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

[Curtis Rueden]

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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