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

Posted by Knecht, David on Feb 02, 2015; 3:00pm
URL: http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5011405.html

Hi Mark- Has there been any progress on opening ND2 files with multiple positions?  I suggested a “split positions” checkbox a while back, but that seems to not have been implemented.    If there is no Z, the system interprets positions as z slices.   At this point, I don’t know a way to open multichannel, multi-z, multi position datasets other than to split them in Elements. Dave

On Feb 2, 2015, at 9:51 AM, Mark Hiner <[hidden email]> wrote:

> 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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Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
Storrs, CT 06269
860-486-2200

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