[ome-users] Question about Matlab Bio-Formats

[Qi Gong]

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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