Zeiss CZI

SOUEDET Nicolas 215310 nicolas.souedet at cea.fr
Tue Nov 18 03:49:59 EST 2014

Hi Benjamin,

We continue to work on the CZI support, but as it is not our main work, we spend only few time to do this.
We hope to be able to submit a first version that can be reviewed before christmas hollidays.

Nicolas Souedet

-----Message d'origine-----
De : openslide-users-bounces+nicolas.souedet=cea.fr at lists.andrew.cmu.edu [mailto:openslide-users-bounces+nicolas.souedet=cea.fr at lists.andrew.cmu.edu] De la part de Benjamin Gilbert
Envoyé : mardi 18 novembre 2014 07:38
À : openslide-users at lists.andrew.cmu.edu
Cc : mario at emmenlauer.de
Objet : Re: Zeiss CZI

On 11/16/2014 03:44 AM, Mario Emmenlauer wrote:
> I've seen an email conversation from summer where support for Zeiss 
> CZI was mentioned - is there (preliminary) support for this format?
> Can I help with some testing or something?

Hi Mario,

Yaël Balbastre and Nicolas Souedet were working on adding CZI support:


As I understand it, their changes are not yet complete, and I haven't heard from them in a while.

For now, the best way to help is by contributing sample slides.  We do have some CZI files provided by the community, but what we really need now is for someone to spend a couple hours with a scanner and collect a set of scans in a rigorous way.  Ideally, we'd like samples of every major feature supported by the format, including:

- A couple JPEG slides
- A couple JPEG XR slides
- An LZW slide, if supported (I am unclear on that)
- A slide with multiple regions of interest, if supported
- Fluorescence scans
- Time-lapse, Z-stacks, etc.

It's best if the scans are of real specimens (instead of a blank slide) but the specimens can be anything that is convenient.

For the scans to be the most useful, we also need a signed permission letter allowing us to distribute these samples in the openslide-testdata dataset.  This allows us to use the samples in automated test cases, and allows others to use them for their own testing.  I can provide the wording for this letter upon request.

--Benjamin Gilbert
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