Niko Sirmpilatze
@nikosirmpilatze.com
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.
Committed to open, collaborative, and reproducible science.
Reposted by Niko Sirmpilatze
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...
brainglobe.info/blog/swc-fem...
February 2, 2026 at 4:59 PM
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...
brainglobe.info/blog/swc-fem...
Reposted by Niko Sirmpilatze
*Trusted by design: set up your research software for community adoption*
By Niko Sirmpilatze @nikosirmpilatze.com
fosdem.org/2026/schedul...
By Niko Sirmpilatze @nikosirmpilatze.com
fosdem.org/2026/schedul...
February 1, 2026 at 1:52 PM
*Trusted by design: set up your research software for community adoption*
By Niko Sirmpilatze @nikosirmpilatze.com
fosdem.org/2026/schedul...
By Niko Sirmpilatze @nikosirmpilatze.com
fosdem.org/2026/schedul...
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.
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.
FOSDEM 2026 - Niko Sirmpilatze
fosdem.org
January 29, 2026 at 1:16 PM
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.
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 Sirmpilatze
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...
Preprint: www.biorxiv.org/content/10.6...
Website: anniegbryant.github.io/subcortex_vi...
January 27, 2026 at 3:04 AM
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...
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...
The second edition will be even more awesome. Remember to apply by the end of January:
neuroinformatics.dev/open-softwar...
January 22, 2026 at 6:25 PM
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...
The second edition will be even more awesome. Remember to apply by the end of January:
neuroinformatics.dev/open-softwar...
Reposted by Niko Sirmpilatze
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
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
January 16, 2026 at 10:14 AM
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
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 Sirmpilatze
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...
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 ...
embl.wd103.myworkdayjobs.com
January 14, 2026 at 9:37 AM
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...
Reposted by Niko Sirmpilatze
The 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
Any and all contributions are welcome! 💕
Early access at: snnbook.net
January 14, 2026 at 10:37 AM
The 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
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!
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!
Bringing together researchers and open source developers of ephys, behaviour and image analysis tools.
neuroinformatics.dev/open-softwar...
Deadline January 31st. Apply now!
January 12, 2026 at 10:06 AM
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!
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!
Reposted by Niko Sirmpilatze
NEW 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.
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.
The golden age of vaccine development - Works in Progress Magazine
The first vaccine was a lucky accident. Now we can design new vaccines in weeks, atom by atom.
worksinprogress.co
January 7, 2026 at 3:20 PM
NEW 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.
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.
Reposted by Niko Sirmpilatze
We've shipped a major update to the JOSS submission scope requirements, affecting what is eligible for submission and what information we require from authors.
You can read more about the changes and our motivations here: blog.joss.theoj.org/2026/01/prep... #joss #opensource #openscience
You can read more about the changes and our motivations here: blog.joss.theoj.org/2026/01/prep... #joss #opensource #openscience
Preparing JOSS for a generative AI future: From code to human creativity and design | Journal of Open Source Software Blog
Blog for the Journal of Open Source Software • <a href='https://joss.theoj.org'>https://joss.theoj.org</a>
blog.joss.theoj.org
January 5, 2026 at 12:31 PM
We've shipped a major update to the JOSS submission scope requirements, affecting what is eligible for submission and what information we require from authors.
You can read more about the changes and our motivations here: blog.joss.theoj.org/2026/01/prep... #joss #opensource #openscience
You can read more about the changes and our motivations here: blog.joss.theoj.org/2026/01/prep... #joss #opensource #openscience
Reposted by Niko Sirmpilatze
you’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.
here’s how to win the war for the soul of the internet, and build the Web We Want.
A Website To End All Websites | Henry From Online
How to win the war for the soul of the internet, and build the Web We Want.
henry.codes
January 1, 2026 at 7:27 PM
you’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.
here’s how to win the war for the soul of the internet, and build the Web We Want.
Reposted by Niko Sirmpilatze
Great 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
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
One Formula That Demystifies 3D Graphics
YouTube video by Tsoding
youtu.be
December 31, 2025 at 8:27 AM
Great 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
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
Reposted by Niko Sirmpilatze
My Ubuntu Summit talk is up! Where I talk about:
1. How Desktop UX is effectively dead
2. Why I hate the term UX/UI with the heat of 1000 suns
3. How OSS can actually innovate in #ux
www.youtube.com/watch?v=1fZT...
1. How Desktop UX is effectively dead
2. Why I hate the term UX/UI with the heat of 1000 suns
3. How OSS can actually innovate in #ux
www.youtube.com/watch?v=1fZT...
Are we stuck with the same Desktop UX forever? | Ubuntu Summit 25.10
YouTube video by Canonical Ubuntu
www.youtube.com
December 12, 2025 at 5:51 AM
My Ubuntu Summit talk is up! Where I talk about:
1. How Desktop UX is effectively dead
2. Why I hate the term UX/UI with the heat of 1000 suns
3. How OSS can actually innovate in #ux
www.youtube.com/watch?v=1fZT...
1. How Desktop UX is effectively dead
2. Why I hate the term UX/UI with the heat of 1000 suns
3. How OSS can actually innovate in #ux
www.youtube.com/watch?v=1fZT...
Reposted by Niko Sirmpilatze
Do 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!
December 23, 2025 at 7:52 PM
Do 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!
Reposted by Niko Sirmpilatze
I've finished my report on burnout in OSS and how to reduce it! Read more (and find the link to the full report) on the Open Source Pledge blog!
Huge thanks to all the OSS devs who shared their perspectives 💜 Let's keep shining a light on this under-recognised issue!
Huge thanks to all the OSS devs who shared their perspectives 💜 Let's keep shining a light on this under-recognised issue!
Burnout in Open Source: A Structural Problem We Can Fix Together | Open Source Pledge
Burnout is affecting the entire Open Source ecosystem. Here's what we could do to make things better.
opensourcepledge.com
November 18, 2025 at 5:01 PM
I've finished my report on burnout in OSS and how to reduce it! Read more (and find the link to the full report) on the Open Source Pledge blog!
Huge thanks to all the OSS devs who shared their perspectives 💜 Let's keep shining a light on this under-recognised issue!
Huge thanks to all the OSS devs who shared their perspectives 💜 Let's keep shining a light on this under-recognised issue!
Reposted by Niko Sirmpilatze
Today, 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...
blog.neurips.cc/2025/12/15/s...
blog.neurips.cc
December 15, 2025 at 1:00 PM
Today, 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...
blog.neurips.cc/2025/12/15/s...
Reposted by Niko Sirmpilatze
If 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...
December 14, 2025 at 11:16 PM
If 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."
Machine learning should not be a replacement for human judgment but rather help us embrace the various assumptions and interpretations that shape behavioral research, write Nedah Nemati and Matthew Whiteway.
#neuroskyence
www.thetransmitter.org/behavioral-n...
#neuroskyence
www.thetransmitter.org/behavioral-n...
Beyond the algorithmic oracle: Rethinking machine learning in behavioral neuroscience
Machine learning should not be a replacement for human judgment but rather help us embrace the various assumptions and interpretations that shape behavioral research.
www.thetransmitter.org
December 8, 2025 at 3:11 PM
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 Sirmpilatze
Pleased 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]
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]
December 8, 2025 at 9:48 AM
Pleased 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]
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]
Reposted by Niko Sirmpilatze
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)
@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)
December 6, 2025 at 7:26 PM
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)
@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
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
December 5, 2025 at 8:42 PM
🧠📢 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
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...
Applications are open for the second Neuroinformatics Unit Open Software Summer School, August 17-28 2025 in London, UK!
Bringing together researchers and developers of open-source software for training and collaboration. Financial support available.
neuroinformatics.dev/open-softwar...
Bringing together researchers and developers of open-source software for training and collaboration. Financial support available.
neuroinformatics.dev/open-softwar...
December 4, 2025 at 11:56 AM
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...
Reposted by Niko Sirmpilatze
@neuroinformatics.dev 's Open Software Week 2025 was a great experience to learn about Neuroinformatics, data science, and hands-on python programming. I thoroughly enjoyed participating in the hack day to come up with a solution for pose skeleton estimation.
Thank you to the whole team!!!
Thank you to the whole team!!!
Great new guest blog post by Pille Wetterauer and @jyoti-bhogal.bsky.social about their summer school project to extract a pose estimation skeleton for C. elegans.
neuroinformatics.dev/blog/worms_o...
neuroinformatics.dev/blog/worms_o...
December 4, 2025 at 10:11 AM
@neuroinformatics.dev 's Open Software Week 2025 was a great experience to learn about Neuroinformatics, data science, and hands-on python programming. I thoroughly enjoyed participating in the hack day to come up with a solution for pose skeleton estimation.
Thank you to the whole team!!!
Thank you to the whole team!!!
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.
November 25, 2025 at 5:17 PM
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.