Implementation of a CZI (Zeiss) driver

[Mathieu Malaterre]

This is indeed a very good implementation of JPEG-XR. It is available
on debian as shared lib (SOVERSIPON set to 0 as per upstream):

http://packages.qa.debian.org/j/jxrlib.html

I had to tweak the build system though.

On Fri, Jun 13, 2014 at 2:08 AM, Adam Goode <adam at spicenitz.org> wrote:
> Regarding JPEG XR: this library looks extremely promising, though it
> would need to get shared library (and probably pkg-config) support.
> Then I suspect it would be packagable in Fedora.
>
> https://jxrlib.codeplex.com/
>
>
> Adam
>
>
> On Thu, Jun 12, 2014 at 2:45 PM, Dmitry Fedorov <fedorov at ece.ucsb.edu> wrote:
>> Hi,
>>
>> We use OpenSlide with the BisQue system for cloud-based management,
>> annotations and analysis and also would like to see CZI whole slide
>> support in OpenSlide. I would support this endeavour and volunteer to
>> help with coding! I agree with Yael in that CZI file format parsing
>> should be written as a separate file/class since additional libraries
>> would already be needed, like jpeg xr.
>>
>> I would suggest one additional requirement for the CZI reader. Since
>> Zeiss CZI file container may hold many 6D image variants and I use
>> another decoder for those it would be great if the openslide would
>> only accept the file if it is a 2D pyramidal tiled RGB image. This is
>> because OpenSlide does not support n-d images nor arbitrary number of
>> channels per image.
>>
>> Dmitry
>>
>>
>> On Thu, Jun 12, 2014 at 8:08 AM, BALBASTRE Yael 237482 Thésard
>> <yael.balbastre at cea.fr> wrote:
>>> Hi,
>>>
>>> Since our lab has acquired a Zeiss Axio-Scan scanner, we are interested in
>>> adding a czi reader to OpenSlide (that we are already using to read other
>>> WSI images). We already had a few contacts with Benjamin Gilbert, but it
>>> must be better to ask my questions using this mailing list.
>>>
>>> The CZI format has been entirely specified by Zeiss and, contrary to most
>>> formats present in OpenSlide, does not use a tiff base, even though the
>>> principles are shared. A file contains several subblocks, each containing a
>>> subimage which can be compressed (jpeg or jpegXR mainly) or not, as well as
>>> metadata stored in the file as xml blocks.
>>>
>>> To follow up the question I asked to Mr Gilbert regarding the file supposed
>>> to host czi-related code, I am not comfortable with having all of it in a
>>> single openslide-zeiss-vendor.c source, especially since it would deal both
>>> with file stream reading (decoding of the hard
>>> directories/subblocks/attachments structure) and with more high-level,
>>> microscopy-related treatment (metadata, grid-building, subimages
>>> decoding...).
>>> I would rather have the stream reading separated and placed in a different
>>> source file along with a clear API (which would resemble the tiff decoder).
>>> I understand that it is different from what has been done before, but maybe
>>> the issue had never been on the table because none of the previous formats
>>> had such a specification ? (the only one I see coming close is MIRAX).
>>> If you still prefer to have everything in one big source, I will obviously
>>> go this way.
>>>
>>> Thanks a lot for your time.
>>>
>>> Best regards,
>>> Yaël Balbastre
>>>
>>> Yaël Balbastre - PhD student
>>> CEA/DSV/I²BM/MIRCen/LMN
>>> Image Processing Team - bioPICSEL
>>> 18 route du Panorama - BP6
>>> 92265 FONTENAY-AUX-ROSES CEDEX
>>> FRANCE
>>> T 33 (1) 46 54 92 83
>>>
>>> _______________________________________________
>>> openslide-users mailing list
>>> openslide-users at lists.andrew.cmu.edu
>>> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users
>>>
>>
>>
>>
>> --
>> __________________________________
>>
>> Dmitry Fedorov Levit <dima at dimin.net>
>> Web: http://www.dimin.net/
>> __________________________________
>>
>> Center for Bio-Image Informatics:
>>   <http://www.bioimage.ucsb.edu/>
>>
>> Vision Research Lab, Electrical and Computer Engineering:
>>   <http://vision.ece.ucsb.edu/>
>>
>> University of California, Santa Barbara
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-- 
Mathieu