SWC/GCNU Neuroinformatics Unit
@neuroinformatics.dev
Research Software Engineering team at the Sainsbury Wellcome Centre and Gatsby Computational Neuroscience Unit, UCL. We build open source software for neuroscience and machine learning.
https://neuroinformatics.dev
Posts by @adamltyson.com
https://neuroinformatics.dev
Posts by @adamltyson.com
Reposted by SWC/GCNU Neuroinformatics Unit
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 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
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...
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...
November 12, 2025 at 2:31 PM
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 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
Reposted by SWC/GCNU Neuroinformatics Unit
Fantastic to see Igor Tatarnikov, Senior Research Software Engineer at SWC, collecting the 2025 International Prize from
@theneuro.bsky.social Irv and Helga Cooper Foundation on behalf of the @brainglobe.info Initiative!
#OpenScience
Read more: sainsburywellcome.org/web/research...
@theneuro.bsky.social Irv and Helga Cooper Foundation on behalf of the @brainglobe.info Initiative!
#OpenScience
Read more: sainsburywellcome.org/web/research...
November 11, 2025 at 3:48 PM
Fantastic to see Igor Tatarnikov, Senior Research Software Engineer at SWC, collecting the 2025 International Prize from
@theneuro.bsky.social Irv and Helga Cooper Foundation on behalf of the @brainglobe.info Initiative!
#OpenScience
Read more: sainsburywellcome.org/web/research...
@theneuro.bsky.social Irv and Helga Cooper Foundation on behalf of the @brainglobe.info Initiative!
#OpenScience
Read more: sainsburywellcome.org/web/research...
Reposted by SWC/GCNU Neuroinformatics Unit
Hear BrainGlobe core developer speak about the project in this keynote lecture.
16:00 EST
16:00 EST
Ready to see how open-source tools are revolutionizing neuroscience?
Join us for Igor Tatarnikov’s talk on The BrainGlobe Initiative, the open-source platform reshaping computational neuroanatomy.
Be part of the future of #OpenScience: buff.ly/p6l83E4
@ucl.ac.uk @sainsburywellcome.bsky.social
Join us for Igor Tatarnikov’s talk on The BrainGlobe Initiative, the open-source platform reshaping computational neuroanatomy.
Be part of the future of #OpenScience: buff.ly/p6l83E4
@ucl.ac.uk @sainsburywellcome.bsky.social
November 10, 2025 at 10:03 AM
Hear BrainGlobe core developer speak about the project in this keynote lecture.
16:00 EST
16:00 EST
Reposted by SWC/GCNU Neuroinformatics Unit
Alongside this new version, Carlo Castoldi wrote a blogpost outlining the changes to how movement calculates displacement.
movement.neuroinformatics.dev/latest/blog/...
movement.neuroinformatics.dev/latest/blog/...
November 10, 2025 at 7:24 AM
Alongside this new version, Carlo Castoldi wrote a blogpost outlining the changes to how movement calculates displacement.
movement.neuroinformatics.dev/latest/blog/...
movement.neuroinformatics.dev/latest/blog/...
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...
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...
November 10, 2025 at 7:20 AM
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...
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...
Reposted by SWC/GCNU Neuroinformatics Unit
A new MRI mouse brain atlas has been added to BrainGlobe!
This atlas from Dorr et al. (2008) is an average of 40 T2-weighted MR images at 32um resolution.
Thanks to Saarah Hussain for adding this atlas.
More details: brainglobe.info/blog/dorr-mo...
Original paper: doi.org/10.1016/j.ne...
This atlas from Dorr et al. (2008) is an average of 40 T2-weighted MR images at 32um resolution.
Thanks to Saarah Hussain for adding this atlas.
More details: brainglobe.info/blog/dorr-mo...
Original paper: doi.org/10.1016/j.ne...
November 6, 2025 at 4:36 PM
A new MRI mouse brain atlas has been added to BrainGlobe!
This atlas from Dorr et al. (2008) is an average of 40 T2-weighted MR images at 32um resolution.
Thanks to Saarah Hussain for adding this atlas.
More details: brainglobe.info/blog/dorr-mo...
Original paper: doi.org/10.1016/j.ne...
This atlas from Dorr et al. (2008) is an average of 40 T2-weighted MR images at 32um resolution.
Thanks to Saarah Hussain for adding this atlas.
More details: brainglobe.info/blog/dorr-mo...
Original paper: doi.org/10.1016/j.ne...
Save the date! The Open Software Summer School returns August 17-28 2026 in London, U.K.
There will be four separate tracks on animal behaviour, extracellular electrophysiology, anatomy and handling large data.
Applications open Dec 1st.
More details:
neuroinformatics.dev/open-softwar...
There will be four separate tracks on animal behaviour, extracellular electrophysiology, anatomy and handling large data.
Applications open Dec 1st.
More details:
neuroinformatics.dev/open-softwar...
October 31, 2025 at 3:25 PM
Save the date! The Open Software Summer School returns August 17-28 2026 in London, U.K.
There will be four separate tracks on animal behaviour, extracellular electrophysiology, anatomy and handling large data.
Applications open Dec 1st.
More details:
neuroinformatics.dev/open-softwar...
There will be four separate tracks on animal behaviour, extracellular electrophysiology, anatomy and handling large data.
Applications open Dec 1st.
More details:
neuroinformatics.dev/open-softwar...
Reposted by SWC/GCNU Neuroinformatics Unit
Register to hear core developer Igor speak about BrainGlobe tools and the community that has been built around them.
Join us at The Neuro’s Open Science Prizes Ceremony for a special lecture by Igor Tatarnikov, Senior Research Software Engineer at the Sainsbury Wellcome Centre, University College London.
🔗 Come be part of the future of open science. buff.ly/p6l83E4
#Neuroscience #Neuroanatomy #OpenScience
🔗 Come be part of the future of open science. buff.ly/p6l83E4
#Neuroscience #Neuroanatomy #OpenScience
October 29, 2025 at 1:46 PM
Register to hear core developer Igor speak about BrainGlobe tools and the community that has been built around them.
Reposted by SWC/GCNU Neuroinformatics Unit
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...
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
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...
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...
Reposted by SWC/GCNU Neuroinformatics Unit
Huge congratulations to the @BrainGlobe.info team for winning the 2025 International Prize awarded by the @theneuro.bsky.social and Helga Cooper Foundation Open Science Prizes Selection Committee 🎉
www.sainsburywellcome.org/web/research...
www.sainsburywellcome.org/web/research...
October 9, 2025 at 2:11 PM
Huge congratulations to the @BrainGlobe.info team for winning the 2025 International Prize awarded by the @theneuro.bsky.social and Helga Cooper Foundation Open Science Prizes Selection Committee 🎉
www.sainsburywellcome.org/web/research...
www.sainsburywellcome.org/web/research...
Reposted by SWC/GCNU Neuroinformatics Unit
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!
Thank you to everyone who has contributed to BrainGlobe over the years!
🏆Announcing the laureates of the Neuro - Irv and Helga Cooper Foundation Open Science Prizes 2025!
🎉 Join us in celebrating the laureates at the award ceremony, featuring a special lecture from International Prize laureate representative from the BrainGlobe initiative.
#OpenScience #Neuroscience
🎉 Join us in celebrating the laureates at the award ceremony, featuring a special lecture from International Prize laureate representative from the BrainGlobe initiative.
#OpenScience #Neuroscience
The Neuro – Irv and Helga Cooper Foundation Open Science Prizes: Meet the winners of an exceptional edition
This year’s edition of the Irv and Helga Cooper Foundation Open Science Prizes at The Neuro, organised by the Tanenbaum Open Science Institute, was exceptional in every way. With a record number of ap...
www.mcgill.ca
October 9, 2025 at 7:06 AM
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!
Thank you to everyone who has contributed to BrainGlobe over the years!
Reposted by SWC/GCNU Neuroinformatics Unit
🏆Announcing the laureates of the Neuro - Irv and Helga Cooper Foundation Open Science Prizes 2025!
🎉 Join us in celebrating the laureates at the award ceremony, featuring a special lecture from International Prize laureate representative from the BrainGlobe initiative.
#OpenScience #Neuroscience
🎉 Join us in celebrating the laureates at the award ceremony, featuring a special lecture from International Prize laureate representative from the BrainGlobe initiative.
#OpenScience #Neuroscience
The Neuro – Irv and Helga Cooper Foundation Open Science Prizes: Meet the winners of an exceptional edition
This year’s edition of the Irv and Helga Cooper Foundation Open Science Prizes at The Neuro, organised by the Tanenbaum Open Science Institute, was exceptional in every way. With a record number of ap...
www.mcgill.ca
October 8, 2025 at 7:29 PM
🏆Announcing the laureates of the Neuro - Irv and Helga Cooper Foundation Open Science Prizes 2025!
🎉 Join us in celebrating the laureates at the award ceremony, featuring a special lecture from International Prize laureate representative from the BrainGlobe initiative.
#OpenScience #Neuroscience
🎉 Join us in celebrating the laureates at the award ceremony, featuring a special lecture from International Prize laureate representative from the BrainGlobe initiative.
#OpenScience #Neuroscience
A new version of fancylog is released (v0.6.0). In this version, the “program” variable passed to the logger has been deprecated in favour of “package”.
This is a breaking change, and support for “program” will be removed in v0.7.0.
github.com/neuroinforma...
This is a breaking change, and support for “program” will be removed in v0.7.0.
github.com/neuroinforma...
Release v0.6.0 · neuroinformatics-unit/fancylog
What's Changed
rename program to package by @AlexandroBerumen in #60
New Contributors
@AlexandroBerumen made their first contribution in #60
Full Changelog: v0.5.2...v0.6.0
github.com
October 3, 2025 at 7:08 AM
A new version of fancylog is released (v0.6.0). In this version, the “program” variable passed to the logger has been deprecated in favour of “package”.
This is a breaking change, and support for “program” will be removed in v0.7.0.
github.com/neuroinforma...
This is a breaking change, and support for “program” will be removed in v0.7.0.
github.com/neuroinforma...
Movement v0.10.0 released!
v0.10.0 enables export of bounding boxes datasets as VIA-tracks csv files which are loadable in our napari GUI and the VGG Image Annotator.
It also includes an example showing how to load 3D data from FreeMoCap into movement.
Release notes:
github.com/neuroinforma...
v0.10.0 enables export of bounding boxes datasets as VIA-tracks csv files which are loadable in our napari GUI and the VGG Image Annotator.
It also includes an example showing how to load 3D data from FreeMoCap into movement.
Release notes:
github.com/neuroinforma...
September 19, 2025 at 3:06 PM
Movement v0.10.0 released!
v0.10.0 enables export of bounding boxes datasets as VIA-tracks csv files which are loadable in our napari GUI and the VGG Image Annotator.
It also includes an example showing how to load 3D data from FreeMoCap into movement.
Release notes:
github.com/neuroinforma...
v0.10.0 enables export of bounding boxes datasets as VIA-tracks csv files which are loadable in our napari GUI and the VGG Image Annotator.
It also includes an example showing how to load 3D data from FreeMoCap into movement.
Release notes:
github.com/neuroinforma...
Reposted by SWC/GCNU Neuroinformatics Unit
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.
and @neuroinformatics.dev 's "Open Software Week".
PS: Code for Thought is a great podcast to follow if you’re into research software.
September 18, 2025 at 9:39 AM
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.
and @neuroinformatics.dev 's "Open Software Week".
PS: Code for Thought is a great podcast to follow if you’re into research software.
Lovely talk by Open Software Week participant @ishratz25.bsky.social on the challenges of using @brainglobe.info tools to identify very small regions, in very large images.
Check out the PyCon Au talk from my team member: @ishratz25.bsky.social on the challenges and solutions(?) of cell counting in whole-brain light sheet images! Also give her a follow, she's new here.
www.youtube.com/watch?v=ccLn...
www.youtube.com/watch?v=ccLn...
"Big Brains, Small Targets: Whole-Brain Image Analysis with Python" - Ishrat Zaman (PyCon AU 2025)
YouTube video by PyCon AU
www.youtube.com
September 17, 2025 at 9:00 AM
Lovely talk by Open Software Week participant @ishratz25.bsky.social on the challenges of using @brainglobe.info tools to identify very small regions, in very large images.
Reposted by SWC/GCNU Neuroinformatics Unit
DeMBA (Developmental Mouse Brain Atlas) has now been added to BrainGlobe!
This includes every developmental stage from P4 to P56. Each of these 53 atlases includes MRI, LSFM and STPT templates.
For more details, see the blog:
brainglobe.info/blog/DeMBA
Paper:
doi.org/10.1038/s414...
This includes every developmental stage from P4 to P56. Each of these 53 atlases includes MRI, LSFM and STPT templates.
For more details, see the blog:
brainglobe.info/blog/DeMBA
Paper:
doi.org/10.1038/s414...
September 15, 2025 at 2:40 PM
DeMBA (Developmental Mouse Brain Atlas) has now been added to BrainGlobe!
This includes every developmental stage from P4 to P56. Each of these 53 atlases includes MRI, LSFM and STPT templates.
For more details, see the blog:
brainglobe.info/blog/DeMBA
Paper:
doi.org/10.1038/s414...
This includes every developmental stage from P4 to P56. Each of these 53 atlases includes MRI, LSFM and STPT templates.
For more details, see the blog:
brainglobe.info/blog/DeMBA
Paper:
doi.org/10.1038/s414...
In our next guest blog, GSoC participant Saarah Hussain talks about her summer working on @brainglobe.info.
neuroinformatics.dev/blog/gsoc_20...
neuroinformatics.dev/blog/gsoc_20...
September 15, 2025 at 1:36 PM
In our next guest blog, GSoC participant Saarah Hussain talks about her summer working on @brainglobe.info.
neuroinformatics.dev/blog/gsoc_20...
neuroinformatics.dev/blog/gsoc_20...
Reposted by SWC/GCNU Neuroinformatics Unit
Have you built any software using a BrainGlobe package? We would love to feature your tool on our "Software built by the community" page.
Get in touch, we would love to hear about your work!
brainglobe.info/community/ex...
Get in touch, we would love to hear about your work!
brainglobe.info/community/ex...
Software built by the community — BrainGlobe
brainglobe.info
September 15, 2025 at 10:50 AM
Have you built any software using a BrainGlobe package? We would love to feature your tool on our "Software built by the community" page.
Get in touch, we would love to hear about your work!
brainglobe.info/community/ex...
Get in touch, we would love to hear about your work!
brainglobe.info/community/ex...
This summer we took part in Google Summer of Code (GSoC) for the first time. In this guest blog, GSoC participant Shrey Singh talks about working on the datashuttle project.
neuroinformatics.dev/blog/datashu...
neuroinformatics.dev/blog/datashu...
September 15, 2025 at 9:14 AM
This summer we took part in Google Summer of Code (GSoC) for the first time. In this guest blog, GSoC participant Shrey Singh talks about working on the datashuttle project.
neuroinformatics.dev/blog/datashu...
neuroinformatics.dev/blog/datashu...
Reposted by SWC/GCNU Neuroinformatics Unit
Version 2 of the "Enhanced and Unified Mouse Brain Atlas" has now been added to BrainGlobe. This popular atlas has been updated with corrected annotations and an isotropic 20um reference volume.
Thanks to Pavel Vychyk for adding this atlas!
brainglobe.info/blog/kim-iso...
Thanks to Pavel Vychyk for adding this atlas!
brainglobe.info/blog/kim-iso...
September 12, 2025 at 10:07 AM
Version 2 of the "Enhanced and Unified Mouse Brain Atlas" has now been added to BrainGlobe. This popular atlas has been updated with corrected annotations and an isotropic 20um reference volume.
Thanks to Pavel Vychyk for adding this atlas!
brainglobe.info/blog/kim-iso...
Thanks to Pavel Vychyk for adding this atlas!
brainglobe.info/blog/kim-iso...
New guest blog by @marcodv.bsky.social about our open software summer school, held at @sainsburywellcome.bsky.social.
neuroinformatics.dev/blog/perspec...
Stay tuned for information about next years event, which will be bigger and better!
neuroinformatics.dev/blog/perspec...
Stay tuned for information about next years event, which will be bigger and better!
September 12, 2025 at 9:36 AM
New guest blog by @marcodv.bsky.social about our open software summer school, held at @sainsburywellcome.bsky.social.
neuroinformatics.dev/blog/perspec...
Stay tuned for information about next years event, which will be bigger and better!
neuroinformatics.dev/blog/perspec...
Stay tuned for information about next years event, which will be bigger and better!
Reposted by SWC/GCNU Neuroinformatics Unit
First day of work back in @istaustria-iof.bsky.social after 2 weeks exchange with the guys at @neuroinformatics.dev. Still processing all the ideas and new information in my brain, I hope to be able to write them down and make something concrete out of all of it very soon!
What an experience, great people, great material and great environment. Thanks for making this possible and I hope this becomes a well established yearly tradition @neuroinformatics.dev
Thank you to everyone who came to Open Software Week. We had a great time, and we hope you all left with new knowledge, ideas or collaborations.
#niu_osw
#niu_osw
August 25, 2025 at 6:13 AM
First day of work back in @istaustria-iof.bsky.social after 2 weeks exchange with the guys at @neuroinformatics.dev. Still processing all the ideas and new information in my brain, I hope to be able to write them down and make something concrete out of all of it very soon!
Reposted by SWC/GCNU Neuroinformatics Unit
Last week I took part in the @neuroinformatics.dev Open Software Week in London. There were great workshops on collaborative coding and deep learning methods for motion tracking. Big thanks to all the organisers, I'd love to be back next year! #niu_osw
On the "Animals in Motion" track, students are learning how to use the Python package, movement, to analyse pose tracks.
Today's course materials: animals-in-motion.neuroinformatics.dev/latest/04-mo...
#niu_osw
Today's course materials: animals-in-motion.neuroinformatics.dev/latest/04-mo...
#niu_osw
August 18, 2025 at 8:32 AM
Last week I took part in the @neuroinformatics.dev Open Software Week in London. There were great workshops on collaborative coding and deep learning methods for motion tracking. Big thanks to all the organisers, I'd love to be back next year! #niu_osw
Reposted by SWC/GCNU Neuroinformatics Unit
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/
All course materials, including hands-on coding exercises, are freely available as an online book:
🔗 animals-in-motion.neuroinformatics.dev/latest/
August 18, 2025 at 6:05 PM
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/
All course materials, including hands-on coding exercises, are freely available as an online book:
🔗 animals-in-motion.neuroinformatics.dev/latest/