http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5011412.html
I uploaded an rather large file when I first reported this. Since the
that one before I upload another one. I cannot do an upload of that size
> 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]
> <mailto:
[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]
> <mailto:
[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/>
>
> <
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 <tel:860-486-2200>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
>
>
>