[ome-users] Can I use Bio-Formats read .CZI file

[Qi Gong]

Hello Sebastien,

I got it. Thank you very much.

Regards,
Qi

On Mon, Jul 25, 2016 at 11:00 AM, Sebastien Besson (Staff) <
s.besson at dundee.ac.uk> wrote:

> Hi Qi,
>
> These ratings are more an appreciation of our support of the file format
> and will
> typically reflect the size/variety of our datasets, the availability of a
> specification
> document...
>
> That being said, all WSI file formats listed in that table are expected to
> be readable
> using Bio-Format. Known limitations like the unsupported JPEG-XR
> compression should
> be described directly in the individual format page - see e.g.
>
> http://www.openmicroscopy.org/site/support/bio-formats5.1/formats/zeiss-czi.html
>
> Best,
> Sebastien
>
>
> On 20 Jul 2016, at 19:36, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>
> Hello Damir,
>
> I have one more question about available image format. On your website I
> find this link
> http://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html
> .
>
> There are a lot of image formats and several rating titles. I want to know
> if I want to load the WSI image to Matlab through Bioformat, I should focus
> on which title? And the rating should be higher than "fair" or "good"?
> Thank you.
>
> Regards,
> Qi
>
>
>
> On Wed, Jun 8, 2016 at 5:27 PM, Damir Sudar <dsudar at lbl.gov> wrote:
>
>> Hi Qi,
>>
>> In general CZI images, including WSI images, are supported by BioFormats
>> and as you know, you need lots of memory allocated. However, internally
>> JPEG-XR-compressed CZI images are currently not yet supported at all. This
>> is expected to change in the near future. Meanwhile, you can save the
>> images in uncompressed format using Zeiss's ZEN application in order to
>> read them with your application with BioFormats.
>>
>> - Damir
>>
>> On Wed, Jun 8, 2016 at 2:00 PM, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>>
>>> Hello everyone,
>>>
>>> Sorry for bother. I want to know could I use Bio-Formats read .czi
>>> format WSI image in matlab? I could read in .svs and .ndpi formats now.
>>> When I used same code to read in .czi file, matlab gave me error. Thank you
>>> very much.
>>>
>>> >> WSI_data = bfGetReader('C:\000_whole_slides\WSIcziexample.czi');
>>>
>>> Warning: *** Insufficient memory detected. ***
>>> *** 352m found ***
>>> *** 512m or greater is recommended ***
>>> *** See http://www.mathworks.com/matlabcentral/answers/92813 ***
>>> *** for instructions on increasing memory allocation. ***
>>>
>>> > In bfCheckJavaMemory (line 53)
>>>   In bfGetReader (line 47)
>>> Error using bfGetReader (line 85)
>>> Java exception occurred:
>>> loci.formats.UnsupportedCompressionException: JPEG-XR not yet supported
>>>
>>> at
>>> loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2936)
>>>
>>> at
>>> loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2908)
>>>
>>> at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:557)
>>>
>>> at loci.formats.FormatReader.setId(FormatReader.java:1426)
>>>
>>> at loci.formats.ImageReader.setId(ImageReader.java:835)
>>>
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
>>>
>>> at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
>>>
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
>>>
>>> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
>>>
>>> Regards,
>>> Qi
>>>
>>> --
>>> mobile phone: 2024060862
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>
>>
>> --
>> Damir Sudar - Staff Scientist
>> Lawrence Berkeley National Laboratory
>> One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
>> T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
>>
>> Visiting Scientist, Oregon Health and Science University
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
>
> --
> mobile phone: 2024060862
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>


-- 
mobile phone: 2024060862
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20160725/d904c9b8/attachment.html>