Re: problem with ND2 reader in latest Bio-Formats in Fiji

Posted by Mark Hiner on Feb 02, 2015; 2:51pm
URL: http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5011404.html

Hi Aryeh,

Thanks for following up on the ImageJ list.

For reference:
- the closed ticket[1]
- commit on develop[2] (Bio-Formats 5.1.x)

>On the OME tracking system, this bug is said to be resolved. If so, then
the corrected bioformats is not yet distributed on the fiji update sites.

Fiji uses Bio-Formats 5.0.x, with the dev version[3] available from the
Bio-Formats development update site[4]. This fix will become part of core
Fiji when there's a 5.1.0 release.

>I also downloaded the appropriate jar files from
>ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
<http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/>

I believe this was the correct place to pull artifacts from to test the ND2
fix, but you should not use 5.0.x jars with 5.1.x. If you want to try
5.1.x, you should replace everything in Fiji.app/jars/bio-formats with its
5.1.x equivalent.

Hope that helps. Good luck!

Best,
Mark

[1] http://trac.openmicroscopy.org.uk/ome/ticket/12548
[2]
https://github.com/openmicroscopy/bioformats/commit/6e6387f8206889b416fe4df9f61d72f782ca0e9e
[3] https://github.com/openmicroscopy/bioformats/tree/dev_5_0
[4] http://imagej.net/List_of_update_sites

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