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

[Damir Sudar]

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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