Re: Latest Bio-Formats in Fiji

Posted by Aryeh Weiss on Oct 01, 2014; 5:07pm
URL: http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5009856.html

On 10/1/14, 6:44 PM, Christophe Leterrier wrote:

> 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?

This may be similar to the bug #12548 on the OME list.

I tried the version pointed by the above link. It has the same problem
as the latest update found by the updater.
In each case, using the 5.0.2 version of the formats-gpl.jar file solves
the problem (at least for my large nd2 files)


--aryeh

> 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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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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