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Hi Qi,
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<div class="">Do you need a thumbnail</div>
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<div class="">On 6 Apr 2015, at 22:11, Qi Gong <<a href="mailto:qigong@gwmail.gwu.edu" class="">qigong@gwmail.gwu.edu</a>> wrote:</div>
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<div dir="ltr" class="">Hello Sebastien,</div>
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Hi Qi,<br class="">
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<div class="">Thank you your your reply. I think it is working.</div>
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Good to hear.</div>
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<div class="">Now, I want to use BIO to get a WSI ( whole slide image) image. But as the WSI is to large more than 2 GB. I can't use bfopen to open it. Melissa told me a could use bfGetPlane to get the image.
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<div>Indeed, if the image is large enough, reading all the planes into memory like boffin does simply does not</div>
<div>scale and you have to read selectively.</div>
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<div class="">But it extract image is 1-by-1 pixel. </div>
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<div class="">If you have a WSI, it is surprising that the command pasted in a previous thread would return a single pixel</div>
<div class="">Can you give us the full dimensions of your image as given by</div>
<div class="">>> r = bfGetReader(‘\path\to\file);</div>
<div class="">>> r.getSizeX()</div>
<div class="">>> r.getSizeY()</div>
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<div class="">>> r.getSizeZ()</div>
<div class="">>> r.getSizeC()</div>
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<div class="">>> r.getSizeT()</div>
<div class="">Also, can you paste the command you use to retrieve this 1-by-1 pixel array?</div>
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<div class="">But some time, we need and thumb image of whole image. Do you know how to extract a 1-by-N image? That means, Extract the whole image (with size 10000x10000), but only display and save in 100x100 size. Thank you.</div>
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<div>Just to be sure, do you want to read a thumbnail for the entire image? Or are you looking for a way to</div>
<div>retrieve a tile i.e. a XY subset of the full image?</div>
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<div class="">Sincerely,</div>
<div class="">Qi </div>
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Best regards,</div>
<div>Sebastien</div>
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<div class="gmail_quote">On Mon, Apr 6, 2015 at 3:26 PM, Sebastien Besson <span dir="ltr" class="">
<<a href="mailto:seb.besson@gmail.com" target="_blank" class="">seb.besson@gmail.com</a>></span> wrote:<br class="">
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<div style="word-wrap:break-word" class="">Hi Qi,
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<div class="">the content of your java.opts looks valid (although you might want to increase the</div>
<div class="">memory settings later). According to the MATLAB documentation, e.g.</div>
<div class=""><a href="http://uk.mathworks.com/help/matlab/matlab_env/java-opts-file.html?refresh=true" target="_blank" class="">http://uk.mathworks.com/help/matlab/matlab_env/java-opts-file.html?refresh=true</a></div>
<div class="">you need to put this file either in the MATLAB startup folder or under the `bin\arch` folder</div>
<div class="">under the MATLAB root path. Locally, I have a `java.opts` under `~/Documents/MATLAB` for</div>
<div class="">instance.</div>
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<div class="">Can you try either of these options and check the output of the following command</div>
<div class="">>> java.lang.Runtime.getRuntime().maxMemory</div>
<div class="">reflects what it in your java.opts</div>
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<div class="">Sebastien</div>
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<div class="">On 6 Apr 2015, at 19:53, Qi Gong <<a href="mailto:qigong@gwmail.gwu.edu" target="_blank" class="">qigong@gwmail.gwu.edu</a>> wrote:</div>
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<div dir="ltr" class="">Hello everyone,
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<div class="">Sorry for bother. I try to use <span style="font-size:12.8000001907349px" class=""> </span><span style="font-size:12.8000001907349px" class="">Matlab version of Bio-Formats. But I face the memory problem, I know, we could add a time named java.opts
to solve the problem. </span></div>
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<div class="">I put the file the java.opts into matlab folder as attachment. But matlab still shows the warning. Could anyone help me check whether my java.opts is correct or not? Thank you.</div>
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<div class="">Sincerely,</div>
<div class="">Qi</div>
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