iiinova — where your digital self keeps evolving

Reposted by SWC/GCNU Neuroinformatics Unit

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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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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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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Pynapple @pynapple.bsky.social · 28/08/2026

Wolf de Wulf (@wulfdewolf.bsky.social) teaching pynapple at the Sainsbury Wellcome Centre’s Open Software Summer School @neuroinformatics.dev ! Students learned to build a reproducible pipeline, starting from raw electrophysiological data and working all the way to answering neuroscience questions.

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 28/08/2026

The last day of the Open Software Summer School is underway. In our final collaboration day, groups are busy trying new tools, analysing data and contributing to open source. #NIU_OSSS_26

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 26/08/2026

Day 3 of Week 2 is underway at our summer school! In the @brainglobe.info track, Igor Tatarnikov is introducing deep learning to analyse whole-brain images. In Extracellular Electrophysiology, Chris Halcrow is teaching the @spikeinterface.bsky.social GUI for visualisation and curation. #NIU_OSSS_26

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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 · 25/08/2026

Day 2 of week 2 ends with our second guest lecture of the summer school. Lucy Collinson from @crick.ac.uk spoke about imaging tissue structure across spatial scales. Lots of beautiful electron microscopy data, and interesting analysis approaches. #NIU_OSSS_26

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SpikeInterface @spikeinterface.bsky.social · 25/08/2026

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...

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 25/08/2026

The second day of Week 2 of our summer school is underway! In the electrophysiology track, Olivier Winter from the @intlbrainlab.bsky.social is introducing recording with neuropixels probes. In the @brainglobe.info track, Harry Carey is talking about brain atlases. #NIU_OSSS_26

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 25/08/2026

Week 2 of the Open Software Summer School has started! This week the two tracks are "Extracellular Electrophysiology" and @brainglobe.info. The first day ended with another excellent symposium, with participants showing off their work. #NIU_OSSS_26

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 21/08/2026

The last day of the first week is underway! Everyone is busy working on their collaboration projects. #NIU_OSSS_26

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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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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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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 19/08/2026

Day 3 of our summer school is underway. In Animals in Motion, participants are being introduced to behavioural segmentation, and in Large Array Data, we are learning how to compress data with Zarr. #NIU_OSSS_26

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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

Day 1 of our summer school ended with a symposium. Lots of fantastic science, from a vast array of fields. #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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BrainGlobe @brainglobe.info · 12/08/2026

A Tawny Dragon brain atlas has been added to BrainGlobe! This lizard has shown great promise for neuroevolutionary research and we hope inclusion of the atlas within BrainGlobe will help researchers understand its brain structure. Read more in the blog: brainglobe.info/blog/tawny-d...

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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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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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BrainGlobe @brainglobe.info · 20/07/2026

Do you use the BrainGlobe Atlas API directly in your work? Have you built a tool on top of BrainGlobe? We will soon release V3 of the API, which changes how brain atlas data is stored and accessed. A release candidate is available for testing, please see our blog: brainglobe.info/blog/atlas-a...

An example of the local and remote directory structure for brainglobe-atlasapi V2 and V3. V2 stores data in large monolithic archives, V3 stores each component separately.

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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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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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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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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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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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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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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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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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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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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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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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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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Niko Sirmpilatze @nikosirmpilatze.com · 09/04/2026

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

youtube.com

movement: a Python toolbox for analysing motion tracking data

YouTube video by COST_TEATIME

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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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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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Niko Sirmpilatze @nikosirmpilatze.com · 17/03/2026

Upcoming talk at TheBehaviourForum.org seminar series. See forum post for details: www.thebehaviourforum.org/t/virtual-wo... Come to see me talk about 'movement', our open-source Python package for analysing motion tracking data.

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

neuroinformatics.dev

Get involved — NIU

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 10/03/2026

Version 0.15.0 of movement released! New features include: - Derivation of bounding boxes from pose tracks - Saving and loading of RoIs via GeoJSON - A new example for scaling pose tracks to real-world coordinates Release notes: github.com/neuroinforma... Docs: movement.neuroinformatics.dev

Screenshots from the new "Scale pose tracks to real-world units" showing the measurement of known lengths in a video.

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 05/03/2026

Are you a neuroscientist with great coding skills, or a software engineer interested in the brain? We are recruiting for a research software engineer to help us build pipelines to process weeks of neural and behavioural recordings from freely moving animals. More details: bit.ly/rse-2026a

Drawing of the "Aeon" project, an open-source platform to study the neural basis of ethological behaviours over naturalistic timescales.

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