[ome-users] question about Bio-Formats.

[Qi Gong]

Hello Sebastien,

Thank you for your email. I am sorry, my description was not clear. It is
not "1-by-1". Now I could extract some sub_area of image, but the extracted
image is *1-to-1 *pixel with WSI. What we want is a thumbnail. In other
word, we want to display the whole WSI or a large part of WSI in a small
size. Thank you.

Sincerely,
Qi

On Mon, Apr 6, 2015 at 6:37 PM, Sebastien Besson (Staff) <
s.besson at dundee.ac.uk> wrote:

>  Hi Qi,
>
>
>  Do you need a thumbnail
>
>
>   On 6 Apr 2015, at 22:11, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>
>  Hello Sebastien,
>
>
>  Hi Qi,
>
>  Thank you your your reply. I think it is working.
>
>
>  Good to hear.
>
>   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.
>
>
>  Indeed, if the image is large enough, reading all the planes into memory
> like boffin does simply does not
> scale and you have to read selectively.
>
>   But it extract image is 1-by-1  pixel.
>
>
>  If you have a WSI, it is surprising that the command pasted in a
> previous thread would return a single pixel
> Can you give us the full dimensions of your image as given by
> >> r =  bfGetReader(‘\path\to\file);
> >> r.getSizeX()
> >> r.getSizeY()
>  >> r.getSizeZ()
> >> r.getSizeC()
>  >> r.getSizeT()
> Also, can you paste the command you use to retrieve this 1-by-1 pixel
> array?
>
>   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.
>
>
>  Just to be sure, do you want to read a thumbnail for the entire image?
> Or are you looking for a way to
> retrieve a tile i.e. a XY subset of the full image?
>
>   Sincerely,
> Qi
>
>
>  Best regards,
> Sebastien
>
>
> 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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>
>
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