Adam Tyson
@adamltyson.com
Head Research Engineer at Sainsbury Wellcome Centre, UCL. I lead @neuroinformatics.dev & @brainglobe.info. We build open source software for neuroscience and machine learning.
Runner, cyclist, sandwich enthusiast.
https://adamltyson.com
Runner, cyclist, sandwich enthusiast.
https://adamltyson.com
Reposted by Adam Tyson
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".
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
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".
Reposted by Adam Tyson
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 Adam Tyson
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 4, 2025 at 2:05 PM
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
Reposted by Adam Tyson
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/...
Reposted by Adam Tyson
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 Adam Tyson
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 Adam Tyson
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...
Reposted by Adam Tyson
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
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
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
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
Reposted by Adam Tyson
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 Adam Tyson
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 11:45 AM
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
Reposted by Adam Tyson
Do you use napari and love @xarray.bsky.social? Or use Xarray but cry when napari ignores the axis names? Read how we will improve this in the future! 🤝
napari.org/island-dispa...
Co-authored by @ianhi.bsky.social and @timmonko.bsky.social, powered by the @scipyconf.bsky.social sprints!
napari.org/island-dispa...
Co-authored by @ianhi.bsky.social and @timmonko.bsky.social, powered by the @scipyconf.bsky.social sprints!
Xarray ❤️ napari — napari blog documentation
napari.org
October 24, 2025 at 3:34 PM
Do you use napari and love @xarray.bsky.social? Or use Xarray but cry when napari ignores the axis names? Read how we will improve this in the future! 🤝
napari.org/island-dispa...
Co-authored by @ianhi.bsky.social and @timmonko.bsky.social, powered by the @scipyconf.bsky.social sprints!
napari.org/island-dispa...
Co-authored by @ianhi.bsky.social and @timmonko.bsky.social, powered by the @scipyconf.bsky.social sprints!
Reposted by Adam Tyson
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help […]
Original post on fosstodon.org
fosstodon.org
October 21, 2025 at 2:34 PM
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help […]
Reposted by Adam Tyson
Very excited about this project: we believe that 3D anatomical atlases have a huge potential for developmental biology. As a starting point, we made the first ever Drosophila wing disc atlas!
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 5:15 PM
Very excited about this project: we believe that 3D anatomical atlases have a huge potential for developmental biology. As a starting point, we made the first ever Drosophila wing disc atlas!
Reposted by Adam Tyson
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 Adam Tyson
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 Adam Tyson
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 Adam Tyson
🏆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
Reposted by Adam Tyson
I cannot understand what these people think the purpose of human life is?
It is *not* "pursue joy, deal justly, love well, try to understand as much and see as much of this beautiful world and of the deepness, richness and variety of human culture and experience as you can before you die"?
It is *not* "pursue joy, deal justly, love well, try to understand as much and see as much of this beautiful world and of the deepness, richness and variety of human culture and experience as you can before you die"?
How is this repeatedly made into a policy issue - by *all* parties - when the blunt fact of the matter is that grown adults who are obliged to pay for their own education, and relentlessly pursued to repay their loans, should be able to study whatever the fuck they want.
October 8, 2025 at 8:22 AM
I cannot understand what these people think the purpose of human life is?
It is *not* "pursue joy, deal justly, love well, try to understand as much and see as much of this beautiful world and of the deepness, richness and variety of human culture and experience as you can before you die"?
It is *not* "pursue joy, deal justly, love well, try to understand as much and see as much of this beautiful world and of the deepness, richness and variety of human culture and experience as you can before you die"?
Reposted by Adam Tyson
Join the new plugin sustainability initiative!
Everyone is invited to fill out this interest form: forms.gle/iwX6P4tuooHK...
Follow along with initial discussion on Zulip: napari.zulipchat.com#narrow/chann...
The first zoom meeting will be this coming week: napari.org/stable/commu...
Everyone is invited to fill out this interest form: forms.gle/iwX6P4tuooHK...
Follow along with initial discussion on Zulip: napari.zulipchat.com#narrow/chann...
The first zoom meeting will be this coming week: napari.org/stable/commu...
Meeting schedule
We hold regular meetings, the timings of which are available on our public calendar. If you are using napari or interested in how napari could be used in your work, please join one of our regular comm...
napari.org
October 6, 2025 at 3:57 AM
Join the new plugin sustainability initiative!
Everyone is invited to fill out this interest form: forms.gle/iwX6P4tuooHK...
Follow along with initial discussion on Zulip: napari.zulipchat.com#narrow/chann...
The first zoom meeting will be this coming week: napari.org/stable/commu...
Everyone is invited to fill out this interest form: forms.gle/iwX6P4tuooHK...
Follow along with initial discussion on Zulip: napari.zulipchat.com#narrow/chann...
The first zoom meeting will be this coming week: napari.org/stable/commu...
Reposted by Adam Tyson
The provisional program for The 6th Crick Bioimage Analysis Symposium (#CBIAS2025) is live!
Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.
Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.
Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
September 23, 2025 at 12:06 PM
The provisional program for The 6th Crick Bioimage Analysis Symposium (#CBIAS2025) is live!
Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.
Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.
Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
Reposted by Adam Tyson
updated version of our paper on bayesian modelling for whole-brain cell count data: elifesciences.org/reviewed-pre....
People spend 1-2 years collecting these kinds of gene-expression/anatomy/IEG data... what's another 1-2 months learning + applying Bayes to get more stats bang for your buck 😍
People spend 1-2 years collecting these kinds of gene-expression/anatomy/IEG data... what's another 1-2 months learning + applying Bayes to get more stats bang for your buck 😍
September 19, 2025 at 6:34 PM
updated version of our paper on bayesian modelling for whole-brain cell count data: elifesciences.org/reviewed-pre....
People spend 1-2 years collecting these kinds of gene-expression/anatomy/IEG data... what's another 1-2 months learning + applying Bayes to get more stats bang for your buck 😍
People spend 1-2 years collecting these kinds of gene-expression/anatomy/IEG data... what's another 1-2 months learning + applying Bayes to get more stats bang for your buck 😍
Reposted by Adam Tyson
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 Adam Tyson
Thrilled to share the first story from my postdoc! 🎉 A wonderful experiment + simulations collaboration. In the Drosophila wing, we find that 3D cell shapes affect signalling range and fine-tune developmental patterning www.biorxiv.org/content/10.1... Thread below ⬇️
August 11, 2025 at 1:18 PM
Thrilled to share the first story from my postdoc! 🎉 A wonderful experiment + simulations collaboration. In the Drosophila wing, we find that 3D cell shapes affect signalling range and fine-tune developmental patterning www.biorxiv.org/content/10.1... Thread below ⬇️
Reposted by Adam Tyson
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 Adam Tyson
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...