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...

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.

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 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. ⌛

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.

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

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...

Bald könnten ALLE Chat-Nachrichten von den Behörden durchsucht werden – selbst ohne Verdacht! Das entscheiden *heute* die Minister*innen. Sag Nein zur Chatkontrolle! Jetzt unterzeichnen ✍️ weact.campact.de/petitions/ch...

Guess what i am just doing ...?

Americans: tell your friends who are worried about Tylenol that there's a safe alternative available in the UK. For a modest fee, I will send them Paracetamol, which is NHS-approved for pregnancy and for children. You can even get it combined with decongestant to make a tasty hot lemon drink.

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 ...

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...

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

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)

#HVO100 und "Bio"-Diesel aus Altspeiseöl ist klimaschädlicher als fossiler Diesel – das ergibt unsere neue Studie. Besonders relevant sind dabei Klimaschäden durch Verlagerungseffekte in der Palmölproduktion. www.duh.de/presse/press...

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...

I don't want it near me and I'm in an AI department FWIW. openletter.earth/open-letter-...

Important letter making an analogy between AI companies and tobacco & petroleum industries.

The 1st working version of my little @napari.org plugin (napari-czitools) is almost ready. It contains sample data, allows to read CZI metadata and can read CZI images (or parts of it) by using the sliders to crop what should be read. Still quite some things to improve ...

Segment any MRI, CTscan, histology, transcriptomic image using CODA using Prof. Kiemen's CODAvision. CODAvision enhances the usability of the CODA algorithm to automatically generating quantitative results and comprehensive reports. More here: www.biorxiv.org/content/10.1...

Amazing 👇

The OME ZARR Team seems to look for developers forum.image.sc/t/more-softw...

100% agree, even if my daily job is being an software architect for AI solutions.

It was a pleasure to be there and see what AI4Life achieved.

Live from the @ai4life.bsky.social community meeting - the new ZEN Microscopy Copilot from @zeiss-microscopy.bsky.social "knows" about BioImageIO :-)

We now published the 1st version of our ZEN API examples from @zeiss-microscopy.bsky.social on our Github page: github.com/zeiss-micros... Control ZEN system from the outside using python (or any other language). Or stream the incoming pixel directly into a an array of online processing :-)

Looking forward to the AI4Life community event in Helsinki. ai4life.eurobioimaging.eu/event/ai4lif...

For all fans of smart, data-driven microscopy: - Guided Acquisition running on a Celldiscoverer 7 - overnight experiment (fully automated) - mitotic events detected in overview image (over time) - 300 3D stacks were acquired using high-resolution water immersion

At @zeiss-microscopy.bsky.social we are offering tools for smart, data-driven microscopy since many years. It started with Experiment Feedback and today we have the Guided Acquistion Module, with allows to automatically detect "rare events" using all kinds of image anylssis tools.

For fun I tried to install @python.org and @napari.org and @pycharm.dev on a chromebook to see if my experimental plugin to view CZI file incl. metadata also would run ... ... and it works :-)

So very true! ✅

Recording from today's live MicroMinute Youtube demo of the ZEISS Microcopy Axioscan and LSM 900 correlative workflow! #microscopy #imageanalysis #bioimaging #science www.youtube.com/live/Po6CIiR...

Naturally-derived & synthetic versions of a chemical are the same chemical. Ex: formaldehyde, formula CH₂O. TRACE levels in some vaccines, <50 micrograms (µg) per dose. YOUR BODY makes 42,520,000 µg formaldehyde a day. (1.5 oz, 850,000-times more than a vaccine). It’s the SAME formaldehyde. 1/

Big news for AI4Life! Our project is a success story by the European Commission! 🇪🇺 The Directorate-General for Research and Innovation (DG RTD) highlights our mission of making AI-powered bioimage analysis accessible to researchers everywhere 🌍 Read more: ai4life.eurobioimaging.eu/ai4life-high...

It is time for Lightfield microscopy! www.zeiss.com/microscopy/e...

An enormous "𝐭𝐡𝐚𝐧𝐤 𝐲𝐨𝐮" goes to the fantastic #MicroSplit team... covering contributions from hard-core method development, over research software engineering mastery, to lots and lots of dataset generation and fruitful discussions on results and possible ways to improve. Thank you all! ❤️

It is Friday again and here is a video on our new AI-assisted labeling tool (SAM-based) on arivis AI (www.apeer.com) from #zeiss_micro. It makes partial labeling to train your models (semantic or instance) even faster. The 1st cell is still annotated the usual way, the others using the new tool.

Hi all, sometimes on Fridays I find some time to play around with some of our new features from ZEN software from #zeiss_micro. Here a demo of using the PixelStream (via ZEN API) to directly "segment" the acquired images by applying an ONNX model to the pixel stream. Hello Feedback Microscopy 😁!

I finally found some time to play around with @marimo.io notebooks (really cool) and my little python project github.com/sebi06/czito.... Here you can see it in action 😜