http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5011469.html
> Hi Aryeh,
>
>>> 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.
>> 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
>> already uploaded is sufficient to continue investigating the issue; we will
>> let you know if not.
> You may have seen this already, but for anyone else following along:
>
>
http://trac.openmicroscopy.org/ome/ticket/12548#comment:11>
> I can confirm that the file you uploaded previously does open with the
> correct stage position, Z section, and channel counts using the files
> from
http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/. With versions of those files that pre-date the fixes mentioned in the ticket,
> I do see the same dimensionality problems that you originally reported.
>
> Please do make sure that all of the steps listed in the ticket comment
> have been performed when updating your Fiji installation - it is really
> easy to forget a file or miss a step.
>
> If that still doesn't work, please upload a Zip file containing your
> Fiji installation directory - this should help us to pinpoint any
> problems that may have occurred during the update.
>
> Regards,
> -Melissa
>
>
> On Mon, Feb 02, 2015 at 03:03:37PM -0600, Curtis Rueden wrote:
>> Hi Aryeh,
>>
>>> 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.
>> 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
>> already uploaded is sufficient to continue investigating the issue; we will
>> let you know if not.
>>
>> Regards,
>> Curtis
>>
>> [1]
https://trac.openmicroscopy.org.uk/ome/ticket/12548#comment:10>>
>>
>> On Mon, Feb 2, 2015 at 12:05 PM, Aryeh Weiss <
[hidden email]> wrote:
>>
>>> 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>>>>>
>>>>>
>>>>
>>>