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...

075

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

042

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...

032

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...

064

Reposted by SWC/GCNU Neuroinformatics Unit

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.

094

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

040

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

Day 3 ends with our second careers clinic, again focussing on non-traditional career paths within research. Thanks to our moderator Niko Sirmpilatze and panellists Ines Perpetuo, Olivier Winter, Stefania Marcotti, and Igor Tatarnikov. #NIU_OSSS_26

000

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

151

Reposted by SWC/GCNU Neuroinformatics Unit

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

1135

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

050

Reposted by SWC/GCNU Neuroinformatics Unit

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...

0144

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

091

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

070

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

070

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

161

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

Day 3 ended with a careers clinic, with a focus on non-traditional roles in research. Special thanks to Ines Perpetuo, Kimberly Meechan and James Bednar for joining us as panellists. #NIU_OSSS_26

011

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

Day 3 continues, with the Animals in Motion track applying the behavioural analysis techniques learnt to real-world data. In the Large Array Data track, guest lecturer James Bednar from Anaconda introducing HoloViz for interactive large data visualisation. #NIU_OSSS_26

120

Reposted by SWC/GCNU Neuroinformatics Unit

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...

092

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

160

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

Day 2 finished with a fantastic guest lecture by Kenneth Harris on spurious correlations in neuroscience. #NIU_OSSS_26

030

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

Day 2 continues, with the Animals in Motion track learning how to use movement (movement.neuroinformatics.dev) and the Large Array Data track being introduced to parallel processing with Dask. #NIU_OSSS_26

120

Reposted by SWC/GCNU Neuroinformatics Unit

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...

082

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

181

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

030

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

A survey of the Animals in Motion participants, show hows broad the field of animal behaviour is. 23 participants, but 15 fields studying 16 species! #NIU_OSSS_26

050

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

Large Array Data starts with a practical to explore the limits of working with data in memory. #NIU_OSSS_26

120

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

Animals in Motion starts with Sofía Miñano with a deep learning primer for computer vision. #NIU_OSSS_26

120

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

163

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 16/08/2026

Very nice. We’re starting to collate a list of tools that work with the NeuroBlueprint data structure, so this is good to know!

010

Reposted by SWC/GCNU Neuroinformatics Unit

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...

062

Reposted by SWC/GCNU Neuroinformatics Unit

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.

0207

Reposted by SWC/GCNU Neuroinformatics Unit

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.

061

Reposted by SWC/GCNU Neuroinformatics Unit

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.

051

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

0137

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

0134

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".

084

Reposted by SWC/GCNU Neuroinformatics Unit

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...

0106

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.

041

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

151

Reposted by SWC/GCNU Neuroinformatics Unit

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

0138

Reposted by SWC/GCNU Neuroinformatics Unit

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.

1142

Reposted by SWC/GCNU Neuroinformatics Unit

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.

185

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.

052

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

If anyone else would like to get involved, please get in touch!

000

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...

041

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

We are building software tools to make it easier and faster to create high quality anatomical atlases for any species. If this sounds interesting to you, please get in touch.

130

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...

162