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

Posted by Aryeh Weiss on Feb 02, 2015; 4:48pm
URL: http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5011410.html

On 2/2/15 5:00 PM, Knecht, David wrote:
> 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 David

You can open multifield ND2 files with bioformats. What you need to maek
it work correctly is the formats-gpl05.0.2.jar file, which still works
correctly with the 5.0.6 distribution. After you insert that, you should
make sure that it does not get updated when you update Fiji.

I can send it to you offlist if you want it. Insert it into
jars/bioformats , and make sure to remove the existing file.

With this workaround, I opened a file with 20 fields, each of which has
3 channels an 17 z-positions.

Best regards,
--aryeh

>> 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
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> Dr. David Knecht
> Professor of Molecular and Cell Biology
> Core Microscopy Facility Director
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
>
> --
> 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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