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

[Qi Gong]

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
>>
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>>
>>
>
>
> --
> 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
>
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