[ome-users] problem reading 14bit JPEG2000

[Curtis Rueden]

Hi Mario,

> I get an error that the jai libraries would be missing. I checked my
> installation of Fiji (fully up-to-date and no local modifications or
> extras) and it brings jai_imageio-1.0.1.jar. Am I doing something
> wrong?

Nope, it was a problem introduced in the Fiji distribution recently.

Short answer: I believe I have fixed it. Please try updating again and let
me know if it works now.

Long answer: Fiji now ships both SCIFIO (http://scif.io/) and Bio-Formats.
Each library has its own version of jai_imageio. Both are forks of the
official jai_imageio. Bio-Formats's fork does *not* shade (i.e., rename)
the packages; SCIFIO's does. Hence, both can be coexist in the same JVM
(but not with the official version). Until just now, the SCIFIO version
(i.e., jai_imageio-1.0.1.jar) was "overwriting" the Bio-Formats one, so
both were not being shipped. I have remedied it by moving the Bio-Formats
version into the "jars/bio-formats" subfolder.

Regards,
Curtis


On Tue, Sep 10, 2013 at 4:59 AM, Mario Emmenlauer <mario at emmenlauer.de>wrote:

>
> Dear Bio-Formats Developers,
>
> I'm not sure if this is an issue with Bio-Formats or with Fiji,
> can you please advise me whether to forward to the correct list?
>
> The following image fails to open for me, and I get an error that
> the jai libraries would be missing. I checked my installation of
> Fiji (fully up-to-date and no local modifications or extras) and it
> brings jai_imageio-1.0.1.jar. Am I doing something wrong?
>
>     http://data.marssoft.de/bCB01-1D08B_wA01_s6_z1_t1_cDAPI_u1.jp2
>
> Thanks and all the best,
>
>     Mario
>
>
>
>
>
>
> --
> Mario Emmenlauer, Dipl.Inf.                  Office: +41-(0)61-26-72110
> Biozentrum Basel
> Klingelbergstrasse 50/70           mailto: mario.emmenlauer * unibas.ch
> CH-4056 Basel                     http://infectx.org/about_us/emmenlau/
>
>
>
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