[ome-users] Question about Matlab Bio-Formats

[Qi Gong]

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
>>  > <problem.png>_______________________________________________
>> > ome-users mailing list
>> > ome-users at lists.openmicroscopy.org.uk
>> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>  _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
>
>
>  --
> mobile phone: 2024060862
>  _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>


-- 
mobile phone: 2024060862
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150415/85abe9e8/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: problem.png
Type: image/png
Size: 36285 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150415/85abe9e8/attachment.png>