http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5010820.html
bioformats-gpl in my recent backups. This most likely means that I was
> issues. And of course testing from multiple different machines might
As long as the workaround works, it is ok. However, that seems like
> [1]
>
http://openmicroscopy.org/site/support/bio-formats5/users/comlinetools/>
> On Thu, Nov 27, 2014 at 1:45 AM, Aryeh Weiss <
[hidden email]
> <mailto:
[hidden email]>> wrote:
>
> On 10/6/14, 11:17 PM, Aryeh Weiss wrote:
>
> Hi Melissa
>
> On 10/6/14, 4:27 PM, Melissa Linkert wrote:
>
> 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).
>
>
> Thank you (and also Mark) for your replies.
> I downloaded the 5.1 builds for all of the jar files in the
> jars/bio-formats directory of my Fiji distribution.
> When I dragged one of my nd2 files into Fiji, bio-formats
> opened, but had the same bug as reported previously.
> When I restored the old bio-formats directory with the 5.0.2
> version of gpl, it worked properly.
> I did not try the 5.0.2 gpl with the 5.1 release, because of
> Melissa warning concerning mixing the two versions.
>
>
> Best regards
> --aryeh
>
>
> 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
>
>
> About two weeks ago, when 5.0.6 was announced, I allowed the Fiji
> updater to update formats-gpl.
> The updated version correctly read my multifield ND2, so I thought
> that this bug was resolved.
> However, yesterday, following an update, the problem reappeared.
> Again,the workaround was to use the 5.0.2 version of
> formats-gpl.
>
> I have not had a chance to search my recent backups for this file
> to see if I can determine exactly when it broke again -- I will
> try to do that.
>
>
> Best regards,
> --aryeh
>
>
>
> 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] <mailto:
[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
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
>