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

[Damir Sudar]

Hi Qi,

I don't know the schedule but I do know some very capable people are
working on it so I expect it will not be too long.

For the interim, note that one of my colleagues has found that doing the
following generates WSI CZI files that are quite manageable:
"I think I just found a better way to deal with large, Axioscan-generated
JPEG-XR images. If I simply select “save as with options” in the Zen file
menu, I can select “uncompressed” and also eliminate some of the pyramid
levels (1 to 3 or 1 to 4 works fine). This reduces the file size by almost
10-fold, and the images successfully import to OMERO (display settings
still don’t transfer yet though). I haven’t noticed a reduction in quality
in the OMERO images."

Cheers,
- Damir

On Wed, Jun 8, 2016 at 2:33 PM, Qi Gong <qigong at gwmail.gwu.edu> wrote:

> Hello Damir,
>
> Thank you very much. Do you know when will that version come? I will try
> uncompressed format.
>
> 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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>>> ome-users at lists.openmicroscopy.org.uk
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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
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
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>>
>>
>
>
> --
> 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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