Niko Sirmpilatze
London-based neuroscientist 🧠 & research software engineer 💻 developing free and open-source tools for studying brains & behaviour, @neuroinformatics.dev @sainsburywellcome.bsky.social at UCL.
Committed to open, collaborative, and reproducible science.
- Reposted by Niko SirmpilatzeNew 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...
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- 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.
- Reposted by Niko SirmpilatzeThe 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...
- Reposted by Niko Sirmpilatzemain 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
- Reposted by Niko SirmpilatzeBig 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...
- Reposted by Niko SirmpilatzeThe field of #neuromorphics is lacking *accessible*, *intuitive*, and *practical* introductions. Ramashish Gaurav, Petruț Antoniu Bogdan, and I are setting out to fix this with a book on Practical Spiking Neural Networks! ✅ Any and all contributions are welcome! 💕 Early access at: snnbook.net
- A quick reminder to apply to this summer school by end of January 👀 It will be a fun mix of hands-on training and collaborative open-source hacking for #neuroskyence and #animalbehaviour I'll be leading the "Animals in Motion" track!
- Three weeks left to apply for the Neuroinformatics Unit Open Software Summer School, August 17-28 2026 in London, UK! Bringing together researchers and open source developers of ephys, behaviour and image analysis tools. neuroinformatics.dev/open-softwar... Deadline January 31st. Apply now!
- Reposted by Niko SirmpilatzeNEW article by me! We can now visualize pathogens down to atoms; design vaccines in weeks; manufacture them in microbial factories; engineer them more precise than ever before. We're living through a golden age of vaccine development, but only if we continue to invest in them.
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- Reposted by Niko Sirmpilatzeyou’re right! it feels mostly awful to Go Online™, these days. the internet in a sad state, for reason after reason after reason. but there is a way to fix it; to trade the voidful howling for a quiet & joyful song. here’s how to win the war for the soul of the internet, and build the Web We Want.
- Reposted by Niko SirmpilatzeGreat to see this workflow. Just my style! Not only is it great to see somebody so confident and comfortable in their editor, but also to explain what's going on so eloquently. Essential viewing! youtu.be/qjWkNZ0SXfo
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- Reposted by Niko SirmpilatzeDo you love quantifying animal behavior as much as we do? We have just the tool for you! Presenting #OCTRON - a pipeline that helps you create rich annotation data and enables training of custom segmentation models. Have a look, particularly if you work with non-model / invertebrate organisms!
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- Reposted by Niko SirmpilatzeToday, the NeurIPS Foundation is proud to announce a $500,000 donation to OpenReview, supporting the infrastructure that makes modern ML research possible. blog.neurips.cc/2025/12/15/s...
- Reposted by Niko SirmpilatzeIf you have to read anything about the prospect of “automating scientific discovery,” “agents for science,” or integrating LLMs into scientific pipelines, please let it be this essay by Kevin T. Baker: artificialbureaucracy.substack.com/p/context-wi...
- This article makes some excellent points, including this one: "Action segmentation ... appears to be a straightforward technical procedure. However, it is a crucial site of scientific judgment where philosophical assumptions about the nature of behavior become embedded in code."
- Reposted by Niko SirmpilatzePleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking. It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems. Preprint: www.biorxiv.org/content/10.6... [1/6]
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Thrilled to start 2026 as faculty in Psych & CS @ualberta.bsky.social + Amii.ca Fellow! 🥳 Recruiting students to develop theories of cognition in natural & artificial systems 🤖💭🧠. Find me at #NeurIPS2025 workshops (speaking coginterp.github.io/neurips2025 & organising @dataonbrainmind.bsky.social) - Reposted by Niko Sirmpilatze🧠📢 New preprint alert Large-scale ephys is exploding but spike sorting remains the computational bottleneck. A 2-hr, 6-probe Neuropixels 2.0 Quad Base session can take over a week to sort on a single machine. Here's a better solution. 🧵 #neuroskyence #compneurosky
- I'll be coordinating the "Animals in Motion" track of this summer school, in August 2026. Apply to join us for some hands-on learning and collaboration on open-source tools for video behavioural analysis. See neuroinformatics.dev/open-softwar...
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- Great track visualisation tool by @teunhuijben.bsky.social and colleagues. Over lunch we discovered that inTRACKtive can handle herds of zebras almost as well as groups of migrating cells.
- Once the tracking is done, visualise in inTRACKtive github.com/royerlab/inT... #CBIAS2025
- Had such a blast at #CBIAS2025 — a meeting full of image-analysis nerds (what more could you want?). If you’d like to learn more about movement, the Python package I presented, my slides are live at neuroinformatics.dev/slides-movem...
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- Reposted by Niko SirmpilatzeThe challenges Neurodata Without Borders faces reflect a broader need for funding that sustains new research tools once they are established. By Lauren Schneider #neuroskyence www.thetransmitter.org/community/ne...
- Reposted by Niko SirmpilatzeAxonal pathfinding of zebrafish retinal ganglion cells forms the optic nerve. Credit to Dr. Matthew Bostock @houartlab.bsky.social. #ZebrafishZunday 🧪
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- Join us tomorrow at the @biig-ucl.bsky.social monthly hybrid seminar, to hear @leaveylab.bsky.social speak on: "From chameleons to sea urchins: Using AI-driven digital dissection tools to study development and evolution".
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- Reposted by Niko SirmpilatzeOur lab is looking for a postdoc! We have interesting projects and cutting-edge techniques such as Neuropixels Opto, Light Beads Microscopy and more. We would be delighted to receive your application. Deadline is 25 November 2025. More info here: www.ucl.ac.uk/cortexlab/po...
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- Reposted by Niko SirmpilatzeDo you use Bonsai and Harp for behaviour acquisition? How easy has it been to interface the outputs with your analysis pipeline? We’re building a high-level Python interface to streamline Bonsai/Harp integration and align data streams. Nearly there, we’d love your input! See thread ⬇️ #neuroskyence
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- Reposted by Niko SirmpilatzeNew preprint from the lab: A reference brain for the clonal raider ant. With this resource, which is based on 40 individual brains, you can register and compare all kinds of samples in a common space. It comes with lots of detailed protocols and a user-friendly GUI. www.biorxiv.org/content/10.1...
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- Reposted by Niko SirmpilatzeIn 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 SirmpilatzeAnd 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...
- 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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- 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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- Reposted by Niko SirmpilatzeCourtney @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 !
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- 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.
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- Reposted by Niko Sirmpilatze🟢 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...
- 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...
- Reposted by Niko SirmpilatzeIn 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.
- As part of this event, I will be running a 2-day hand-on workshop, for folks that want to use open-source software to study "Animals in Motion". Thanks to the generous support of @softwaresaved.bsky.social & @sainsburywellcome.bsky.social More info at neuroinformatics.dev/open-software-week
- Reposted by Niko SirmpilatzeExcited to share our new pre-print on bioRxiv, in which we reveal that feedback-driven motor corrections are encoded in small, previously missed neural signals.
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