http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5010804.html
> 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
That is very odd. It would be great if you could somehow isolate the
difference between the working version of Fiji vs. the non-working
tool [1], which would rule out any Fiji-specific installation issues. And
> 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]>
>>>> 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>