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Hi Qi,
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</div>
<div class="">thanks for testing this. First of all, upgrade can sometimes be tricky as old JAR s</div>
<div class="">are still present in the MATLAB class path. Could you double check that you are</div>
<div class="">using the latest release version by verifying the output of:</div>
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</div>
<div class="">
<div class="">>> [~, v] = bfCheckJavaPath</div>
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</div>
<div class="">v =</div>
<div class=""><br class="">
</div>
<div class="">5.1.0</div>
</div>
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</div>
<div class="">Once you have confirmed the version and assuming the error still persists for the</div>
<div class="">large NPDI files, could you also paste the stack trace of the error? In this case,</div>
<div class="">we will also need the original file to help you further with the underlying issue. Since</div>
<div class="">the image is larger than 2 GB, we will contact you privately with FTP information</div>
<div class="">to upload examples of failing files.</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class="">Sebastien</div>
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<div>
<blockquote type="cite" class="">
<div class="">On 14 Apr 2015, at 22:34, Qi Gong <<a href="mailto:qigong@gwmail.gwu.edu" class="">qigong@gwmail.gwu.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<div dir="ltr" class="">Hello Sebastien,
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</div>
<div class="">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.</div>
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<div class="">Sincerely,</div>
<div class="">Qi </div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Tue, Apr 14, 2015 at 5:07 PM, Sebastien Besson (Staff)
<span dir="ltr" class=""><<a href="mailto:s.besson@dundee.ac.uk" target="_blank" class="">s.besson@dundee.ac.uk</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Qi,<br class="">
<br class="">
thanks for your feedback.<br class="">
The stack trace attached to your email suggests you are using<br class="">
Bio-Formats 5.0.8 or earlier. Your error is very similar to the<br class="">
one reported in <a href="http://trac.openmicroscopy.org.uk/ome/ticket/12367" target="_blank" class="">
http://trac.openmicroscopy.org.uk/ome/ticket/12367</a>.<br class="">
<br class="">
The latter issue has been fixed in the 5.1.0 release of Bio-Formats.<br class="">
Could you try upgrading your version of Bio-Formats MATLAB to this<br class="">
release as described in<br class="">
<a href="https://www.openmicroscopy.org/site/support/bio-formats5.1/users/matlab/index.html#upgrading" target="_blank" class="">https://www.openmicroscopy.org/site/support/bio-formats5.1/users/matlab/index.html#upgrading</a><br class="">
and try accessing the WSI tile again? Let us know if this resolves the<br class="">
issue.<br class="">
<br class="">
Best regards,<br class="">
Sebastien<br class="">
<div class="">
<div class="h5"><br class="">
> On 14 Apr 2015, at 18:19, Qi Gong <<a href="mailto:qigong@gwmail.gwu.edu" class="">qigong@gwmail.gwu.edu</a>> wrote:<br class="">
><br class="">
> Hello everyone,<br class="">
><br class="">
> 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.<br class="">
><br class="">
> If I change<br class="">
> I=bfGetPlane(reader,2,3179,79516,454,454); to<br class="">
> I=bfGetPlane(reader,2,3179,40000,454,454);<br class="">
><br class="">
> It could work. But I think 79516 is inside the image as reader.getSizeY() = 93184.<br class="">
> Does anyone know why this happen? Thank you.<br class="">
><br class="">
> Sincerely,<br class="">
> Qi<br class="">
> --<br class="">
> mobile phone: 2024060862<br class="">
</div>
</div>
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