I just got our new stickers from our COP Python at Zeiss (@zeiss-microscopy.bsky.social is of course part of It).

Cool, isn't it :-)

Amazing to see you go all in.

Since @napari.org just released 0.7.0 I also checked if my to little plugins still work and released new versions with some small updates.

pypi.org/project/napa...

pypi.org/project/napa...

Friday fun with:

pyapp-kit.github.io/ndv/latest/

pymmcore-plus.github.io/ome-writers/

github.com/zeiss-micros...

- run an acquisition in ZEN
- capture the pixel stream via ZEN API
- write it directly to an OME-ZARR using ome-writers
- display it in the NDV viewer.

Also works with @napari.org 😉

Hi all fans of #smart #microscopy,

we from @zeiss-microscopy.bsky.social have just published a new application note: "Study Mitotic Progression with Guided Acquisition – Rare Event Detection"

go2.zeiss.com/ODk2LVhNUy03...

For more details: forum.image.sc/t/applicatio...

Any slides available already?

I tried out my updated image readers for CZI files with the new (at least for me) NDV viewer: github.com/pyapp-kit/ndv and I am really impressed.
This several GBs multi-dimension stack open super quickly (dask lazy arrays) and navigation works nicely.

Congratulations and all the best for you!

Cool. What is the major advantage over pyapp-kit.github.io/magicgui/ ?

Congrats! This is really cool.

Amazing and super, super important!

Wow!

I really hate it when scientists keep saying that “we need to rebuild trust in science,” because it implies that scientists are to blame for the mistrust rather than the millions of dollars of dark money that have funded political attacks on science in order to advance a far right agenda.

I am still digesting all the info from the OME-NGFF hackathon last week.

So I decided to make a little UI for some of the code created there (just to play around), which one can easily show to interested colleagues 😜.

CZI --> OME-ZARR with some options ...

By far not perfect but still fun!

ZEISS Microscopy development team of ZEISS Lightfield 4D microscope system

ZEISS Lightfield 4D has been nominated for the prestigious Thuringian Innovation Award! 🎉The jury has made their selections - now it's your turn to decide on the "Audience Award 2025". 👉 Support us with a "thumbs up" : zeiss.ly/innovationspreis2025-voting
Voting is open until Nov 21, 2025. ⌛

Vote for this really cool system (totally biased opinion) :-)

It was an amazing event and I learned a lot which will help me to drive our discussions about OME-ZARR at @zeiss-microscopy.bsky.social

Thanks for having me there.

Hi @nkiaru.bsky.social ping me :-)

Hi Fans of Feedback Microscopy,

what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?

Btw, it works as well in Fiji&ImageJ :-)

Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.

I honestly think that a clear and smart regulation of AI can be a strong competive advantage for Europe.

Unregulated AI in contrast might destroy the world we know and love ...

I count on you @florianjug.bsky.social

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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