From chenw1 at uthscsa.edu  Fri Oct  7 12:17:34 2022
From: chenw1 at uthscsa.edu (Wei Chen)
Date: Fri, 7 Oct 2022 11:17:34 -0500
Subject: Support Zeiss CZI format
Message-ID: <d1b63b66-6a96-595d-9dbe-ab211a4204a5@uthscsa.edu>

Hi,

I am working on Zeiss CZI driver.

https://github.com/venklab/openslide/tree/axioscan7

It reads bright field CZI file in JPEG XR and uncompressed format.
The microscope is AxioScan7. I can only make it generates these two
formats. Cannot find an option to produce JPEG or LZW or ZSTD CZI
therefor these decoders are not included in the driver.

It works for slide with single or multiple sections, or scenes, in CZI's
term. Slide label is also recognized and available in associated images.

AxioScan7 is able to capture multiple channels, such as multiple
grayscale channels for fluorescence. Its default is 14bits grayscale. I
need test downscale them to 8bits then remix grayscale channels into
single ARGB.

The JPEG XR decoder is from jxrlib, which is included in CentOS, Debian
and Ubuntu. Because CentOS7, Debian 10 and 11, Ubuntu < 22 are all
missing pkg-config file, an autogen.sh script is included to generate
libjxr.pc for configure.

I will send pull request after more testing.


Best,
Wei

From bgilbert+openslide at cs.cmu.edu  Sun Oct  9 11:54:44 2022
From: bgilbert+openslide at cs.cmu.edu (Benjamin Gilbert)
Date: Sun, 9 Oct 2022 11:54:44 -0400
Subject: Support Zeiss CZI format
In-Reply-To: <d1b63b66-6a96-595d-9dbe-ab211a4204a5@uthscsa.edu>
References: <d1b63b66-6a96-595d-9dbe-ab211a4204a5@uthscsa.edu>
Message-ID: <CANioFnhH=NsPTw90q2h34nmmrfq60ggWAHrAEO2ke1UMyXQb+w@mail.gmail.com>

On Fri, Oct 7, 2022 at 12:17 PM Wei Chen <chenw1 at uthscsa.edu> wrote:
> I am working on Zeiss CZI driver.

Thanks for getting in touch.  Did you use the official Zeiss CZI
format documentation to create the driver?  If so, AND if Zeiss still
requires agreeing to a license or click-through agreement before
receiving the documentation, AND if that license is similar to the
license text they've used in the past, then we will not be able to
merge your code.  The CZI documentation license has historically
included some language which appears to forbid using it to create open
source code and documentation.  Feel free to email me to discuss this
in more detail.

> The JPEG XR decoder is from jxrlib, which is included in CentOS, Debian
> and Ubuntu.

Unfortunately, jxrlib doesn't seem to have an active upstream
maintainer.  Some Linux distributions do package it, but without a
reliable upstream we'd probably need to make JPEG XR support optional.

Best,
--Benjamin Gilbert

From chenw1 at uthscsa.edu  Sun Oct  9 12:30:21 2022
From: chenw1 at uthscsa.edu (Wei Chen)
Date: Sun, 9 Oct 2022 11:30:21 -0500
Subject: Support Zeiss CZI format
In-Reply-To: <CANioFnhH=NsPTw90q2h34nmmrfq60ggWAHrAEO2ke1UMyXQb+w@mail.gmail.com>
References: <d1b63b66-6a96-595d-9dbe-ab211a4204a5@uthscsa.edu>
 <CANioFnhH=NsPTw90q2h34nmmrfq60ggWAHrAEO2ke1UMyXQb+w@mail.gmail.com>
Message-ID: <e76c7c25-6754-bac0-18d3-5ce0be6178be@uthscsa.edu>

Hi Benjamin,

On 10/09/2022 10:54 AM, Benjamin Gilbert wrote:
> Thanks for getting in touch.  Did you use the official Zeiss CZI
> format documentation to create the driver?  If so, AND if Zeiss still
> requires agreeing to a license or click-through agreement before
> receiving the documentation, AND if that license is similar to the
> license text they've used in the past, then we will not be able to
> merge your code.  The CZI documentation license has historically
> included some language which appears to forbid using it to create open
> source code and documentation.  Feel free to email me to discuss this
> in more detail.
>

I got the CZI format document 1.1(2012) from our Zeiss support
specialist. He didn't mention any license or agreement limitation. I
tried several times to get an updated version from Zeiss website but
haven't heard from them yet. Also Zeiss website interface may have
changed, I went through several steps to create service ticket. And
didn't see any click-through agreement option.

In this 1.1 version document, I cannot find any word mention what I
cannot do. It only describes the format.

>> The JPEG XR decoder is from jxrlib, which is included in CentOS, Debian
>> and Ubuntu.
>
> Unfortunately, jxrlib doesn't seem to have an active upstream
> maintainer.  Some Linux distributions do package it, but without a
> reliable upstream we'd probably need to make JPEG XR support optional.
>

Sure, I can do it in configure.

Now this driver can read uncompressed, BGR24, BGR48, and fluorescence 
image in Gray8 and Gray16, at most three fluorescence channels though.


Best,
Wei

From chenw1 at uthscsa.edu  Mon Oct 10 11:52:52 2022
From: chenw1 at uthscsa.edu (Wei Chen)
Date: Mon, 10 Oct 2022 10:52:52 -0500
Subject: Support Zeiss CZI format
In-Reply-To: <92a0b6b94e8747d0828672c184d023e9@cea.fr>
References: <d1b63b66-6a96-595d-9dbe-ab211a4204a5@uthscsa.edu>
 <CANioFnhH=NsPTw90q2h34nmmrfq60ggWAHrAEO2ke1UMyXQb+w@mail.gmail.com>
 <e76c7c25-6754-bac0-18d3-5ce0be6178be@uthscsa.edu>
 <92a0b6b94e8747d0828672c184d023e9@cea.fr>
Message-ID: <1133abfd-26e6-9ad5-a50f-115986e26a20@uthscsa.edu>

Hi Nicolas,

I am super excited to see your message. It is like finally meet you,
although not in person :). I learned a lot, especially on how to use the
range grid, by studying your code!


On 10/10/22 3:36 AM, SOUEDET Nicolas wrote:
> A few years ago (in 2016, I guess), we tried to integrate CZI ZEISS support to OpenSlide and we had exactly the same problem than you.
> The main issue is that ZEISS is too restrictive in its licence and the only way we found was to fork openslide and to integrate CZI ZEISS support in a separated github project. Our repository is based upon an old OpenSlide version, but if you want to have look it is available here : https://github.com/MIRCen/openslide
> 

I am not aware any limitation on using CZI doc. In fact, I won't accept
the CZI format document in the first place, if it has any restriction
attached. The 1.1 version I used also looks very similar to the top
search result when google "ZISRAW file format", at least for the file
and segment header part I am interested.

Although I wrote the driver mainly for our research, I do hope upstream
can integrate it so people in the future can spend more time working on
scientific problems rather than preparing to solve them.


Best,
Wei

From bgilbert at cs.cmu.edu  Tue Oct 11 22:57:30 2022
From: bgilbert at cs.cmu.edu (Benjamin Gilbert)
Date: Tue, 11 Oct 2022 22:57:30 -0400
Subject: Support Zeiss CZI format
In-Reply-To: <e76c7c25-6754-bac0-18d3-5ce0be6178be@uthscsa.edu>
References: <d1b63b66-6a96-595d-9dbe-ab211a4204a5@uthscsa.edu>
 <CANioFnhH=NsPTw90q2h34nmmrfq60ggWAHrAEO2ke1UMyXQb+w@mail.gmail.com>
 <e76c7c25-6754-bac0-18d3-5ce0be6178be@uthscsa.edu>
Message-ID: <CANioFnjGuaCzHW9hUqnY2BVqxHHrE9UgihAvZTHHbOf2PHi-kA@mail.gmail.com>

On Sun, Oct 9, 2022 at 12:30 PM Wei Chen <chenw1 at uthscsa.edu> wrote:
> I got the CZI format document 1.1(2012) from our Zeiss support
> specialist. He didn't mention any license or agreement limitation. I
> tried several times to get an updated version from Zeiss website but
> haven't heard from them yet. Also Zeiss website interface may have
> changed, I went through several steps to create service ticket. And
> didn't see any click-through agreement option.
>
> In this 1.1 version document, I cannot find any word mention what I
> cannot do. It only describes the format.

Okay, great.  Thanks for the additional context.

Best,
--Benjamin Gilbert