[ome-users] question about Bio-Formats.

Wed Apr 8 19:08:38 BST 2015

Hello Sebastien,

now I just use the command
"reader = bfGetReader('C:\000_whole_slides\tissue40x-8B.ndpi');
plane = reader.openThumbBytes(1);"
to get the thumbnail. But the output is a vector. 12288 x1. in the
bfGetPlane function, you use the reshape function to transfer it to 2-D
image. But in that function we know the size of image. And now I don't know
the size (width and height). Do you know how to transfer it to image? Thank
you.

Sincerely,
Qi

On Wed, Apr 8, 2015 at 5:45 AM, Sebastien Besson (Staff) <
s.besson at dundee.ac.uk> wrote:

>  Hi Qi,
>
>  all understood and this certainly makes sense.
> The Bio-Formats API has a method to return bytes corresponding to a
> thumbnail instead of a full plane, see
>
> http://downloads.openmicroscopy.org/bio-formats/5.1.0/api/loci/formats/FormatReader.html#openThumbBytes(int)
>
>  This method can be used in the same way that bfGetPlane() makes use
> openBytes() to retrieve a single
> plane. Here, the final array would have to be resized by the thumbnail
> size, typically 128 x 128, instead
> of the full plane dimensions
>
>  Note however that the way to get thumbnails for almost all of the
> readers is to read the pixels data
> and scale it internally. For very large WSI, calling this method will
> likely be restricted to the same memory
> limitations as reading full planes.
>
>  Best regards,
> Sebastien
>
>  On 7 Apr 2015, at 15:53, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>
>   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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