Niko Sirmpilatze
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nikosirmpilatze.com
Niko Sirmpilatze
@nikosirmpilatze.com
380 followers 880 following 19 posts
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.
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nikosirmpilatze.com
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."
December 8, 2025 at 3:11 PM
Reposted by Niko Sirmpilatze
zimengwu33.bsky.social
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]
December 8, 2025 at 9:48 AM
Reposted by Niko Sirmpilatze
eringrant.me
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)
December 6, 2025 at 7:26 PM
Reposted by Niko Sirmpilatze
alleninstitute.org
🧠📢 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
December 5, 2025 at 8:42 PM
nikosirmpilatze.com
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...
neuroinformatics.dev SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 7d
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...
An overview of the Open Software Summer School 2026 schedule. There are two tracks in the first week, "Animals in Motion" and "Large Array Data". "BrainGlobe" and "Extracellular Electrophysiology" will be run in the second week. Each week starts with a symposium on the Monday afternoon, followed by 3 days of the course, and then a 2 days of collaboration, bringing together researchers and engineers to use, and improve neuroscience open source software.
December 4, 2025 at 11:56 AM
Reposted by Niko Sirmpilatze
jyoti-bhogal.bsky.social
@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!!!
neuroinformatics.dev SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 4d
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...
A schematic to show the combination of the SAM-2 model and scikit-image to analyse images of C. Elegans.
December 4, 2025 at 10:11 AM
nikosirmpilatze.com
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
nikosirmpilatze.com
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...
November 25, 2025 at 5:01 PM
Reposted by Niko Sirmpilatze
mastodon.mastodon.social.ap.brid.gy
Hey everyone, we have some pretty big news to share. You might remember that we announced a big restructuring for the Mastodon team earlier this year. Today marks an important milestone in this transition.

#mastodon #fediverse #socialweb
November 18, 2025 at 8:05 AM
Reposted by Niko Sirmpilatze
thetransmitter.bsky.social
The 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...
Neurophysiology data-sharing system faces funding cliff
After the primary grant supporting Neurodata Without Borders ends in March 2026, the platform may no longer be maintained or kept up to date.
www.thetransmitter.org
November 17, 2025 at 9:38 PM
Reposted by Niko Sirmpilatze
zebrafishrock.bsky.social
Axonal pathfinding of zebrafish retinal ganglion cells forms the optic nerve. Credit to Dr. Matthew Bostock @houartlab.bsky.social. #ZebrafishZunday 🧪
November 16, 2025 at 8:30 PM
Reposted by Niko Sirmpilatze
leaveylab.bsky.social
Full chameleon cranial atlas article out now in @anatrecord.bsky.social ! doi.org/10.1002/ar.7... 🦎✨️
3D anatomical atlas of the heads of male and female adult Chamaeleo calyptratus
The veiled chameleon is a model organism in reptile development research. Utilizing contrast-enhanced microCT and deep learning segmentation models, we have generated the first digital atlases of the...
doi.org
November 15, 2025 at 9:28 AM
nikosirmpilatze.com
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".
leaveylab.bsky.social Alice Leavey @leaveylab.bsky.social · Nov 5
I have been invited to speak at the UCL BioImage Interest Group meeting on Nov 14 - find the Zoom information on this link, open for anyone wanting to learn about AI-driven digital dissection tools (www.ucl.ac.uk/science-tech...)
UCL BioImage Interest Group
The UCL BIIG - BioImage Interest Group - aims to share knowledge, expertise and foster discussion and collaborations around the topics of bioimaging and bioimage analysis in an informal setting.
www.ucl.ac.uk
November 13, 2025 at 8:14 PM
Reposted by Niko Sirmpilatze
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Niko Sirmpilatze
carandinilab.net
Our 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...
November 12, 2025 at 3:41 PM
Reposted by Niko Sirmpilatze
carlocastoldi.bsky.social
Today I came back from holidays but my first day at the office was happier than expected!

@neuroinformatics.dev just released a new version of movement, a software for #motion tracking #analysis, that includes my PR on which I worked during the Open Software Week 2025
neuroinformatics.dev SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 28d
movement v0.11.0 released!

v0.11.0 includes an update on how movement computes displacement vectors and adds support for 3D DLC files.

movement can now also be installed in one line with pip/uv.

More details: github.com/neuroinforma...
An overview of the movement data processing pipeline, from data loading, filtering, viualisation and analysis.
November 12, 2025 at 2:31 PM
Reposted by Niko Sirmpilatze
neuroinformatics.dev
movement v0.11.0 released!

v0.11.0 includes an update on how movement computes displacement vectors and adds support for 3D DLC files.

movement can now also be installed in one line with pip/uv.

More details: github.com/neuroinforma...
An overview of the movement data processing pipeline, from data loading, filtering, viualisation and analysis.
November 10, 2025 at 7:20 AM
Reposted by Niko Sirmpilatze
zamakany.bsky.social
Part of a startup project funded by Max Planck Innovation's MAX!mize program, we're developing next-generation software for automated analysis of animal social behavior. We have this opening:
Software Engineer (m/f/d) (80 - 100 %) Behavioral Analysis Platform Development
Details : lnkd.in/ewXgnBmV
November 7, 2025 at 4:46 PM
Reposted by Niko Sirmpilatze
sepikeshavarzi.bsky.social
Do 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
October 29, 2025 at 5:05 PM
Reposted by Niko Sirmpilatze
erickratamero.com
If you've ever worked with OME things, it is worth reading this update from Jason Swedlow on image.sc about the evolving OME governance. The TL;DR is that an interim leadership team has been assembled and new governance structures are coming sooner rather than later. forum.image.sc/t/ome-transi...
OME Transition-- Update
Dear All- Over the past two decades, OME has grown into a vibrant and global community dedicated to developing open standards, tools, and resources for the management, sharing, and analysis of micros...
forum.image.sc
October 22, 2025 at 4:28 AM
Reposted by Niko Sirmpilatze
danielkronauer.bsky.social
New 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...
October 17, 2025 at 5:35 PM
Reposted by Niko Sirmpilatze
marcodv.bsky.social
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
October 10, 2025 at 6:59 AM
Reposted by Niko Sirmpilatze
brainglobe.info
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...
October 10, 2025 at 10:40 AM
Reposted by Niko Sirmpilatze
brainglobe.info
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!
October 9, 2025 at 7:06 AM
Reposted by Niko Sirmpilatze
simonwillison.net
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
October 9, 2025 at 3:40 AM