Niko Sirmpilatze

Screenshots from the new "Scale pose tracks to real-world units" showing the measurement of known lengths in a video.

Version 0.15.0 of movement released!

New features include:

- Derivation of bounding boxes from pose tracks
- Saving and loading of RoIs via GeoJSON
- A new example for scaling pose tracks to real-world coordinates

Release notes: github.com/neuroinforma...

Docs: movement.neuroinformatics.dev

BIG UPDATES!
OCTRON now supports the new SAM3 models (alongside SAM2)!
We’ve also added a global switch for Detection vs. Segmentation: Use the same annotations to train either lightweight detection or full segmentation models. Plus, we’ve added support for the new YOLO26 models. ⤵️
1/12

Come work with us, it's fun! #neuroskyence

Drawing of the "Aeon" project, an open-source platform to study the neural basis of ethological behaviours over naturalistic timescales.

Are you a neuroscientist with great coding skills, or a software engineer interested in the brain?

We are recruiting for a research software engineer to help us build pipelines to process weeks of neural and behavioural recordings from freely moving animals.

More details: bit.ly/rse-2026a

🚀 New workshop before FENS in Barcelona!
Join the Flatiron Institute Center for Computational Neuroscience of the Simons Foundation for a hands-on workshop on pynapple & NeMoS.
Learn to analyze and model neural data with open-source tools.
Accommodation & meals included.
Details ⬇️

The screenshot of the release notes reads: A new version of TeX Live Utility is available! TeX Live Utility 1.55 is now available-you have 1.54. Would you like to download it now? Release Notes: Changes Since 1.54 • Fix bug 137, homepage link in Help Book. • First release in a long time, since I don't use TeX anymore and resent the very idea of paying Apple annually for the privilege of giving away free and open-source software. Also, I'm really lazy. Please accept my apologies for all the annoying issues you've encountered in this mission-critical software. • Updated mirror list, which was three years out of date. • Added missing legacy mirrors, which was even more out of date. • Added an alert on startup when user tries Homebrew's lobotomized MacTex, because those lunatics left timgr but removed its database. Thanks for nothing, guys. Bug 142 and 144. • Use a custom user-agent to work around the Anubis bot trap on texlive.info. Can't wait to see what else breaks because of this, thanks to the profusion of degenerate Artificial Insemination fetishists scraping websites to feed their models. • Lists of countries in Repository/Continent are now sorted. No idea how you people let me get away with that one for the last fifteen years.

There's a "is anyone even reading this" sort of honesty you get in the software update release notes from a project that's been around for a long time.

Triple paper drop from the inimitable @willydorrell.bsky.social :

1) A normative theory of prefrontal working memory slots.

2) A comprehensive review of normative theories of why grid cells look like grid cells.

3) A new theory of convex efficient coding.

(0/3)

Using BORIS to annotate animal behaviour and want a model to automate it? 🐦

DL classifiers need short, focused clips — not hour-long recordings. 𝗯𝗼𝗿𝗶𝘀-𝗰𝗹𝗶𝗽 extracts those from your `.boris` files, ready for BehaveAI, Octron, and friends. 🤖

roald-arboel.com/boris-clip/

#ComputationalEthology

"You see what you look for, and you look for what you know."

We are proud to release FOCUS: a 100 μm deformable human subcortical atlas precisely registered to MNI space.

www.biorxiv.org/content/10.6...

Want to spend this summer improving open-source tools for neuroscience 🧠📈 and animal behaviour 🐭🐒? Apply to work with us on BrainGlobe, movement and others.

We particularly welcome researchers who want to sharpen their software dev skills and contribute to the open-source ecosystem.

GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile

Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package:

- fully bootstrapped Java setup (just pip install)
- lazy, repeatably-indexable Array object
- fully spec-compliant OME-Zarr group obj.
- xarray/dask exports

github.com/imaging-form...
v0.0.rc1 on PyPI

👀

A precise atlas of the human subcortex | bioRxiv www.biorxiv.org/content/10.6...

[PERF] Replace np.column_stack with np.vstack().T by crabby-rathbun · Pull Request #31132 · matplotlib/matplotlib This PR addresses issue #31130 by replacing specific safe occurrences of np.column_stack with np.vstack().T for better performance. IMPORTANT: This is a more targeted fix than originally proposed. ...

holy shit

PR from an ‘agent’ gets closed so it writes a blog post with a personal takedown

Some interesting comments from the maintainers too

Slop machine go brr, dead internet theory x1000

github.com/matplotlib/m...

Folding Flow 19 (2021)

#rstats and #ggplot2

Part 3 of my "Trusted by design" blog series is live at neuroinformatics.dev/blog/trusted...

Open-source software is public, yet much of the communication around it may happen in private channels. What if communication were radically open—visible to anyone who cares to look?

FOSDEM 2026 - Trusted by design: set up your research software for community adoption

Part 3 will follow next week.

In the meantime, you can watch the recording of my talk at @fosdem.org and get the gist of the whole blog series:

fosdem.org/2026/schedul...

Part 2 of the "Trusted by design" blog series is out today @neuroinformatics.dev.

'Release early, release often' is an often-repeated mantra, but...

How early? How often? And why is this so critical to establishing and maintaining trust?

See neuroinformatics.dev/blog/trusted...

New blogpost outlining our work with @athenaakrami.bsky.social at @sainsburywellcome.bsky.social to build light-microscopy based atlases of the rat brain.

brainglobe.info/blog/swc-fem...

*Trusted by design: set up your research software for community adoption*

By Niko Sirmpilatze @nikosirmpilatze.com

fosdem.org/2026/schedul...

Parts 2 and 3 to follow in the next few weeks (will post under this thread).

Part 1 is about finding your software's mission and scope.

Open-source software is a vast web of inter-connected tools. When creating a new tool, your first job is to carve out its place in the web openly and from the outset. How can you approach that?

See neuroinformatics.dev/blog/trusted...

While prepping the talk, I realised there was much to say on this topic, so I've also prepared a 3-part blog post series.

You can find the overview here: neuroinformatics.dev/blog/trusted...

In this 2nd talk, I'll distil lessons learnt through my transition from academic research to research software engineering with @neuroinformatics.dev

Tune in if you've written code that solves a problem—maybe for your own analysis, maybe for your lab—and hope it can be useful to others.

FOSDEM 2026 - Trusted by design: set up your research software for community adoption

The second talk is on Sunday, in the Open Research devroom @FosdemResearch.

fosdem.org/2026/schedul...

It's titled: "Trusted by design: set up your research software for community adoption".

FOSDEM 2026 - Movement: a Python toolbox for analysing motion tracking data

My first talk is on Saturday, in the Bioinformatics & Computational Biology devroom.

fosdem.org/2026/schedul...

I'm presenting movement, our Python package for analysing animal motion.

FOSDEM 2026 - Niko Sirmpilatze

I'm heading to @fosdem.org this weekend to present 2 research software-related talks.

Come say hi, tune into the livestream, or watch the recordings later. #FOSDEM

fosdem.org/2026/schedul...

I'm also using this as a chance to kick off a short blog post series.

Details in the thread.

Nine subcortical/cerebellar atlases included in the subcortex_visualization Python package (and subcortexVisualizationR package in R). The atlases are depicted in two-dimensional vector graphic format.

The extended version of my thesis procrastination project/subcortex visualization package is out now in both Python and R, now that I’ve graduated 🤠 This figure shows the 9 atlases included (and counting)!

Preprint: www.biorxiv.org/content/10.6...
Website: anniegbryant.github.io/subcortex_vi...

Read the story behind the first @neuroinformatics.dev Open Software Week, in a series of blogposts for @softwaresaved.bsky.social

The second edition will be even more awesome. Remember to apply by the end of January:

neuroinformatics.dev/open-softwar...

main goal for this year: find a new job! 🙂

looking for a role with fun & complex technical challenges & within a great community. my main expertise is in signal processing/EEG/MEG, but topic-wise I am quite flexible.

science/industry both great! starting mid-year. nschawor.github.io/cv

Scientific Workflows Developer The European Molecular Biology Laboratory (EMBL) is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service teams covering the ...

Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...