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
I can't stop thinking about this essay: akamatsu.leaflet.pub/3mkwouogdzs2j
If so much of research is going to come from large companies, then maybe the way academia survives is to take advantage of our yet unrealized potential for open collaboration
If so much of research is going to come from large companies, then maybe the way academia survives is to take advantage of our yet unrealized potential for open collaboration
A protocol for attributable modular research contribution
akamatsu.leaflet.pub
September 9, 2026 at 9:29 AM
I can't stop thinking about this essay: akamatsu.leaflet.pub/3mkwouogdzs2j
If so much of research is going to come from large companies, then maybe the way academia survives is to take advantage of our yet unrealized potential for open collaboration
If so much of research is going to come from large companies, then maybe the way academia survives is to take advantage of our yet unrealized potential for open collaboration
Reposted by Niko Sirmpilatze
We are excited to share that the first session of London BIIG will be on Friday 11th September at 12pm at the LMCB!
Talks: Yongjoo Kim (UCL) & Nina Thornton (Crick) #l-biig
Refreshments will be provided. Directions for LMCB can be found on our website.
Talks: Yongjoo Kim (UCL) & Nina Thornton (Crick) #l-biig
Refreshments will be provided. Directions for LMCB can be found on our website.
August 17, 2026 at 8:40 AM
We are excited to share that the first session of London BIIG will be on Friday 11th September at 12pm at the LMCB!
Talks: Yongjoo Kim (UCL) & Nina Thornton (Crick) #l-biig
Refreshments will be provided. Directions for LMCB can be found on our website.
Talks: Yongjoo Kim (UCL) & Nina Thornton (Crick) #l-biig
Refreshments will be provided. Directions for LMCB can be found on our website.
Reposted by Niko Sirmpilatze
Just released a new version of nwb4edu, an online resource for educators and self-guided learners to use @nwb.org datasets, to adapt for the loss of Dandihub 😢
nwb4edu.github.io
nwb4edu.github.io
nwb4edu.github.io
September 4, 2026 at 6:55 PM
Just released a new version of nwb4edu, an online resource for educators and self-guided learners to use @nwb.org datasets, to adapt for the loss of Dandihub 😢
nwb4edu.github.io
nwb4edu.github.io
Reposted by Niko Sirmpilatze
Super nice site for a Friday afternoon!!! bookofshapes.com 🔥
Book of Shapes
A curated gallery of generative patterns. Discover, customize, and download unique algorithmic art.
bookofshapes.com
September 4, 2026 at 3:20 PM
Super nice site for a Friday afternoon!!! bookofshapes.com 🔥
Reposted by Niko Sirmpilatze
We are hiring! Come join us in the Straw Lab at the @biologyunifreiburg.bsky.social . Seeking a scientist to work on the neural and computational mechanisms of visual navigation in honey bees. uni-freiburg.de/en/job/00005...
September 4, 2026 at 2:57 PM
We are hiring! Come join us in the Straw Lab at the @biologyunifreiburg.bsky.social . Seeking a scientist to work on the neural and computational mechanisms of visual navigation in honey bees. uni-freiburg.de/en/job/00005...
Reposted by Niko Sirmpilatze
Textbook: tracking position during navigation is primarily the job of the hippocampus. Recent findings suggest a more complicated story.
Recording >20k neurons brainwide, we indeed find spatial representations in every region!
With @kenneth-harris.bsky.social and @carandinilab.net
Recording >20k neurons brainwide, we indeed find spatial representations in every region!
With @kenneth-harris.bsky.social and @carandinilab.net
September 4, 2026 at 6:22 AM
Textbook: tracking position during navigation is primarily the job of the hippocampus. Recent findings suggest a more complicated story.
Recording >20k neurons brainwide, we indeed find spatial representations in every region!
With @kenneth-harris.bsky.social and @carandinilab.net
Recording >20k neurons brainwide, we indeed find spatial representations in every region!
With @kenneth-harris.bsky.social and @carandinilab.net
Reposted by Niko Sirmpilatze
Heads-up: Doris Tsao is hiring 15 scientists/engineers to work on the neuroscience of consciousness at her new venture (Astera).
astera.org/careers/#box...
astera.org/careers/#box...
Careers
astera.org
September 3, 2026 at 2:01 AM
Heads-up: Doris Tsao is hiring 15 scientists/engineers to work on the neuroscience of consciousness at her new venture (Astera).
astera.org/careers/#box...
astera.org/careers/#box...
Reposted by Niko Sirmpilatze
⬡ Today, we become the Institute for Research Software.
For 15 years, we've worked as the Software Sustainability Institute to make research software more sustainable and properly recognised.
For 15 years, we've worked as the Software Sustainability Institute to make research software more sustainable and properly recognised.
September 1, 2026 at 9:46 AM
⬡ Today, we become the Institute for Research Software.
For 15 years, we've worked as the Software Sustainability Institute to make research software more sustainable and properly recognised.
For 15 years, we've worked as the Software Sustainability Institute to make research software more sustainable and properly recognised.
Reposted by Niko Sirmpilatze
Interested in image analysis and a service role in a dynamic and growing facility? Come and joy our image analysis team!
Feel free to reach out for any questions or doubts.
ista.ac.at/en/job/?titl...
Feel free to reach out for any questions or doubts.
ista.ac.at/en/job/?titl...
Job details
Job details
ista.ac.at
August 27, 2026 at 3:20 PM
Interested in image analysis and a service role in a dynamic and growing facility? Come and joy our image analysis team!
Feel free to reach out for any questions or doubts.
ista.ac.at/en/job/?titl...
Feel free to reach out for any questions or doubts.
ista.ac.at/en/job/?titl...
Reposted by Niko Sirmpilatze
Teaching extracellular #ephys analysis and #spikesorting with SpikeInterface at @neuroinformatics.dev Open Software Summer School at @sainsburywellcome.bsky.social in London this week!
Course material is available here: neuroinformatics.dev/course_ephys...
Course material is available here: neuroinformatics.dev/course_ephys...
August 25, 2026 at 10:51 AM
Teaching extracellular #ephys analysis and #spikesorting with SpikeInterface at @neuroinformatics.dev Open Software Summer School at @sainsburywellcome.bsky.social in London this week!
Course material is available here: neuroinformatics.dev/course_ephys...
Course material is available here: neuroinformatics.dev/course_ephys...
Reposted by Niko Sirmpilatze
Neuromatch is hiring a #remote, temporary, part-time Curriculum Specialist!
🤓 Help adapt our existing #NeuroAI course for a new audience, bringing important AI and neuroscience concepts to high school students!
➡️ Learn more and apply before 30 August: neuromatch.io/careers/
🤓 Help adapt our existing #NeuroAI course for a new audience, bringing important AI and neuroscience concepts to high school students!
➡️ Learn more and apply before 30 August: neuromatch.io/careers/
August 24, 2026 at 2:30 PM
Neuromatch is hiring a #remote, temporary, part-time Curriculum Specialist!
🤓 Help adapt our existing #NeuroAI course for a new audience, bringing important AI and neuroscience concepts to high school students!
➡️ Learn more and apply before 30 August: neuromatch.io/careers/
🤓 Help adapt our existing #NeuroAI course for a new audience, bringing important AI and neuroscience concepts to high school students!
➡️ Learn more and apply before 30 August: neuromatch.io/careers/
Reposted by Niko Sirmpilatze
A personal essay about how I’ve been feeling and thinking about this new technology that I’m contributing to and what it might to do to us all.
togelius.blogspot.com/2026/08/losi...
togelius.blogspot.com/2026/08/losi...
Losing my religion
In spring 2025 I had a crisis of faith. I thought about what the technology I'm helping to create might do to our future, and got scared. M...
togelius.blogspot.com
August 22, 2026 at 3:33 PM
A personal essay about how I’ve been feeling and thinking about this new technology that I’m contributing to and what it might to do to us all.
togelius.blogspot.com/2026/08/losi...
togelius.blogspot.com/2026/08/losi...
Reposted by Niko Sirmpilatze
Every illustration in the British Library's 19th-century book images dataset now has an instance mask: 1.02M clean cutouts of public-domain engravings, no image generation involved!
One small segmentation model, $3.24 of compute. Model, masks and a search Space with cutout view all open.
One small segmentation model, $3.24 of compute. Model, masks and a search Space with cutout view all open.
August 20, 2026 at 10:42 AM
Every illustration in the British Library's 19th-century book images dataset now has an instance mask: 1.02M clean cutouts of public-domain engravings, no image generation involved!
One small segmentation model, $3.24 of compute. Model, masks and a search Space with cutout view all open.
One small segmentation model, $3.24 of compute. Model, masks and a search Space with cutout view all open.
Reposted by Niko Sirmpilatze
What regulates the urge to sleep? William Joo and colleagues identified brain regions that reflect how long mice have been awake. Strikingly, inhibiting one of these regions reduces sleep by 70%, without the major behavioral deficits associated with sleep deprivation. www.nature.com/articles/s41...
Wake-activated neuronal populations that regulate sleep drive - Nature
Whole-brain activity mapping, targeted cell manipulations and electrophysiology in mice identify wake-activated neuronal populations that are crucial for sleep drive and can persistently red...
www.nature.com
August 19, 2026 at 3:41 PM
What regulates the urge to sleep? William Joo and colleagues identified brain regions that reflect how long mice have been awake. Strikingly, inhibiting one of these regions reduces sleep by 70%, without the major behavioral deficits associated with sleep deprivation. www.nature.com/articles/s41...
Reposted by Niko Sirmpilatze
The BioImage Interest Group is expanding! London-BIIG is bringing together microscopists and computational scientists across UCL, Crick, KCL and Imperial. Follow us for updates on bioimage analysis talks (@LMCB & Zoom) as well as next year's networking event! 🔬🧫 #L-BIIG
August 17, 2026 at 8:30 AM
The BioImage Interest Group is expanding! London-BIIG is bringing together microscopists and computational scientists across UCL, Crick, KCL and Imperial. Follow us for updates on bioimage analysis talks (@LMCB & Zoom) as well as next year's networking event! 🔬🧫 #L-BIIG
Reposted by Niko Sirmpilatze
BrainGlobe Atlas API V3 is out!
After 6 years, this is the first major change in how BrainGlobe works. Each atlas component is fetched independently, meaning all BrainGlobe tools will work faster, and more reliably.
Read more at: brainglobe.info/blog/braingl...
After 6 years, this is the first major change in how BrainGlobe works. Each atlas component is fetched independently, meaning all BrainGlobe tools will work faster, and more reliably.
Read more at: brainglobe.info/blog/braingl...
August 11, 2026 at 2:34 PM
BrainGlobe Atlas API V3 is out!
After 6 years, this is the first major change in how BrainGlobe works. Each atlas component is fetched independently, meaning all BrainGlobe tools will work faster, and more reliably.
Read more at: brainglobe.info/blog/braingl...
After 6 years, this is the first major change in how BrainGlobe works. Each atlas component is fetched independently, meaning all BrainGlobe tools will work faster, and more reliably.
Read more at: brainglobe.info/blog/braingl...
Reposted by Niko Sirmpilatze
All BrainGlobe atlases now have Neuroglancer links so that you can explore atlases in the browser without needing to download them first!
All links here: brainglobe.info/documentatio...
Here you can view our Eurasian Blackcap atlas:
neuroglancer-demo.appspot.com#!https://bra...
All links here: brainglobe.info/documentatio...
Here you can view our Eurasian Blackcap atlas:
neuroglancer-demo.appspot.com#!https://bra...
August 5, 2026 at 3:57 PM
All BrainGlobe atlases now have Neuroglancer links so that you can explore atlases in the browser without needing to download them first!
All links here: brainglobe.info/documentatio...
Here you can view our Eurasian Blackcap atlas:
neuroglancer-demo.appspot.com#!https://bra...
All links here: brainglobe.info/documentatio...
Here you can view our Eurasian Blackcap atlas:
neuroglancer-demo.appspot.com#!https://bra...
Reposted by Niko Sirmpilatze
New Toettchlab paper alert!
Harrison Oatman just published his beautiful work combining software design for "smart" microscopy+optogenetics and some really beautiful work understanding EGFR-driven collective cell migration.
www.cell.com/cell-systems...
Harrison Oatman just published his beautiful work combining software design for "smart" microscopy+optogenetics and some really beautiful work understanding EGFR-driven collective cell migration.
www.cell.com/cell-systems...
July 24, 2026 at 2:47 PM
New Toettchlab paper alert!
Harrison Oatman just published his beautiful work combining software design for "smart" microscopy+optogenetics and some really beautiful work understanding EGFR-driven collective cell migration.
www.cell.com/cell-systems...
Harrison Oatman just published his beautiful work combining software design for "smart" microscopy+optogenetics and some really beautiful work understanding EGFR-driven collective cell migration.
www.cell.com/cell-systems...
Reposted by Niko Sirmpilatze
Microscopy Nodes 3.1 is out for Blender 5.2! 🎉
This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation!
Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...
This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation!
Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...
July 24, 2026 at 1:49 PM
Microscopy Nodes 3.1 is out for Blender 5.2! 🎉
This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation!
Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...
This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation!
Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...
Reposted by Niko Sirmpilatze
Launch of our brand-new website for 𝐃𝐞𝐞𝐩𝐎𝐅! 🚀
👉 Explore: deepof.ai
👉 Explore: deepof.ai
DeepOF � Supervised and Unsupervised Behavioral Analysis
DeepOF: An open-source Python library for mouse behavioral analysis.
deepof.ai
July 14, 2026 at 7:50 AM
Launch of our brand-new website for 𝐃𝐞𝐞𝐩𝐎𝐅! 🚀
👉 Explore: deepof.ai
👉 Explore: deepof.ai
Reposted by Niko Sirmpilatze
We do an awful lot of looooong video recordings in our lab and have long wanted an easy way to clip, compress and combine videos for our workflows.
So here's #croppy! 🦀 I hope others will find it useful too - I'd love to hear if you do! And would appreciate if you give it a star on Github! 🌟
So here's #croppy! 🦀 I hope others will find it useful too - I'd love to hear if you do! And would appreciate if you give it a star on Github! 🌟
Our postdoc @roald-arboel.com made a thing! #Croppy is #free and awesome for fast and
effective #video #editing and it has a #GUI!
Need to crop a part of a video? Need to trim a video? Need to combine videos? Need to
compress a video? roald-arboel.com/croppy/
effective #video #editing and it has a #GUI!
Need to crop a part of a video? Need to trim a video? Need to combine videos? Need to
compress a video? roald-arboel.com/croppy/
July 7, 2026 at 4:22 PM
We do an awful lot of looooong video recordings in our lab and have long wanted an easy way to clip, compress and combine videos for our workflows.
So here's #croppy! 🦀 I hope others will find it useful too - I'd love to hear if you do! And would appreciate if you give it a star on Github! 🌟
So here's #croppy! 🦀 I hope others will find it useful too - I'd love to hear if you do! And would appreciate if you give it a star on Github! 🌟
I'll be in Barcelona for #FENS2026 next week, presenting a poster about movement, and also hanging around our team's other posters (details in quoted post).
Drop by if you want to chat about any of these projects or just to say hi!
Drop by if you want to chat about any of these projects or just to say hi!
July 2, 2026 at 5:20 PM
I'll be in Barcelona for #FENS2026 next week, presenting a poster about movement, and also hanging around our team's other posters (details in quoted post).
Drop by if you want to chat about any of these projects or just to say hi!
Drop by if you want to chat about any of these projects or just to say hi!
Reposted by Niko Sirmpilatze
Working with OME-Zarrs in @napari.org ? Check out the newest release of napari-ome-zarr-navigator to make your life easier & allow more interactive ways to write back to OME-Zarrs.
Follow the thread for more
(1/5 🧵)
Follow the thread for more
(1/5 🧵)
June 30, 2026 at 12:31 PM
Working with OME-Zarrs in @napari.org ? Check out the newest release of napari-ome-zarr-navigator to make your life easier & allow more interactive ways to write back to OME-Zarrs.
Follow the thread for more
(1/5 🧵)
Follow the thread for more
(1/5 🧵)
Reposted by Niko Sirmpilatze
The University of Exeter have announced a programme of academic staff cuts, including all of www.exeter.ac.uk/research/gro... Sign the open letter of support at docs.google.com/forms/d/e/1F...
@crab-exeter.bsky.social
@crab-exeter.bsky.social
Centre for Research in Animal Behaviour (CRAB) | Research Groups | University of Exeter
www.exeter.ac.uk
June 29, 2026 at 3:00 AM
The University of Exeter have announced a programme of academic staff cuts, including all of www.exeter.ac.uk/research/gro... Sign the open letter of support at docs.google.com/forms/d/e/1F...
@crab-exeter.bsky.social
@crab-exeter.bsky.social
Reposted by Niko Sirmpilatze
🌟 NEW OCTRON RELEASE! 🌟
Want to track your animals using the command line? You can now train models and predict videos with single prompts in a terminal! Ideal for batch jobs, headless servers, and remote machines.
Big shout-out to @roald-arboel.com for helping with this release!
Want to track your animals using the command line? You can now train models and predict videos with single prompts in a terminal! Ideal for batch jobs, headless servers, and remote machines.
Big shout-out to @roald-arboel.com for helping with this release!
June 29, 2026 at 9:40 PM
🌟 NEW OCTRON RELEASE! 🌟
Want to track your animals using the command line? You can now train models and predict videos with single prompts in a terminal! Ideal for batch jobs, headless servers, and remote machines.
Big shout-out to @roald-arboel.com for helping with this release!
Want to track your animals using the command line? You can now train models and predict videos with single prompts in a terminal! Ideal for batch jobs, headless servers, and remote machines.
Big shout-out to @roald-arboel.com for helping with this release!