Juan Nunez-Iglesias

As good as a time as any to announce: After a great time at @poldresden.bsky.social I'm looking forward to starting my new position at @gerbi-gmb.de as a software developer for @openmicroscopy.org 🔬😀!

Scalable #RDM solutions in the ome-zarr-verse, here we come!

Kushaan! How are you! *Where* are you??? 😂

A huge exaggeration, but I’ll allow it. 😂🥰

How I’d put it: we really do all learn *so much* from each other. ❤️‍🔥

They’re building rainbow cycle tunnels in Norway. With no cars. Nice video by Critical Mass Bergen.

This is so wrong. It is all so wrong. And it gets worse, but I can't even say because I don't know if people impacted want it in public domain. These actions are unjust & have repercussions way beyond the impacts of those immediately involved. It's not a story, it is people's lives

What’s a technology that you think is overhyped? I’m going to give a sideways answer to this, which is that the venture capital business model needs to be understood as requiring hype. You can go back to the Netscape IPO, and that was the proof point that made venture capital the financial lifeblood of the tech industry. Venture capital looks at valuations and growth, not necessarily at profit or revenue. So you don’t actually have to invest in technology that works, or that even makes a profit, you simply have to have a narrative that is compelling enough to float those valuations. So you see this repetitive and exhausting hype cycle as a feature in this industry. A couple of years ago, you would have been asking me about the metaverse, then last year, you would have asked me about Web3 and crypto, and for each of these inflection points there’s an Andreessen Horowitz manifesto. It’s not simply that one piece of technology is overhyped, it’s that hype is a necessary ingredient of the current business ecosystem of the tech industry. We should examine how often the financial incentive for hype is rewarded without any real social returns, without any meaningful progress in technology, without these tools and services and worlds ever actually manifesting. That’s key to understanding the growing chasm between the narrative of techno-optimists and the reality of our tech-encumbered world.

Stand by this: www.politico.com/newsletters/...

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a few things I learned from this thread:

- https://endof10.org/places/ has a list of a lot of Linux cafes etc in Europe
- some cities in North America have a FreeGeek organization
- https://tinker.sh/ is a Linux distro that's just for distraction-free writing

(3/?)

GitHub - live-image-tracking-tools/geff: Reference implementation of the Graph Exchange File Format Reference implementation of the Graph Exchange File Format - live-image-tracking-tools/geff

There will be so many good things spanning from these efforts, short term. We worked on a universal file format for tracking data, GEFF github.com/live-image-t...

This will facilitate exchanging data between algorithms and tools, and greatly accelerate and facilitate analysis of timelapse data

Saying goodbye to beautiful @hhmijanelia.bsky.social, after an intense two weeks trackhathon. Organized by legends Caroline Malin-Mayor and Morgan Schwartz in the @janfunkey.bsky.social.

It has been awesome and productive. Thank you!!

I am thrilled to share that our dartR team is a finalist in the prestigious 2025 Australian Museum @eurekaprizes.bsky.social, in the Excellence in Research #Software category!!! 🤓💻🧬

30 sec video ⬇️; more details in the link in comments

Congrats to fellow finalists! How good is it to have software work recognised??? 😭😭😭🙏🙏🙏

Hey I just saw you’re at Monash! We should hang out! 😃 Feel free to send me an email. 📧 (Also feel free to ignore me! LOL)

*global collaborations with a significant Australian component. 😅 It's always after you send that you want to edit it, no matter how long you took to write it. 😂 bsky urgently needs an edit button!

Again, a not-so-small thread cannot do justice to the monumental effort and spirit of collaboration of so many people to get to this point (and still so much work to do!), and I apologise if you read this thread and feel left out — please reach out and let me know! More writing to come…

Even deeper history: napari predates my CZI fellowship (which was for scikit-image) (thanks to @mentat.za.net for his mentorship!) and I also owe the last 8 years of my career to Ian Harper at Monash Micro Imaging who took a chance on me and gave me freedom and support to work on FOSS. 🙏🙏🙏

I also want to thank @cziscience.bsky.social which has funded me over the past ~7 years, and is funding the napari community through a new 4 year grant (more soon!), @numfocus.bsky.social, the fiscal home of @napari.org, and all @scientific-python.org for the environment in which napari has thrived.

Community There are several different ways to be a part of the napari community. From being a code or documentation contributor, to creating educational content or examples, you are welcome to help develop and ...

(Draga, Wouter-Michiel, and I think (?) also @czaki-pl.bsky.social are still currently finishing their PhD! 😅)

I point this out because you 🫵 can also contribute! Check out our community page to find out how:

napari.org/stable/commu...

and join our Zulip chat and open community meetings.

Little known fact: most of the team were/are *not* professional software developers, but PhD students, postdocs, and even faculty improving napari for their own use. CC @alisterburt.bsky.social @czaki-pl.bsky.social @psobolewskiphd.bsky.social @kevinyamauchi.bsky.social @timmonko.bsky.social

Screenshot of a napari core team meeting on Zoom, including Grzegorz Bokota, Juan Nunez-Iglesias, Wouter-Michiel Vierdag, Tim Monko, Peter Sobolewski, Draga Doncila Pop, Melissa Weber Mendonça, Kevin Yamauchi, Lorenzo Gaifas, Carol Willing, Kyle Harrington, and Ashley Anderson.

World map with pictures of past (black and white) and present core team member photos overlaid. Includes: Kira Evans, Nick Sofroniew (emeritus), Kyle Harrington, Alister Burt (emeritus), Loïc Royer (emeritus), Carol Willing, Tim Monko, Andy Sweet (emeritus), Talley Lambert (emeritus), Peter Sobolewski, Ashley "I am not, in fact, a cactus" Anderson, Melissa Weber Mendonça, Kevin Yamauchi, Lorenzo Gaifas, Wouter-Michiel Wierdag, Grzegorz Bokota, Juan Nunez-Iglesias, Genevieve Buckley, Draga Doncila Pop, and Lucy Liu (emeritus).

And when I wrote that post, there were 15 contributors to napari — we're now at 180+ and counting! I can't thank you all individually 😅 but I want to shout out to the core team past and present.

napari.org/stable/commu...

When I wrote that post, napari didn't have a plugin system. We now have 500+ plugins, thanks to the plugin systems created by @talley.codes. 🙏! And that's only one of many, many improvements from Talley, including magicgui, evented models, and app-model, which he's spun out into pyapp-kit.github.io.

Longer term, it's been almost 6y since I wrote my blog post announcing napari to the world* and… I've basically written nothing of substance since. 😅 I'm long overdue for another post, but in the meantime this thread will have to do!

*: ilovesymposia.com/2019/10/24/i...

I also need to thank @ardc.edu.au in general and Paula Martinez specifically for recognising the importance of research software to science. 🙏 And this year specifically for updating the eligibility requirements to include global collaborations! Which is exactly what @napari.org is!

Most proximally, thanks to Dave Mellert (from @jacksonlab.bsky.social), @trackingactions.bsky.social, @cppape.bsky.social, and Junel Solis (from @turkubioimaging.bsky.social) for writing references for our submission that brought tears to my eyes. Thank your maintainers, they will appreciate it! 🥹🥰

It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇

Oh WHAT! That’s awesome. Very clever to offset t along z. 🤩

There’s probably some cool viz theory to be done to work out the optimal offset direction for a given dataset and view direction… 🧠⚙️⚙️

Renfe publica los informes de puntualidad de sus servicios Los datos mensuales de puntualidad pueden descargarse en el apartado de “Gobierno corporativo y transparencia” de Renfe.com.

Se habla mucho de la puntualidad de Renfe y hemos decidido dar el paso de publicar los datos con total transparencia.

www.renfe.com/es/es/grupo...

YouTube video by Brian Northan Pixi and Napari-Easy-augment-Batch-DL

I just published a new video demonstrating how to use Pixi and Napari-Easy-Augment-Batch-DL for repeatable and reproducible deep learning segmentation. In this example, I use Pixi to set up a Python environment then launch Napari to explore and compare Cellpose3 and Micro-SAM. youtu.be/3ObAnSTBri8

Cell tracking is never perfect, and it's important to understand the types of errors your solution contains.

Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...

You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.

I'm not sure if this is an attempt at political messaging for an audience of policymakers who need everything framed in terms of competitive advantage or national win/loss (if so, why is it in The Transmitter?). But I think it is wrong and, frankly, a bit ugly.

A three-dimensional view of the Kocher lab’s bumblebee brain atlas visualised with brainrender-napari.

The brain atlas of the bumblebee Bombus impatiens created by the @kocherlab.bsky.social is now part of BrainGlobe!

This is our first insect brain atlas. Thanks to Scott Wolf for adding it!

More details: brainglobe.info/blog/bee-atl...

Original paper: doi.org/10.1016/j.cu...

first data from the new LLSM in PertzLab @olivierpertz.bsky.social! i always thought nuclei were spherical but they are pancakes???? so much more to see in 3d, but data volume produced is insane, we will have to rethink our analysis pipelines. tips welcome! here shown in @napari.org