[ome-users] question about Bio-Formats.

[Qi Gong]

Hello Sebastien,

Thank you your your reply. I think it is working. 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. But it extract image is 1-by-1  pixel. 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.

Sincerely,
Qi

On Mon, Apr 6, 2015 at 3:26 PM, Sebastien Besson <seb.besson at gmail.com>
wrote:

> Hi Qi,
>
> the content of your java.opts looks valid (although you might want to
> increase the
> memory settings later). According to the MATLAB documentation, e.g.
>
> http://uk.mathworks.com/help/matlab/matlab_env/java-opts-file.html?refresh=true
> you need to put this file either in the MATLAB startup folder or under the
> `bin\arch` folder
> under the MATLAB root path. Locally, I have a `java.opts` under
> `~/Documents/MATLAB` for
> instance.
>
> Can you try either of these options and check the output of the following
> command
> >> java.lang.Runtime.getRuntime().maxMemory
> reflects what it in your java.opts
>
>
> Sebastien
>
> On 6 Apr 2015, at 19:53, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>
> Hello everyone,
>
> Sorry for bother. I try to use  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.
>
> 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.
>
> Sincerely,
> Qi
>
>
>  <matlab folder.png><memory warning.png><java.opts>
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