Posted by
Melissa Linkert-2 on
Oct 06, 2014; 1:27pm
URL: http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5009918.html
Hi Aryeh,
> >> You are correct. We will be switching over to 5.1.x, but in the mean time
> >> it looks like the nd2 fix
> >> <
https://github.com/openmicroscopy/bioformats/commit/> >> 3c857c2e5743e9b23801408bd61de49697716b4d>
> >> you're looking for only affected the formats-gpl component. You should be
> >> able to just download that specific jar, and replace the
> >> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
> >> version will just be called "formats-gpl.jar" if you still have the
> >> Bio-Formats update site enabled).
> >>
> >
> > How can I turn this into the formats-gpl.jar file?
> > If I can do that, I will replace my version 5.0.2 file, and see if it
> > works properly
Instead of compiling from source, you can also download the latest 5.1
builds from:
http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/For anyone trying this though, please do note that mixing 5.1 and 5.0
files is not supported and very unlikely to work, so you will need to
update all files to 5.1. Be aware that this can cause problems with
other plugins that use Bio-Formats, as there are API differences between
the two versions (though we have not yet released 5.1.0).
We are also considering this fix for a 5.0.6 release of Bio-Formats, which
would eliminate the need to manually update files.
Regards,
-Melissa
On Mon, Oct 06, 2014 at 07:52:39AM -0500, Mark Hiner wrote:
> Hi Aryeh,
>
> >How can I turn this into the formats-gpl.jar file?
>
> Great question! I'm cc'ing the list because I think this information is of
> general interest.
>
> The Bio-Formats site has a page with instructions for downloading and
> building the jars from source:
>
https://www.openmicroscopy.org/site/support/bio-formats5/developers/building-bioformats.html>
> After cloning the Bio-Formats repository
> <
http://git-scm.com/book/en/Git-Basics-Getting-a-Git-Repository#Cloning-an-Existing-Repository>,
> you can either:
> * Check out a specific tag
> <
http://stackoverflow.com/questions/791959/download-a-specific-tag-with-git>
> or
> * Check out a specific commit
> <
http://stackoverflow.com/questions/2007662/rollback-to-an-old-commit-using-git>
>
> Or it should be fine to just build the "develop" branch, since the patch in
> question was merged.
>
> After building Bio-Formats, all the output .jars will be in the /artifacts
> sub-directory of your Bio-Formats checkout.
>
> Let me know if you have any more questions, and thank you for taking the
> time to test this!
>
> Regards,
> Mark
>
>
> On Sat, Oct 4, 2014 at 3:03 PM, Aryeh Weiss <
[hidden email]> wrote:
>
> > Hi Mark
> >
> > On 10/1/14, 10:21 PM, Mark Hiner wrote:
> >
> >> Hi Christophe,
> >>
> >> As far as I understand, the current dailies are 5.0, not 5.1 yet
> >>>
> >> You are correct. We will be switching over to 5.1.x, but in the mean time
> >> it looks like the nd2 fix
> >> <
https://github.com/openmicroscopy/bioformats/commit/> >> 3c857c2e5743e9b23801408bd61de49697716b4d>
> >> you're looking for only affected the formats-gpl component. You should be
> >> able to just download that specific jar, and replace the
> >> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
> >> version will just be called "formats-gpl.jar" if you still have the
> >> Bio-Formats update site enabled).
> >>
> >
> > How can I turn this into the formats-gpl.jar file?
> > If I can do that, I will replace my version 5.0.2 file, and see if it
> > works properly
> >
> > thanks and best regards
> > --aryeh
> >
> >
> > --
> > Aryeh Weiss
> > Faculty of Engineering
> > Bar Ilan University
> > Ramat Gan 52900 Israel
> >
> > Ph: 972-3-5317638
> > FAX: 972-3-7384051
> >
> >
>
> --
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