iiinova — where your digital self keeps evolving

Reposted by Adam Tyson

BrainGlobe @brainglobe.info · 23/09/2026

An atlas for the Danionella cerebrum fish has been added to BrainGlobe! Read more in the blog: brainglobe.info/blog/danione... Take a look at the atlas with Neuroglancer: neuroglancer-demo.appspot.com#!https://bra...

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 21/09/2026

Our final Google Summer of Code project is by Soumya Snigdha Kundu, who worked to make cellfinder, a cell detection tool in the @brainglobe.info ecosystem, usable with more types of data. Read more in Soumya's blog: neuroinformatics.dev/blog/gsoc_20...

neuroinformatics.dev

GSoC 2026: single-channel support in cellfinder — NIU

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 21/09/2026

Our second Google Summer of Code project is by Varun Singh who worked on improving the maintainability of the @brainglobe.info project. Read more in Varun's blog: neuroinformatics.dev/blog/gsoc_20...

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 21/09/2026

Our Google Summer of Code participants have been writing up their projects. First up, Anna Teruel-Sanchis who built an interactive GUI in @napari.org for correcting pose estimation tracks directly within the movement framework. Read more in Anna's blog: neuroinformatics.dev/blog/gsoc_20...

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BrainGlobe @brainglobe.info · 11/08/2026

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...

A figure illustrating the use of the new BrainGlobe Atlas API. Lazy fetching of components for analysis. To draw the hippocampus inside a transparent brain, V2 pulled a 7.4 GB archive containing every image and every mesh in the atlas. V3 fetches the two meshes the render actually uses, 2.3 MB

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 20/08/2026

Day 4 of our summer school has been a busy one! We ran an introduction to version control with Git and started our project collaborations. The day ends with Niko Sirmpilatze giving a talk on "Trusted by design: set up your research software for community adoption". #NIU_OSSS_26

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napari @napari.org · 20/08/2026

Sizzling Summer Series 4 - global 🌍️ napari 0.9.0 is about ready to fly out the door! ✈️ We would be grateful if you tried out the pre-release: Install into an environment with `pip install "napari[all]>=0.9.0rc1"` or try with uv in a temp environment with `uvx "napari[all]>=0.9.0rc1"`.

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Reposted by Adam Tyson

BrainGlobe @brainglobe.info · 19/08/2026

Nine new developmental rat brain atlases from Duke University have been added to BrainGlobe, covering P0-P80 Read more in the blog: brainglobe.info/blog/duke-de... Take a look at the P0 atlas with Neuroglancer: neuroglancer-demo.appspot.com#!https://bra...

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Reposted by Adam Tyson

BrainGlobe @brainglobe.info · 18/08/2026

The MRI-based, high-resolution Duke Mouse Brain Atlas has been added to BrainGlobe! Read more in our blog: brainglobe.info/blog/duke-mo... View the atlas in Neuroglancer: neuroglancer-demo.appspot.com#!https://bra...

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 18/08/2026

Day 2 of our summer school has started! This morning, in the Animals in Motion track, participants are learning how to use SLEAP for pose estimation, and in Large Array Data, the OME-Zarr spec for storing image data is being introduced. #NIU_OSSS_26

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 17/08/2026

The Neuroinformatics Unit Open Software Summer School starts today! Week one starts with: - Animals in Motion, how to use open source tools to quantify animal behaviour - Large Array Data, working with very large scientific datasets neuroinformatics.dev/open-softwar... #NIU_OSSS_26

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Reposted by Adam Tyson

Fabrizio Musacchio @fabmusacchio.bsky.social · 16/08/2026

Awesome work by @neuroinformatics.dev! #datashuttle is a #Python tool for standardized #DataManagement in #neuroscience. It helps create, validate, & transfer structured project folders, bridging the gap between messy lab-specific folder systems and full standards like #BIDS or #NWB 👌

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Adam Tyson @adamltyson.com · 11/08/2026

Very excited about what the new version of BrainGlobe will enable: faster, more reliable data access, more atlases, web-based tools and streamlined development in the future. Read more in the BrainGlobe blog: brainglobe.info/blog/braingl...

brainglobe.info

brainglobe-atlasapi V3 is here! — BrainGlobe

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Reposted by Adam Tyson

BrainGlobe @brainglobe.info · 05/08/2026

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...

Screenshot of the Neuroglancer preview of the BrainGlobe Eurasian Blackcap atlas.

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Reposted by Adam Tyson

Max Farnworth @maxfarnworth.bsky.social · 23/07/2026

🚨 I am very happy (and relieved!) to announce that I secured Emmy Noether funding by the @dfg.de to start my own group at @unimainz.bsky.social , hosted by Marion Silies & Jakob von Engelhardt in August! 🚨 Website coming soon - open for name/logo suggestions. They better be funny tho!

static.klipy.com

Sophia Petrillo with Megaphone in Golden Girls

ALT: Sophia Petrillo with Megaphone in Golden Girls

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Adam Tyson @adamltyson.com · 20/07/2026

If you use the BrainGlobe Atlas API directly (i.e. not through brainreg, brainrender etc), please test out the new version of the API. V3 should be backwards compatible, but we want to catch any bugs before full release.

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Reposted by Adam Tyson

Aidan Horner @aidanhorner.bsky.social · 16/07/2026

New preprint! Work led by Doug Hardman on the Barkley Marathons. This was a lot of fun, reading lots of rich qualitative data from interviews and reports. Navigating the Barkley Marathons #psychscisky #neuroskyence #cognition 🧪

osf.io

OSF

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BrainGlobe @brainglobe.info · 16/07/2026

Nice Claude skill to create basic neuroanatomical visualisations with BrainGlobe & blender: github.com/SamedVossber... The single prompt "Use the allen mouse brain atlas to create an animation to show primary visual cortex and primary motor cortex" gives:

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 02/07/2026

The Neuroinformatics Unit is going to #FENS2026. Come and chat to us if you're interested in open source neuroscience software!

Neuroinformatics Unit at FENS 2026

PS01-07AM-562 AN OPEN-SOURCE THREE-DIMENSIONAL DIGITAL BRAIN ATLAS OF THE MIGRATORY EURASIAN BLACKCAP
N. Sirmpilatze1, A. Felder1, D. Abdulazhanova2,3, L. Schwigon2,3, I. Tatarnikov1, K. Haase2,3, I. Musielak2,3, T. Margrie1, H. Mouritsen2,3, D. Heyers2,3, A. Tyson1,4, S. Weiler1

PS05-09AM-022 HIGH-RESOLUTION 2-PHOTON MICROSCOPY-BASED RAT BRAIN ATLAS INTEGRATED INTO THE BRAINGLOBE ECOSYSTEM
V.M. Plattner1,2, A. Felder2, N. Sirmpilatze2, A. Akrami1, A. L. Tyson2

PS05-09AM-023 MODERNISING AND EXPANDING BRAINGLOBE’S NEUROANATOMICAL ATLAS INFRASTRUCTURE
A. Felder1, I. Tatarnikov1, H. Carey1,2, V. Plattner1, N. Sirmpilatze1, A. Tyson1

PS05-09AM-024 MAKING BRAINGLOBE MORE ACCESSIBLE: SUPPORTING PARTIAL BRAIN REGISTRATION AND ACCELERATING HIGH-THROUGHPUT CELL DETECTION
I. Tatarnikov1, A. Felder1, M. Einhorn2, S. Hussain1, N. Sirmpilatze1, A. Tyson1

PS05-09AM-025 PHOTONMOSAIC: A FLEXIBLE, MODULAR AND INTEROPERABLE SOFTWARE FRAMEWORK FOR MULTIPHOTON I

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Reposted by Adam Tyson

Niko Sirmpilatze @nikosirmpilatze.com · 02/07/2026

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!

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Adam Tyson @adamltyson.com · 02/07/2026

If you're at #FENS2026 and want to chat about these projects or any others, please get in touch.

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 16/06/2026

datashuttle is now published in JOSS! A tool to automate the creation, validation & transfer of standardised neuroscience project folders — GUI or Python API. The GUI works on all operating systems, even remotely via SSH! More details: datashuttle.neuroinformatics.dev #neuroscience #openscience

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Reposted by Adam Tyson

Journal of Open Source Software @joss-openjournals.bsky.social · 16/06/2026

Just published in JOSS: 'datashuttle: automated data management for experimental neuroscience' doi.org/10.21105/joss.09642

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 10/06/2026

v0.17.0 of movement released! 🧠🧪 This version includes new path analysis functions along with a number of bug fixes. Importantly there are some small breaking changes, so please read the release notes to see how your code may be affected. More details: github.com/neuroinforma...

Schematic summarising new path analysis functions, including "path straightness", "path deviation" and "directional change".

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Reposted by Adam Tyson

Sepiedeh Keshavarzi @sepikeshavarzi.bsky.social · 21/05/2026

Together with @roozbehkiani.bsky.social and @athenaakrami.bsky.social, we published a Nature correspondence highlighting our open letter’s core message: the academic community must speak out against attacks on academic institutions. doi.org/10.1038/d415... Open access version: rdcu.be/fju9B

doi.org

Support academic institutions under attack

Letter to the Editor

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Reposted by Adam Tyson

BrainGlobe @brainglobe.info · 21/05/2026

As part of this effort, we've just released three new atlases from v2 of the Allen mouse CCF - the brain atlas, fiber tract atlas and developmental brain atlas. Most pipelines have moved to CCFv3, but adding v2 allows atlas comparison and reproducing old analyses. brainglobe.info/blog/ccfv2-a...

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Reposted by Adam Tyson

Kenneth Harris @kenneth-harris.bsky.social · 19/05/2026

New method for identifying the fine transcriptomic types of thousands of neurons recorded in vivo!

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 19/05/2026

Introducing driftplots—a tool for creating customisable, interactive drift maps from Kilosort or @spikeinterface.bsky.social output. Read more: driftplots.neuroinformatics.dev

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 19/05/2026

driftplots is particularly useful for checking probe alignment across sessions (e.g. before unit matching) as well as assessing within-session drift.

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Reposted by Adam Tyson

BrainGlobe @brainglobe.info · 18/05/2026

We've started an effort to bring every 3D (non-human) anatomical atlas that exists into BrainGlobe. Get in touch if there's an atlas we've missed, or you think there's a specific atlas we should prioritise. Read more in our blog: brainglobe.info/blog/the-sys...

brainglobe.info

The Systematic Atlas Packaging Project — BrainGlobe

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Adam Tyson @adamltyson.com · 14/05/2026

Fantastic to see @brainglobe.info recognised. Thank you to everyone who's helped build it, and thank you to the RMS.

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Reposted by Adam Tyson

BrainGlobe @brainglobe.info · 13/05/2026

Great writeup from our collaborators at UCL Advanced Research Computing on our joint work to make building novel 3D brain atlases faster, more reproducible, and accessible to more labs. 🧠 www.ucl.ac.uk/advanced-res...

ucl.ac.uk

BrainGlobe Template Builder

Atlas building is complex and time-consuming. To help the BrainGlobe team meet growing demand, we streamlined the first stage: generating a high-quality, standardised 3D reference template.

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Reposted by Adam Tyson

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 07/05/2026

The Cimini lab is hiring for both postdocs and interns! The postdoc role will cover bioimage analysis projects and educational material creation; the intern will be working on our Bilayers project for helping distribute and access deep learning tools for bioimage analysis. Click below to learn more!

forum.image.sc

Postdoctoral Associate and Data Science Intern roles - Broad Institute, Cambridge MA USA

The Broad Institute Imaging Platform (the team behind CellProfiler, Piximi, and Bilayers) is currently hiring for postdoctoral and intern roles! Postdoc role: we are looking for 1-2 candidates who ha...

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 05/05/2026

We're very excited about this new collaboration with the @intlbrainlab.bsky.social to build general-purpose systems neuroscience software infrastructure for the community.

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 23/04/2026

Movement v0.16.0 released! This version now comes with the ability to draw, save, and load Regions of Interest in the GUI, and load_dataset can now automatically detect the source software. See the release notes for more info and a full list of changes: github.com/neuroinforma...

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Reposted by Adam Tyson

BrainGlobe @brainglobe.info · 23/04/2026

This is the first of many collaborations to build novel anatomical atlases. We want to expand advanced computational anatomy to new fields. If this sounds interesting, get in touch!

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 23/04/2026

New NIU paper in @currentbiology.bsky.social, in collaboration with @neuroweiler.bsky.social and colleagues at the University of Oldenburg. We built the first anatomical atlas for the Eurasian blackcap. Paper: www.cell.com/current-biol... More details: brainglobe.info/projects/bla...

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Niko Sirmpilatze @nikosirmpilatze.com · 20/04/2026

Mapping brains never gets old, especially when the territory is new 🐦🧠🗺️. Loved being drawn into this collaboration by @neuroweiler.bsky.social and learning about birds and their magnetic senses. Stay tuned for more new atlases coming to @brainglobe.info

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Sainsbury Wellcome Centre @sainsburywellcome.bsky.social · 20/04/2026

A migratory bird brain, the Eurasian blackcap, has been mapped for the first time using high-resolution light microscopy. The open-source software tools developed form a foundation for new brain atlases to be built for any species, providing a valuable resource.

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 14/04/2026

Managing neuroscience data just got easier! Datashuttle keeps your research data organised, generating standardised folders and seamlessly transferring data. v0.8.0 is out now and supports Google Drive and AWS storage. Check it out at datashuttle.neuroinformatics.dev

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Adam Tyson @adamltyson.com · 09/04/2026

Last chance to apply for this fantastic workshop! Just before FENS, learn how to analyse neural data from the developers of pynapple and NeMoS.

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 13/03/2026

We have three neuroscience research software engineering jobs available at @sainsburywellcome.bsky.social, two joint with the Advanced Microscopy Facility. All positions start ASAP, funded until Sept 2028 in the first instance. Salary £54-64k. More details: neuroinformatics.dev/get-involved

neuroinformatics.dev

Get involved — NIU

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Society of RSE @society-rse.org · 26/03/2026

Remember to check out our #vacancies page if you are looking for an RSE (or related) role, or if you have one to share. We've currently got jobs at the Sainsbury Wellcome Centre, one at the British Antarctic Survey and one at Forschungszentrum Jülich in Germany. society-rse.org/careers/vaca...

society-rse.org

Vacancies - Society of Research Software Engineering

You can post a vacancy here for any role that involves a significant element of writing software for research, or supports the role of RSEs. Vacancies anywhere in the world are welcome. We have also…

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 26/03/2026

Two weeks left to apply for three research software engineering jobs at the Sainsbury Wellcome Centre. Closing date April 12th, salary £54-64k For more details see: neuroinformatics.dev/get-involved #neuroscience #rse

neuroinformatics.dev

Get involved — NIU

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 17/03/2026

Don't miss NIU Senior Research Software Engineer @nikosirmpilatze.com talking about our Python package for behavioural quantification, movement. April 2nd, 12h30-14h00 CET. Online on Zoom, registration needed: helsinki.zoom.us/meeting/regi...

Poster advertising the talk, with a photo of the speaker.

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Reposted by Adam Tyson

BrainGlobe @brainglobe.info · 17/03/2026

BrainGlobe has a new roadmap! Somewhat overdue, the March 2026 roadmap summarises our recent progress, and our priorities for the coming year. Read more: brainglobe.info/community/ro...

An illustration of many of the atlases supported by BrainGlobe.

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Reposted by Adam Tyson

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 17/03/2026

The deadline for all these positions is now April 12th. Please do not be put off by the "Senior" in the job title. We have hired people at different career stages into roles at this grade, what matters is whether you can do the job!

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Adam Tyson @adamltyson.com · 16/03/2026

Such a fantastic idea, and by the right people to make this work.

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