http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5011465.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
. With versions of those files that pre-date the fixes mentioned in the ticket,
> 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> >>>
> >>>
> >>
> >>
> >>
> > --
> > Aryeh Weiss
> > Faculty of Engineering
> > Bar Ilan University
> > Ramat Gan 52900 Israel
> >
> > Ph: 972-3-5317638
> > FAX: 972-3-7384051
> >
> >
> >