[ome-devel] Make LOCI data browser default IJ / Fiji viewer ?

Thu Dec 12 20:51:01 GMT 2013

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 <ctrueden at 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.mary at 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 <ctrueden at 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.mary at 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-devel at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>>>
>>>>
>>>
>>
>
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