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Niko Sirmpilatze

@niksirbi.neuromatch.social.ap.brid.gy

5 followers 1 following 34 posts

London-based neuroscientist 🧠 & research software engineer 💻 developing free and Open Source tools for studying brains & behaviour, @neuroinformatics at UCL […] 🌉 bridged from ⁂ neuromatch.social/@niksirbi, follow @ap.brid.gy to interact

Posts Replies Media

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 22/09/2026

RE: mastodon.online/@neuroinformatics/1… It was a pleasure working with Anna on this project! She has added lots of cool new features to our GUI. Keep an eye out for a fresh movement release this autumn 🍁😉 Details in her blog below.

mastodon.online

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 22/09/2026

RE: mastodon.online/@neuroinformatics/1… It was such a pleasure having Anna work on this project over the summer. She’s added lots of cool new features to our GUI. Keep an eye out for a fresh movement release this autumn 🍁 Details in her blog, linked below.

mastodon.online

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 02/07/2026

RE: mastodon.online/@neuroinformatics/1… I'll be in Barcelona for #FENS2026 next week, presenting a poster about movement.neuroinformatics.dev, and also hanging around our team's other posters (details in quoted post). Drop by if you want to chat about any of […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 23/04/2026

RE: mastodon.online/@neuroinformatics/1… Drawing regions of interest has been among our most-requested features, and a long time in the making. Building it on top of @napari was fun. Drawing and editing shapes is such a joy!

mastodon.online

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 20/04/2026

RE: neuromatch.social/@SWC_Neuro/116437… Mapping brains never gets old, especially when the territory is new 🐦🧠🗺️. Loved being drawn into this collaboration by Simon Weiler and learning about birds and their magnetic senses. Stay tuned for more new atlases coming to @brainglobe

neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 09/04/2026

For those who missed the talk: the recording is now available on YouTube: www.youtube.com/watch?v=RUDhXB1ZZIg

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 17/03/2026

RE: mastodon.online/@neuroinformatics/1… Upcoming talk at TheBehaviourForum.org seminar series. See forum post for details: www.thebehaviourforum.org/t/virtual… Come to see me talk […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 13/03/2026

RE: mastodon.online/@neuroinformatics/1… If you're interested in the intersection of neuroscience 🧠 and software engineering 👩‍💻, these are excellent opportunities. Great teams and a supportive working environment. Can't recommend them enough! #neuroscience #python

mastodon.online

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 20/02/2026

RE: mastodon.online/@neuroinformatics/1… 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 […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 11/02/2026

@neuroinformatics @FosdemResearch Part 3 of my "Trusted by design" blog series is live at neuroinformatics.dev/blog/trusted-b… Open-source software is public, yet much of the communication around it may happen in private emails, internal Slack channels and meetings […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 04/02/2026

@neuroinformatics Part 3 will follow next week. In the meantime, you can watch the recording my talk at @FosdemResearch, containing the gist of the whole blog series: fosdem.org/2026/schedule/event/VPJH…

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

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 04/02/2026

@neuroinformatics Part 2 of the "Trusted by design" blog series is out today. 'Release early, release often' is an often-repeated mantra, but I hadn't fully grasped its significance until I switched from academic research to full-time software development. How early? How often? And why is […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 29/01/2026

@neuroinformatics Part 1 is all about finding your software's mission and scope. No project exists in a vacuum. Open-source software is a vast web of inter-connected and inter-dependent tools. When creating a new tool, your number one job is to carve out its place in the web consciously […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 29/01/2026

@fosdem @FosdemResearch @neuroinformatics 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. The general overview and the first of three parts are already published at […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 29/01/2026

@fosdem @FosdemResearch In it, I'll try to distil the lessons learnt through my transition from academic research to research software development with @neuroinformatics 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 […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 29/01/2026

@fosdem The second talk is on Sunday, in the Open Research devroom @FosdemResearch fosdem.org/2026/schedule/event/VPJH… It's titled: "Trusted by design: set up your research software for community adoption".

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

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 29/01/2026

@fosdem My first talk is on Saturday, in the Bioinformatics & Computational Biology devroom. fosdem.org/2026/schedule/event/9VLS… I'm presenting movement, our Python package for analysing animal motion.

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

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 29/01/2026

I'm heading to @fosdem over the weekend to present 2 research software-related talks. Come say hi if you're in Brussels, tune into the livestream, or watch the recordings later. Find all the info here: fosdem.org/2026/schedule/speaker/ni… I'm also using this as a chance […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 22/01/2026

RE: mastodon.social/@SoftwareSaved/1159… I really enjoyed recounting the story behind the first @neuroinformatics Open Software Week. The second edition will be even more awesome. Remember to apply by the end of January […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 22/01/2026

You can read my account of last year's event in a blogpost I wrote for @SoftwareSaved : www.software.ac.uk/blog/animals-mot…

Animals in Motion: empowering behavioural researchers with open-source tools | Software Sustainability Institute

I organised the first Animals in Motion workshop in London, which was the central goal of my Software Sustainability Institute (SSI) Fellowship.

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 12/01/2026

RE: mastodon.online/@neuroinformatics/1… 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 #neuroscience #animalbehavior #opensource I'll be leading the "Animals in […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 04/12/2025

Note that while icons of mice are used for illustration, the course content should be applicable to any animal species.

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 04/12/2025

This workshop is designed for researchers and students who have collected — or plan to collect — videos of animal behaviour. It is aimed at those interested in using free and open-source tools for tracking animal motion and extracting quantitative behavioural measures.

A schematic overview of topics covered in the "Animals in Motion" workshop. These include computer vision-based tools for animal detection and tracking (e.g. SLEAP), Python packages for motion quantifications (e.g. movement), and supervised behaviour segmentation. While icons of mice are used for illustration, the course content should be applicable to any animal species.

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 04/12/2025

RE: mastodon.online/@neuroinformatics/1… I'll be coordinating the "Animals in Motion" track of this summer school, returning to London in August 2026. Apply to join us for some hands-on learning and collaboration on open-source tools for video behavioural analysis […]

neuromatch.social

Original post on neuromatch.social

Reposted by Niko Sirmpilatze

cirlo @cirlo.mastodon.uno.ap.brid.gy · 12/11/2025

RE: mastodon.online/@neuroinformatics/1… Today I came back from holidays but my first day at the office was happier than expected! @neuroinformatics just released a new version of `movement`, a software for #motion tracking #analysis, that includes my PR on which I […]

Original post on mastodon.uno

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 10/11/2025

RE: mastodon.online/@neuroinformatics/1… Thanks for the contribution @cirlo, and for the blogpost!

mastodon.online

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 30/10/2025

RE: mastodon.online/@TheCSCCE/115463442… Taking part in the Birdaro programme by @TheCSCCE on behalf of movement.neuroinformatics.dev has been such a great experience so far. I'm learning tons about open-source governance and community building, and meeting a brilliant […]

neuromatch.social

Original post on neuromatch.social

Reposted by Niko Sirmpilatze

Lincoln Russell @linc.phpc.social.ap.brid.gy · 08/10/2025

I’ve been thinking about community software most of my life. 23 years ago, I started organizing communities. 15 years ago, I joined the wave of "next-generation" forums that popularized community as an enterprise feature. 7 years ago, I began reflecting on everything I'd learned in a notebook […]

Original post on phpc.social

Reposted by Niko Sirmpilatze

petersuber @petersuber.fediscience.org.ap.brid.gy · 10/09/2025

The University of Utrecht is cancelling the #WebOfScience and offering training sessions on #OpenAlex. www.uu.nl/en/news/access-to-web-of-… "Discontinuing Web of Science is a logical step that fits in with the UU vision on #OpenScience. Closed commercial […]

fediscience.org

Original post on fediscience.org

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 18/09/2025

I enjoyed chatting with Peter about my @SoftwareSaved fellowship. Tune in for the backstory behind animals-in-motion.neuroinformatics.… and @neuroinformatics's "Open Software Week". PS: Code for Thought is a great podcast to follow if you’re into research software […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 18/08/2025

Had a blast teaching the "Animals in Motion" course last week as part of @neuroinformatics Open Software Week! All course materials—including hands-on coding exercises—are freely available as an online book: 🔗 […] [Original post on neuromatch.social]

Reposted by Niko Sirmpilatze

djspiewak.fosstodon.org.ap.brid.gy @djspiewak.fosstodon.org.ap.brid.gy · 11/07/2025

One of my coworkers refers to Open Source as “the most incredible thing humanity has ever accomplished.” When he says that, he’s not making a socioeconomic or political statement, nor is he ignoring technical shortcomings. Rather, he is making an observation about how millions of people have […]

Original post on fosstodon.org

Reposted by Niko Sirmpilatze

Henrik Schönemann @lavaeolus.fedihum.org.ap.brid.gy · 03/07/2025

For everyone in the #US and able to visit some national parks in the coming days/weeks: We need your help in preserving history: #SaveOurSigns fedihum.org/@SafeguardingResearch/1…

Safeguarding Research/Culture (@SafeguardingResearch@fedihum.org)

Data comes in many forms, but not every time there is a dataset ready to be saved: We, together with @datarescueproject.org@bsky.brid.gy and partners need YOUR help in preserving American history – but this time, we need you to put on your ranger hat and boots, and trek to your local national park to #SaveOurSigns https://saveoursigns.org #NationalPark #NPS #SafeguardingResearch Please share widely! <3

Reposted by Niko Sirmpilatze

Julia Evans @b0rk.social.jvns.ca.ap.brid.gy · 26/06/2025

new zine: The Secret Rules of the Terminal jvns.ca/blog/2025/06/24/new-zine--t…

New zine: The Secret Rules of the Terminal

Reposted by Niko Sirmpilatze

Alper Çuğun-Gscheidel @alper.rls.social.ap.brid.gy · 06/06/2025

“Nightmare bicycle” is a concept that I won’t get out of my head quickly. www.geoffreylitt.com/2025/03/03/the…

geoffreylitt.com

Avoid the nightmare bicycle

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 19/05/2025

Reminder to register for our @neuroinformatics "Open Software Week" this August in London, for some hands-on training and hacking on open-source Python tools for analysing animal motion, whole-brain microscopy (with @brainglobe), or big imaging data. Spaces are limited but registration and food […]

neuromatch.social

Original post on neuromatch.social

Reposted by Niko Sirmpilatze

Djoerd Hiemstra 🍉 @djoerd.idf.social.ap.brid.gy · 11/05/2025

The Journal of Open Source Education is an educator friendly journal for publishing open-source educational materials and software. jose.theoj.org

Journal of Open Source Education

Journal of Open Source Education (JOSE) is an educator friendly journal for publishing open-source educational materials and software.

Reposted by Niko Sirmpilatze

jonny (nonvenomous) @jonny.neuromatch.social.ap.brid.gy · 24/04/2025

Helping a labmate stream a video from python that gets processed framewise as a series of arrays to the browser for some dashboard, and the amount of tutorials that encourage you to encode every frame as a b64 JPEG and dynamically update the `src` attribute on an `img` element are too damn high […]

neuromatch.social

Original post on neuromatch.social

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 17/04/2025

As part of this week-long event, I will be hosting a 2-day “Animals in Motion” workshop in London, with the generous support of @SoftwareSaved. It’s for anyone who wants to get hands-on experience with using open-source software to track animals from video footage and analyse their motion […]

neuromatch.social

Original post on neuromatch.social

Reposted by Niko Sirmpilatze

jonny (nonvenomous) @jonny.neuromatch.social.ap.brid.gy · 09/04/2025

to any academics who want their work to outlast their current hype cycle, the next publisher downsizing, or government book burning: * make your work available for free. * as a PDF or HTML document (or, fine, JATS) * from a URL that requires no login or javascript to access. having […]

neuromatch.social

Original post on neuromatch.social

Reposted by Niko Sirmpilatze

Tom Gauld @tomgauld.bsky.social · 06/04/2025

My cartoon for this week’s @newscientist.com

Caption: The Tardigrade can survive the heat of a volcano and the vacuum of space, but it prefers an open fire, a good book and a chilled Sancerre.

Image: A tardigrade (a cute, plump micro-animal with eight legs - six of which are in view) sits in a tiny armchair, reading with a glass of wine in one hand and a smile on its face.

Reposted by Niko Sirmpilatze

Kee Hinckley @nazgul.infosec.exchange.ap.brid.gy · 06/04/2025

Now there's a protest sign you don't see often.

Person holding a cardboard sign which reads "Hand off working COBOL code"

Reposted by Niko Sirmpilatze

Julia Evans @b0rk.social.jvns.ca.ap.brid.gy · 02/04/2025

every core unix command I use

basic file stuff

touch - create file
mkdir - create directory
cp - copy
mv - move
rm - delete
ln - create symlink
ls - list directory

how big is it
wc - word count
du - file size in bytes
df - filesystem usage

slice & dice files
sed - replace regex
tr - replace character
grep - search file
cut - get column
awk - get column (+ more)
sort - sort lines
uniq - unique lines
head - first 10 lines
tail - last 10 lines

filesystems
mount - mount a filesystem
umount - unmount
dd - copy data to a disk

manage processes
ps - list processes
lsof - list open files
kill - send a signal
pkill - fancy `kill`
top - who's using CPU?
uptime - time since reboot

permissions
chown - change owner
chmod - change permissions

time stuff
time - measure runtime
date - current time
sleep - wait X seconds
cal - cute calendar

useful with pipes
less - scroll text
cat - print file contents
tee - stdin -> file + stdout
xargs - run cmd for each line

compression
tar - make/extract tar files
gzip - compress with gzip
gunzip - decompress
zip - compress with zip
unzip - decompress

& more
which - find cmd on PATH
man - read man page
crontab - edit crontab
md5sum - calculate md5sum
diff - diff files

shell builtins (not programs)

export - set env var
alias - create an alias
source - eval code from file
cd - change directory
type - is cmd a builtin?
history - view history
echo - print text
printf - like C printf
disown - TODO

Reposted by Niko Sirmpilatze

jonny (nonvenomous) @jonny.neuromatch.social.ap.brid.gy · 14/03/2025

don't fuck up and think that disappearing Mahmoud Khalil and leveling Columbia is anything but trying to crush leftist organizing full stop. They don't give a shit about antisemitism, and they're not even doing it because they love Israel. They're going after campus organizers because […]

neuromatch.social

Original post on neuromatch.social

Reposted by Niko Sirmpilatze

jonny (nonvenomous) @jonny.neuromatch.social.ap.brid.gy · 12/03/2025

Happy #FetchAllReplies day to those that celebrate (everyone)

Niko Sirmpilatze @niksirbi.neuromatch.social.ap.brid.gy · 11/03/2025

This was among the most fun projects I’ve worked on! Borrowing some methods from MRI and applying them to whole-brain microscopy data of outstanding quality. Check out these beautiful (and magnetoreceptive) bird brains! #anatomy #neuroscience From: @adamltyson […]

neuromatch.social

Original post on neuromatch.social

Reposted by Niko Sirmpilatze

Julian Fietkau @fietkau.me · 04/03/2025

I'm finally unveiling the #ActivityPub project that has been consuming my weekends: Encyclia, an #ORCID bridge that will make ORCID records followable and interactable on the fediverse. 🙂 It's early-stage and the ORCID following function is not publicly available yet. We're seeking community […]

Original post on fietkau.social