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

[Sebastien Besson (Staff)]

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<mailto: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<mailto: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<mailto: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

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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<tel:510%2F486-5346> - F: 510/486-5586<tel:510%2F486-5586> - E: DSudar at lbl.gov<mailto:DSudar at lbl.gov>

Visiting Scientist, Oregon Health and Science University

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