Re: Latest Bio-Formats in Fiji

Posted by Mark Hiner on Oct 06, 2014; 12:52pm
URL: http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5009916.html

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: [phone]
>
>

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