http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5011414.html
> I uploaded an rather large file when I first reported this. Since the
Thank you for the clarification. I have reopened ticket #12548 with your
and Dave's comments from this thread [1]. I expect that the data you
> Hi Curtiss
>
> I uploaded an rather large file when I first reported this. Since the
> files are quite large (2-4GB), please let me know if you still have that
> one before I upload another one. I cannot do an upload of that size from
> home.
>
> Best regards
> --aryeh
>
>
> On 2/2/15 7:35 PM, Curtis Rueden wrote:
>
> Hi Aryeh,
>
> > The latest update of Bio-formats still does not read my multifield ND2
> > files correctly.
>
> Very sorry to hear that there are still problems reading your data.
>
> I spoke with Melissa briefly about this issue. The OME developers will
> need a sample non-working dataset in order to debug the issue. The best
> place to follow up is via the OME support channels:
>
> -
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/> -
http://qa.openmicroscopy.org.uk/qa/upload/>
> Regards,
> Curtis
>
> On Mon, Feb 2, 2015 at 10:48 AM, Aryeh Weiss <
[hidden email]> wrote:
>
>> 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: 972-3-7384051
>
>
>