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Reposted by Niko Sirmpilatze

Marco Dalla Vecchia @marcodv.bsky.social · 23h

New blog post!

Last year, I wrote some data visualization tips and pitfalls for a workshop, and I now ported it over to a @quarto.org manuscript with references and source code for the figures.

Check it out here!
marcodallavecchia.gitlab.io/web/blog/dos...

Dos and Don’ts of data visualization – marcodallavecchia/web

A few sample cases to understand the importance of proper data visualization

marcodallavecchia.gitlab.io

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BrainGlobe @brainglobe.info · 20h

BrainGlobe branches out!

New blog outlining our collaborative work with @giuliapaci.bsky.social from @lmcb-ucl.bsky.social to build anatomical atlases for developmental mechanobiology.

brainglobe.info/blog/drosoph...

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BrainGlobe @brainglobe.info · 1d

We are incredibly proud to receieve this award, especially as it recognises the hard work of the entire BrainGlobe community.

Thank you to everyone who has contributed to BrainGlobe over the years!

Le Neuro (Institut-Hôpital neurologique de Montréal) @theneuro.bsky.social · 2d

🏆Announcing the laureates of the Neuro - Irv and Helga Cooper Foundation Open Science Prizes 2025!

🎉 Join us in celebrating the laureates at the award ceremony, featuring a special lecture from International Prize laureate representative from the BrainGlobe initiative.

#OpenScience #Neuroscience

The Neuro – Irv and Helga Cooper Foundation Open Science Prizes: Meet the winners of an exceptional edition

This year’s edition of the Irv and Helga Cooper Foundation Open Science Prizes at The Neuro, organised by the Tanenbaum Open Science Institute, was exceptional in every way. With a record number of ap...

www.mcgill.ca

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Simon Willison @simonwillison.net · 2d

I figured out a uv recipe for running tests for any project with pyproject.toml or setuppy using any Python version:

uv run --python 3.14 --isolated --with-editable '.[test]' pytest

I've wrapped it in a uv-test script:

uv-test -p 3.11

Full details here: til.simonwillison.net/python/uv-te...

setup.py

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Niko Sirmpilatze @nikosirmpilatze.com · 4d

This is cool! I didn’t know you could use Marimo together with Quarto like that!

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Saloni @scientificdiscovery.dev · 12d

In general I think it's hard to combat scientific misinformation when some of the best research is locked behind an academic paywall, while lots of nonsense gets published free for everyone to read in predatory journals.

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Reposted by Niko Sirmpilatze

Sainsbury Wellcome Centre @sainsburywellcome.bsky.social · 11d

At SWC, we’re not afraid to ask bold questions. We’re striving to understand how the brain gives rise to behaviour.

Join us for your PhD!

🧠 World-class training in systems neuroscience
💰 Fully-funded 4-year programme

Apply by 3 Nov ⬇️

www.sainsburywellcome.org/web/content/...

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Ann Kennedy @antihebbiann.bsky.social · 22d

And we are live!

Excited to announce the 2025 Multi-Agent Behavior Challenge on cross-lab supervised action recognition in mice 🐁🐀🖱️

Running on Kaggle until December 15th, with a $50,000 prize pool going to the top five submissions!

www.kaggle.com/competitions...

https://www.kaggle.com/competitions/MABe-mouse-behavior-detection

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Niko Sirmpilatze @nikosirmpilatze.com · 22d

I enjoyed chatting with Peter about my @softwaresaved.bsky.social fellowship. Tune in for the backstory behind animals-in-motion.neuroinformatics.dev
and @neuroinformatics.dev 's "Open Software Week".

PS: Code for Thought is a great podcast to follow if you’re into research software.

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 28d

New guest blog by @marcodv.bsky.social about our open software summer school, held at @sainsburywellcome.bsky.social.

neuroinformatics.dev/blog/perspec...

Stay tuned for information about next years event, which will be bigger and better!

Some of the summer school participants, gathered after the summer school hackday.

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UCL BioImage Interest Group @biig-ucl.bsky.social · Sep 8

BIIG seminars are back! 🎉

12-1pm on 12th September:
- Kaixiang Shuai (LMCB, UCL): Creating the first Drosophila imaginal wing disc atlas
- Aikta Sharma (UCL Mechanical Engineering): Predicting Osteoarthritis in the Tibial Epiphysis with Synchrotron X-ray CT and Digital Volume Correlation

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Niko Sirmpilatze @nikosirmpilatze.com · Aug 18

This would not have been possible without support from @sainsburywellcome.bsky.social @softwaresaved.bsky.social @society-rse.org and @aibio-uk.bsky.social

Software Sustainability Institute (@softwaresaved.bsky.social)

The Software Sustainability Institute is the first organisation in the world that was dedicated to improving software in research.

softwaresaved.bsky.social

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Niko Sirmpilatze @nikosirmpilatze.com · Aug 18

Thanks to our amazingly engaged participants, including @carlocastoldi.bsky.social, @rebeccalowes.bsky.social, @annthomp.bsky.social and many many others.

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Niko Sirmpilatze @nikosirmpilatze.com · Aug 18

Had a blast teaching "Animals in Motion" last week, together with my @neuroinformatics.dev colleagues.

All course materials, including hands-on coding exercises, are freely available as an online book:
🔗 animals-in-motion.neuroinformatics.dev/latest/

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 15

Thank you to everyone who came to Open Software Week. We had a great time, and we hope you all left with new knowledge, ideas or collaborations.

#niu_osw

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Giulia Paci @giuliapaci.bsky.social · Aug 14

Courtney @courtneyl7a7.bsky.social has written a lovely piece on this wonderful community initiative we’ve been running for 5 years at UCL - have a read! And follow @biig-ucl.bsky.social !

FocalPlane @focalplane.bsky.social · Aug 14

📢New post on FocalPlane - Connecting Researchers Through Bioimaging: Reflections from UCL’s BioImage Interest Group

Courtney Lancaster @courtneyl7a7.bsky.social‬ reflects on the success of the BioImage Interest Group at UCL, offering a template for other communities.

Connecting Researchers Through Bioimaging: Reflections from UCL’s BioImage Interest Group - FocalPlane

Connecting Researchers Through Bioimaging: Reflections from UCL’s BioImage Interest Group -

focalplane.biologists.com

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 12

The BrainGlobe track started with an introduction to image analysis with @napari.org, and then tutorials on how to use @brainglobe.info to register data to atlases, and how to detect cells in whole-brain microscopy images.

All our tutorials are online: brainglobe.info/tutorials

#niu_osw

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The Transmitter @thetransmitter.bsky.social · Aug 5

How can birds keep enough control to fly while drifting in and out of sleep? In an excerpt from their new book published today, @evoneuro.bsky.social and Georg Striedter explore this and other questions about neural mechanisms that regulate bird sleep.

bit.ly/45mfwgn

#neuroskyence

‘Bird Brains and Behavior,’ an excerpt

In their new book, published today, Georg Striedter and Andrew Iwaniuk dive deep into the latest research on the neural mechanisms of avian behavior. This excerpt from Chapter 2 explores how birds…

www.thetransmitter.org

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Niko Sirmpilatze @nikosirmpilatze.com · Aug 4

Not quite scientific history, but I’ve really enjoyed reading “The Cathedral and the Bazaar”–a collection of essays about the open-source movement.

www.catb.org/esr/writings...

The Cathedral and the Bazaar

My third book

www.catb.org

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Niko Sirmpilatze @nikosirmpilatze.com · May 19

Still a few weeks to register for some hands-on training and hacking on open-source tools for analysing animal motion, whole-brain microscopy with @brainglobe.info, and big imaging data. 🧠📈

Aug 11-15 at @sainsburywellcome.bsky.social in London.

"Free as in beer" and travel stipends available.

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Apr 16

We're excited to announce the Neuroinformatics Unit Open Source Week, August 11-15 2025 in London, UK.

Bringing together researchers and developers of open-source software for training, community-building and hacking.

No cost and travel stipends available.

neuroinformatics.dev/open-softwar...

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Center for Open Science @cos.io · May 1

🛠️ Calling all open source developers!

COS is looking to fund small dev projects that help improve the Open Science Framework (OSF).

Python, Django, Angular.js devs—this one’s for you.

Proposals due: May 14th, 2025.

🔗 http://cos.io/pose

#DevGrants #OpenSource #OpenScience

Funding for Open-Source Development to Advance OSF Integrations

The Center for Open Science (COS) is seeking proposals for open-source development projects that will improve usability, interoperability, and research workflows on the Open Science Framework (OSF)—a free, open-source platform maintained by COS to support researchers throughout the entire research lifecycle.

cos.io

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Software Sustainability Institute @softwaresaved.bsky.social · Apr 28

🟢 Applications are now open for two SSI Fellows' events: Niko Sirmpilatze's "Animals in Motion" and Alessandro Felder's "Big Imaging Data". These events will take place during the NIU Open Software Week running between Monday 11 and Friday 15 August in London.
www.software.ac.uk/news/ssi-fel...

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Niko Sirmpilatze @nikosirmpilatze.com · Apr 25

Had a blast at #ASABSpring2025, presenting movement and meeting many enthusiastic early career researchers.

If you're into tracking animal movements in videos, do apply for the "Animals in Motion" workshop I'm organising in London this August: neuroinformatics.dev/open-softwar...

A schematic representation of "Movement: a Python Toolbox for Analysing Motion Tracking Data".

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Max-Planck-Gesellschaft @maxplanck.de · Apr 22

In an open letter of support to the President of @harvard.edu, Max Planck President Patrick Cramer @patrick-cramer.maxplanck.de has expressed his full support of the University in its stance against demands by the Trump administration to change its policies in order to retain federal funding.

A photo of Max Planck President Patrick Cramer and the words: "Threats to science anywhere are threat to science everywhere".

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