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

[Hadrien Mary]

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
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20131211/a5b28266/attachment-0001.html>