[ome-users] Question about Matlab Bio-Formats

[Melissa Linkert]

Hi Qi,

> I try it. But it still has problem as attachment. I will send the image to
> you. Thank you.

Thank you for sending the file.  I can confirm the problem, and there is
now a ticket for this problem on our issue tracking system:

https://trac.openmicroscopy.org/ome/ticket/12839

You have been CC'd on the ticket, and so will automatically be notified
of changes to the ticket's status.  If you prefer not to receive
notifications, please let us know.

Regards,
-Melissa

On Wed, Apr 15, 2015 at 11:47:58AM -0400, Qi Gong wrote:
> Hello Sebastien,
> 
> I try it. But it still has problem as attachment. I will send the image to
> you. Thank you.
> 
> Sincerely,
> Qi
> 
> On Wed, Apr 15, 2015 at 10:27 AM, Sebastien Besson (Staff) <
> s.besson at dundee.ac.uk> wrote:
> 
> >  Hi Qi,
> >
> >  thanks for testing this. First of all, upgrade can sometimes be tricky
> > as old JAR s
> > are still present in the MATLAB class path. Could you double check that
> > you are
> > using the latest release version by verifying the output of:
> >
> >  >> [~, v] = bfCheckJavaPath
> >
> >  v =
> >
> >  5.1.0
> >
> >  Once you have confirmed the version and assuming the error still
> > persists for the
> > large NPDI files, could you also paste the stack trace of the error? In
> > this case,
> > we will also need the original file to help you further with the
> > underlying issue. Since
> > the image is larger than 2 GB, we will contact you privately with FTP
> > information
> > to upload examples of failing files.
> >
> >  Best regards,
> > Sebastien
> >
> >  On 14 Apr 2015, at 22:34, Qi Gong <qigong at gwmail.gwu.edu> wrote:
> >
> >  Hello Sebastien,
> >
> >  Thank you for your reply. It is still doesn't work and has same problem.
> > Actually, For some .ndpi files, we could extract anywhere from highest
> > resolution WSI. But for some in highest resolution, we could only reach
> > about 2/3 in Y directory, and could reach whole X directory. For example,
> > if WSI image is 30000 * 30000. We could extract [1:30000,1:20000] area. For
> > [1:30000,20001:30000], we face the problem. I try Bio-formats by 5 WSI, 3
> > of them work well. Well the other two have this problem. And only the two
> > files don't work have more than 3 GB size. Don't you think that is the
> > reason? Thank you.
> >
> >  Sincerely,
> > Qi
> >
> > On Tue, Apr 14, 2015 at 5:07 PM, Sebastien Besson (Staff) <
> > s.besson at dundee.ac.uk> wrote:
> >
> >> Hi Qi,
> >>
> >> thanks for your feedback.
> >> The stack trace attached to your email suggests you are using
> >> Bio-Formats 5.0.8 or earlier. Your error is very similar to the
> >> one reported in http://trac.openmicroscopy.org.uk/ome/ticket/12367.
> >>
> >> The latter issue has been fixed in the 5.1.0 release of Bio-Formats.
> >> Could you try upgrading your version of Bio-Formats MATLAB to this
> >> release as described in
> >>
> >> https://www.openmicroscopy.org/site/support/bio-formats5.1/users/matlab/index.html#upgrading
> >> and try accessing the WSI tile again? Let us know if this resolves the
> >> issue.
> >>
> >> Best regards,
> >> Sebastien
> >>
> >> > On 14 Apr 2015, at 18:19, Qi Gong <qigong at gwmail.gwu.edu> wrote:
> >> >
> >> > Hello everyone,
> >> >
> >> > Sorry for bother. I have a question about Matlab Bio-formats. I want to
> >> use bfGetPlane function to extract a area for WSI. But I face a problem as
> >> attachment. I believe I choose a area inside the image, But it shows error.
> >> >
> >> > If I change
> >> > I=bfGetPlane(reader,2,3179,79516,454,454); to
> >> > I=bfGetPlane(reader,2,3179,40000,454,454);
> >> >
> >> > It could work. But I think 79516 is inside the image as
> >> reader.getSizeY() =  93184.
> >> > Does anyone know why this happen? Thank you.
> >> >
> >> > Sincerely,
> >> > Qi
> >> > --
> >> > mobile phone: 2024060862
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> >>
> >>
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> >
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