Sebi

Ah, I see. Cool.

napari-czitools/src/napari_czitools/_io.py at 2e587ae0a46c5128c97573c487574d3f5a7d9935 · sebi06/napari-czitools napari plugin to open CZI image files and their metadata - sebi06/napari-czitools

Hi @jni.codes I thought you mean what I (try) do here:

github.com/sebi06/napar...

I just meant that a while ago i started to read CZI images into Xarrays.

Before that I had to use custom code to label the axis sliders in Napari, but now this just works out-of-the-box thanks to labelled arrays.

GitHub - sebi06/napari-czitools: napari plugin to open CZI image files and their metadata napari plugin to open CZI image files and their metadata - sebi06/napari-czitools

This works already, doesn't it.

In my (experimental) github.com/sebi06/napar... I was nicely surprised to see that using Xarrays made my custom code to label axes in Napari based on dimension order useless :-)

It works now out of the box

Finally - the latest release of our pylibCZIrw supports also MacOS.

Check: pypi.org/project/pyli...

My favorite thingy: Direct data streaming and stage control from Java!

nice to see our ZEN API from @zeiss-microscopy.bsky.social in action. *.proto Files --> Java --> Pixel Stream in Fiji 😉

If you want more info check

github.com/zeiss-micros...

github.com/sebi06/ZEN_P...

That’s Mifobio Spirit @gdrimabio.bsky.social … fun sample thanks Frédéric Bolze

GitHub - sebi06/ZEN_Python_CZI_Smart_Microscopy_Workshop: Material to showcase and test several tools and packages releated to ZEN, OAD, ZEN-API. CZI image files and python packages related to those t... Material to showcase and test several tools and packages releated to ZEN, OAD, ZEN-API. CZI image files and python packages related to those topics - sebi06/ZEN_Python_CZI_Smart_Microscopy_Workshop

Getting ready for the Smart Microscopy Workshop at the EPFL in Lausanne. Cannot wait to get started ... 😀

www.zeiss.ch/mikroskopie/...

The code for the ZEN API & Python related topics can be found here:

github.com/sebi06/ZEN_P...

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You need to add our ZEN API interface to that site?

github.com/zeiss-micros...

Kind off .... but by rahter by showing off out ZEN API at an AiryScan Demo.

Guess what i am just doing ...?

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The first day is open for all (while day 2 and 3 will be hands-on with a limited number of people)

- Learn about concepts and tools available
- AI tools within ZEISS ecosystem
- Guided Acquisition without coding
- ZEN Scripting
- ZEN API - Control ZEN via Python

and more!

Hi Fans of Smart Microscopy,

Are you ready to automate your next large scale microscopy experiment and work smarter, not harder?

Join us for the Smart Microscopy workshop organized by EPFL Bio-Imaging Platform (Lausanne) and @zeiss-microscopy.bsky.social

www.zeiss.ch/mikroskopie/...

I saw this in my vaccation in a cafe in France.
As a person creating AI software tools I hope that is not true but I am not so sure anymore ...

And now the real challenge starts - the data analysis :-)

From #ome-ngff-validator you can open open #OME-Zarr images in a bunch of viewers, and neuroglancer's rendering of multi-channel images just got a lot nicer: ome.github.io/ome-ngff-val... - See github.com/google/neuro...

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Table 1. Below some of the typical terminological disarray is untangled. Importantly, none of these terms are orthogonal nor do they exclusively pick out the types of products we may wish to critique or proscribe.

Protecting the Ecosystem of Human Knowledge: Five Principles

Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...

We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
1/n

Ah OK. Slow means it takes too much time for a single DF3 run?

What exactly is not convincing and should be improved? And did you try the Microscopy Copilot?

ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets Barbiero et al., (2025). ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. Journal of Open Source Software, 10(109), 7882, https://doi.org/10.21105/joss.07882

We’re excited to share that ez_zarr now supports Zarr v3! 🚀 Huge thanks to @mbstadler.bsky.social & @csoneson.bsky.social who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting 📊
📄 joss.theoj.org/papers/10.2110… (1/3)

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Another topic is that Smart Microscopy often requires dedicated (even low level) hardware control. Therefore making all those solutions "interoperable" across imaging system will be really, really, really hard ...

I think one reason for the fragmentation is that it so much fun to create "your own smart microscopy solutions" (I know what I am talking about 😜). This is also the reason why existing commercial solutions are often not used ...

Plus the publishing issue that new is "cooler" than "re-use".

I finally managed to upload the first version of the napari-czitools plugin (still in alpha - expect issues...)

- open complete CZI images or subsets
- read CZI metadata

pypi.org/project/napa...

or

github.com/sebi06/napar...

Available Tools:

- Guided Acquisition incl. AI Segmentation
- Experiment Feedback
- Automated Photomanipulation
- ZEN Internal Scripting Interface
- ZEN API: Control ZEN "from the outside" using Python & more incl. direct access to Pixel Stream

Maybe they should be mentioned there as well 😜?

As you might know I am big fan of smart microscopy because I worked on that topic in academia and also in several industry position (still do).

Therefore I have to point out that @zeiss-microscopy.bsky.social offers several tools that are not mentioned as "Industry Implementations".

Are the slides available?