[ome-users] question about Bio-Formats.

Wed Apr 8 20:20:44 BST 2015

Hi Qi,

to convert the thumbnail array returned from openThumBytes, you should be able to use
the same steps as in bfGetPlane to convert the int8 array into an array of the correct type.
For the final reshaping step, you can read the thumbnail dimensions from the reader with:

I = reshape(I, [reader.getThumbSizeX() reader.getThumbSizeY()])’;

Best,
Sebastien

> On 8 Apr 2015, at 19:08, Qi Gong <qigong at gwmail.gwu.edu> wrote:
> 
> 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 <mailto: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) <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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <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 <mailto: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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