iiinova — where your digital self keeps evolving

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Simon Cleary @simoncleary.bsky.social · 9h

Nikon: '"At this time, we don't see that any rules were violated," it said in a statement.' www.bbc.co.uk/news/article...

bbc.co.uk

Tiny image sparks big backlash in Nikon photo contest

Dr Ning Xu denies he broke the rules of Nikon's annual Small World In Motion contest.

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Sebi @sebi06.bsky.social · 30/09/2026

Hi all, prototype of a napari-zenapi-streaming plugin is working using @zeiss-microscopy.bsky.social and @napari.org. - stream pixels from ZEN into multi-dim array and display live - stream pixels from ZEN directly into OME-ZARR (see video) For viewing I used: find-nuclei.github.io

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Sebi @sebi06.bsky.social · 22/09/2026

I just learned something new at the Lab of the Future Meeting. Beyond FAIR data there is now CLEAR data. - Contextualized - Lineaged - Evaluated - Accountable - Regulated "FAIR gets the data to the machine, CLEAR let's the machine act on it." I must say I agree.

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jmutterer.bsky.social @jmutterer.bsky.social · 28/08/2026

I've made a video about Fig_Space, the next version of FigureJ. It has nice new features, I hope you like it. youtu.be/bTKcXN4p-JM

youtu.be

FigSpace Fiji plugin demo

YouTube video by jerome mutterer

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Sebi @sebi06.bsky.social · 25/08/2026

I extended the pypi.org/project/czit... package with a little extra tool that allows to quickly inspect all the well & HCS data from a CZI file. Very useful as a pre-flight check for further processing or when converting to on #OME-ZARR with HCS layout.

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Sebi @sebi06.bsky.social · 24/08/2026

Hi all, I updated pypi.org/project/czit... (0.21.0) and pypi.org/project/napa... (0.12.1) again. Now in @napari.org also opening large CZI files should work much better when using the plugin. The image shown in the video is about 100 GB on disk.

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Sebi @sebi06.bsky.social · 19/08/2026

ZEISS arivis Cloud preprint is now available on bioRxiv! We are excited to share that our manuscript preprint on ZEISS arivis Cloud is now available on bioRxiv. www.biorxiv.org/content/10.6... Kudos to my colleagues for this.

Annotation interface in ZEISS arivis Cloud showing partial annotations for mitochondria (yellow) and background (purple) classes on a FIB-SEM slice of a HeLa cell. Partial annotations allow users to label only the most informative regions rather than every pixel in the training image. Sample courtesy of Anna Steyer and Yannick Schwab, EMBL.

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Sebi @sebi06.bsky.social · 02/08/2026

czitools 0.20.1 is out! 🎉 Improved CZI/HCS → OME-Zarr export, lazy Dask reading, lighter imports, better napari notebook support, and NDV visualization. Github: github.com/sebi06/czito... PyPi: pypi.org/project/czit...

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#DerApotheker 🥷 @derapotheker.bsky.social · 11/07/2026

Es spielt keine Rolle, wie beliebt die Homöopathie ist, ob sie erstattet wird oder nicht, SIE HAT KEINE WIRKUNG, DIE ÜBER DEN PLACEBOEFFEKT HINAUSGEHT. Heute nicht, morgen nicht und übermorgen auch nicht. Das wird sich auch niemals ändern. Niemals. #DerApotheker 🥷

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Danielle Beckman @daniellebeckman.bsky.social · 20/05/2026

Beautiful work published by my new Lab at @nature.com today! @dorie00.bsky.social et al. created MouseMapper, an AI-powered tool that identifies & maps cells/tissues throughout the whole mouse body. We can now use this for different diseases, such as #LongCovid. This is AI being used the right way!

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Sebi @sebi06.bsky.social · 14/04/2026

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 :-)

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Sebi @sebi06.bsky.social · 29/03/2026

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...

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Sebi @sebi06.bsky.social · 27/03/2026

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 😉

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Sebi @sebi06.bsky.social · 19/03/2026

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...

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Sebi @sebi06.bsky.social · 12/03/2026

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.

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Dr. Lucky Tran @luckytran.com · 19/11/2025

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.

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Sebi @sebi06.bsky.social · 19/11/2025

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!

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ZEISS Microscopy @zeiss-microscopy.bsky.social · 19/11/2025

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. ⌛

ZEISS Microscopy development team of ZEISS Lightfield 4D microscope system

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Sebi @sebi06.bsky.social · 07/11/2025

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.

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Sebi @sebi06.bsky.social · 23/10/2025

Finally - the latest release of our pylibCZIrw supports also MacOS. Check: pypi.org/project/pyli...

pypi.org

Client Challenge

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Nicolas Chiaruttini @nkiaru.bsky.social · 17/10/2025

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

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Lordil-Microscopie @lordil-microscopie.bsky.social · 14/10/2025

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

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Sebi @sebi06.bsky.social · 07/10/2025

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...

weact.campact.de

Chatkontrolle stoppen!

Die EU-Kommission will Messenger-Dienste wie WhatsApp und Signal zwingen, alle privaten Nachrichten und Fotos in Echtzeit zu scannen. Angeblich zum Kinderschutz. In Wahrheit bedeutet die Chatkontrolle...

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Sebi @sebi06.bsky.social · 01/10/2025

Guess what i am just doing ...?

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Julia Sero @cellmorphosero.bsky.social · 27/09/2025

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.

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Sebi @sebi06.bsky.social · 26/09/2025

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/...

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Sebi @sebi06.bsky.social · 16/09/2025

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 ...

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will-j-moore.bsky.social @will-j-moore.bsky.social · 08/09/2025

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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Olivia Guest · Ολίβια Γκεστ @olivia.science · 06/09/2025

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

Abstract: Under the banner of progress, products have been uncritically adopted or
even imposed on users — in past centuries with tobacco and combustion engines, and in
the 21st with social media. For these collective blunders, we now regret our involvement or
apathy as scientists, and society struggles to put the genie back in the bottle. Currently, we
are similarly entangled with artificial intelligence (AI) technology. For example, software updates are rolled out seamlessly and non-consensually, Microsoft Office is bundled with chatbots, and we, our students, and our employers have had no say, as it is not
considered a valid position to reject AI technologies in our teaching and research. This
is why in June 2025, we co-authored an Open Letter calling on our employers to reverse
and rethink their stance on uncritically adopting AI technologies. In this position piece,
we expound on why universities must take their role seriously toa) counter the technology
industry’s marketing, hype, and harm; and to b) safeguard higher education, critical
thinking, expertise, academic freedom, and scientific integrity. We include pointers to
relevant work to further inform our colleagues.

Figure 1. A cartoon set theoretic view on various terms (see Table 1) used when discussing the superset AI
(black outline, hatched background): LLMs are in orange; ANNs are in magenta; generative models are
in blue; and finally, chatbots are in green. Where these intersect, the colours reflect that, e.g. generative adversarial network (GAN) and Boltzmann machine (BM) models are in the purple subset because they are
both generative and ANNs. In the case of proprietary closed source models, e.g. OpenAI’s ChatGPT and
Apple’s Siri, we cannot verify their implementation and so academics can only make educated guesses (cf.
Dingemanse 2025). Undefined terms used above: BERT (Devlin et al. 2019); AlexNet (Krizhevsky et al.
2017); A.L.I.C.E. (Wallace 2009); ELIZA (Weizenbaum 1966); Jabberwacky (Twist 2003); linear discriminant analysis (LDA); quadratic discriminant analysis (QDA).

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

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Silvia Barbiero @silviabarbiero.bsky.social · 15/08/2025

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)

joss.theoj.org

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

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Deutsche Umwelthilfe @umwelthilfe.bsky.social · 22/08/2025

#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...

duh.de

Deutsche Umwelthilfe belegt: HVO100 aus Altspeiseöl klimaschädlicher als fossiler Diesel

• Neue Studie im Auftrag der DUH: HVO100 und „Bio“-Diesel aus Altspeiseöl in der Gesamtbetrachtung von der Produktion bis zum Verbrauch noch klimaschädlicher als fossiler Diesel• Versprechen von fast ...

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Sebi @sebi06.bsky.social · 20/08/2025

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...

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Olivia Guest · Ολίβια Γκεστ @olivia.science · 01/08/2025

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

openletter.earth

Open Letter: Stop the Uncritical Adoption of AI Technologies in Academia

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paveltomancak.bsky.social @paveltomancak.bsky.social · 02/08/2025

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

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Sebi @sebi06.bsky.social · 30/07/2025

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 ...

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Denis Wirtz @deniswirtz.bsky.social · 07/06/2025

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...

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Sebi @sebi06.bsky.social · 30/05/2025

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

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Sebi @sebi06.bsky.social · 28/05/2025

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

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Sebi @sebi06.bsky.social · 28/05/2025

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

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Sebi @sebi06.bsky.social · 26/05/2025

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 :-)

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