Re: Latest Bio-Formats in Fiji

Posted by lechristophe on Oct 01, 2014; 3:44pm
URL: http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5009852.html

Hi Mark,

I am indeed looking for a particular fix regarding large nd2 files:
https://github.com/openmicroscopy/bioformats/pull/1351

Melissa Linkert was kind enough to solve the problem and pointed me to get
it at:
http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/

I had some problem manually replacing files in Fiji's jar folder in the
past, so I'd have preferred to get it via the updater. As far as I
understand, the current dailies are 5.0, not 5.1 yet, which is where the
fix I'm looking for is right now?

Thanks for your help,

Christophe

2014-10-01 16:29 GMT+02:00 Mark Hiner <[hidden email]>:

> Hi Christophe,
>
> >checking the "Bio-Formats" update site should do that, or did I
> misunderstood something?
>
> You understood perfectly. The Bio-Formats update site should give you the
> latest Bio-Formats libraries.
>
> >I checked the update site but it doesn't seem to update Bio-Formats beyond
> the current Fiji version.
>
> Can you clarify what behavior you're expecting? I just tested the update
> site. The Wiki page <http://imagej.net/Bio-Formats#Daily_builds> mentioned
> earlier in the thread you referenced also has instructions for checking the
> version of your Bio-Formats - and mine went from 5.0.5 to 5.0.5-DEV, as
> expected.
>
> The 5.0.5 release was fairly recent, so I'm not sure what, if anything,
> will be different on the daily build. Is there a specific fix you were
> looking for that seems to be missing though?
>
> Hope this helps,
> Mark
>
> On Wed, Oct 1, 2014 at 2:54 AM, Christophe Leterrier <
> [hidden email]> wrote:
>
> > Hi,
> >
> > I'd like to know how to get the latest Bio-Formats (something like daily
> > builds) in Fiji. According to an email Curtis Rueden sent at the
> transition
> > between version 4 and 5 (
> >
> >
> http://imagej.1557.x6.nabble.com/Fiji-s-Bio-Formats-will-be-updated-to-5-0-0-tp5006701p5006787.html
> > ),
> > checking the "Bio-Formats" update site should do that, or did I
> > misunderstood something? I checked the update site but it doesn't seem to
> > update Bio-Formats beyond the current Fiji version.
> >
> > Thanks for your help,
> >
> > Christophe
> >
> > --
> > Christophe Leterrier
> > Researcher
> > Axonal Domains Architecture Team
> > CRN2M CNRS UMR 7286
> > Aix Marseille University, France
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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