled answer Curtis !
-- Hadrien Mary Ph.D student in Biology Tournier-Gachet Team CNRS - LBCMCP - UMR 5088 Université de Toulouse - Bât. 4R3B1 118, route de Narbonne - 31062 Toulouse On Thu, Dec 12, 2013 at 9:28 PM, Curtis Rueden <ctrue...@wisc.edu> wrote: > Hi Hadrien, > > [Cross-posting with imagej-devel since this discussion is relevant there > too.] > > > 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. > > Ah. So at minimum, what you need is a way to wrap an ImageJ hyperstack > back into a Data Browser window again. You can do that with this Beanshell > one-liner: > > new loci.plugins.util.DataBrowser(IJ.getImage()); > > Paste that line into the script editor and save as (e.g.) > data-browser.bsh. When you run it, the currently active image window will > be converted to a Data Browser window. > > You can even install the script into the menus and map a shortcut key to > it, although of course that's still not completely automatic. For a totally > seamless override of the default image viewer you'll have to 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... > > Yes, we are working toward more of a gradual release schedule. Rather than > releasing "ImageJ2" as one monolithic thing (which it really isn't), we > want to start integrating the already polished parts of it into Fiji as > soon as possible. We are currently working on the "legacy" interoperability > layer to facilitate this. > > > 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 > > That is essentially what we are doing, yes. ImageJ2 is the core software; > several parts of Fiji core infrastructure have migrated into ImageJ2. So at > heart, Fiji is now a big collection of life sciences plugins -- i.e., an > ImageJ update site. As such, you can currently obtain a working Fiji > installation by downloading ImageJ2, running the updater, and toggling the > Fiji update site. > > Fiji and ImageJ2 are fundamentally the same software, using the same > launcher. It's just that if you download "Fiji" and run it, it currently > starts up in ImageJ1 mode at the moment. But Fiji ships with ImageJ2 and > you can launch it in that mode instead if you prefer -- or switch to > ImageJ2 mode after launching using the "Switch to Modern Mode" command > under the Help menu. > > Ultimately, we probably do not want to get rid of the two distinct web > sites and project names though, since people are familiar with both. That > said, we are integrating resources when feasible: e.g., wiki.imagej.netand > fiji.sc are really both the same wiki with a different skin, to make > cross-linking more seamless. But we want to ensure it is clear that ImageJ2 > is not a life-sciences-specific project, whereas Fiji is. Historically, > because Fiji has a life sciences focus, there have been some users who > refused to switch from vanilla ImageJ1 to Fiji even though Fiji makes > users' lives easier in lots of ways. > > Regards, > Curtis > > > On Wed, Dec 11, 2013 at 3:41 PM, Hadrien Mary <hadrien.m...@gmail.com>wrote: > >> Thansk for the answer Curtis !o >> >> 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. >> >> 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... >> >> 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. >> >> Best, >> >> >> -- >> Hadrien Mary >> >> Ph.D student in Biology >> Tournier-Gachet Team >> CNRS - LBCMCP - UMR 5088 >> >> Université de Toulouse - Bât. 4R3B1 >> 118, route de Narbonne - 31062 Toulouse >> >> >> On Wed, Dec 11, 2013 at 10:26 PM, Curtis Rueden <ctrue...@wisc.edu>wrote: >> >>> Hi Hadrien, >>> >>> > Is there is a way to make LOCI data browser the default viewer on IJ / >>> > Fiji ? >>> >>> 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. >>> >>> 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. >>> >>> 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. >>> >>> > Or at least use LOCI data browser when an OME Tiff file is detected ? >>> >>> 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. >>> >>> 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. >>> >>> Regards, >>> Curtis >>> >>> 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. >>> >>> >>> On Wed, Dec 11, 2013 at 1:29 PM, Hadrien Mary <hadrien.m...@gmail.com>wrote: >>> >>>> Hi, >>>> >>>> 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 >>>> ? >>>> >>>> Best, >>>> >>>> -- >>>> Hadrien Mary >>>> >>>> Ph.D student in Biology >>>> Tournier-Gachet Team >>>> CNRS - LBCMCP - UMR 5088 >>>> >>>> Université de Toulouse - Bât. 4R3B1 >>>> 118, route de Narbonne - 31062 Toulouse >>>> >>>> _______________________________________________ >>>> ome-devel mailing list >>>> ome-de...@lists.openmicroscopy.org.uk >>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel >>>> >>>> >>> >> >
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