[ome-users] Question about Matlab Bio-Formats

[Sebastien Besson (Staff)]

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<mailto: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<mailto: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<mailto: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
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