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.

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...

In our next guest blog, GSoC participant Saarah Hussain talks about her summer working on @brainglobe.info. neuroinformatics.dev/blog/gsoc_20...

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...

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...

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!

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

The third day of Open Software Week is underway. On the @brainglobe.info track, students are learning how to use the BrainGlobe Python ecosystem to write their own scripts. Starting with creating visualisations using brainglobe-heatmap: brainglobe.info/documentatio... #niu_osw

The BrainGlobe track started with an introduction to image analysis with @napari.org, and then tutorials on how to use @brainglobe.info to register data to atlases, and how to detect cells in whole-brain microscopy images. All our tutorials are online: brainglobe.info/tutorials #niu_osw

Second day of Open Software Week starts soon! Today we split into two parallel tracks: Animals in Motion: Using open source tools to track and analyse animal motion from videos BrainGlobe: Using the @brainglobe.info ecosystem of tools to process and analyse whole-brain microscopy images #niu_osw

Today is the first day of the Neuroinformatics Unit Open Software Week, bringing together researchers from around the world for a week of training and collaborating on open source neuroscience software. First day is a Python programming workshop. neuroinformatics.dev/open-softwar... #niu_osw

Version 2.3.0 of the BrainGlobe Atlas API released! Nothing exciting, but lots of minor bug fixes. This release included work by 11 contributors. Thanks to everyone in the community for their hard work. To update: "pip install brainglobe-atlasapi -U" Release notes: github.com/brainglobe/b...

The brain atlas of the bumblebee Bombus impatiens created by the @kocherlab.bsky.social is now part of BrainGlobe! This is our first insect brain atlas. Thanks to Scott Wolf for adding it! More details: brainglobe.info/blog/bee-atl... Original paper: doi.org/10.1016/j.cu...

Hey, it's out! doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:

A new version of datashuttle is out! Datashuttle helps organise neuroscience experiments by automating folder creation and data transfer. Version 0.7.0 adds automatic validation, extends the available datatypes and several other improvements. Check it out at datashuttle.neuroinformatics.dev!

BrainGlobe has a new atlas, the "CCFv3 augmented mouse atlas"! This atlas is an extended version of the CCFv3, designed to cover the rostral and caudal tips of the mouse brain and includes Nissl templates. More details: brainglobe.info/blog/CCFv3BB... Original paper: doi.org/10.1162/imag...

Join us for the @neuroinformatics.dev Open Software Week at SWC this summer! This event will bring together researchers, developers and users of open-source software for some hands-on training, community-building and hacking. Find out more and apply: neuroinformatics.dev/open-softwar...

Still a few weeks to register for some hands-on training and hacking on open-source tools for analysing animal motion, whole-brain microscopy with @brainglobe.info, and big imaging data. 🧠📈 Aug 11-15 at @sainsburywellcome.bsky.social in London. "Free as in beer" and travel stipends available.

Fully funded (including travel and accomodation) BrainGlobe course in London. Applications close June 6th. Any questions, get in touch.

We’ve received additional funding for this, so we expect to be able to fully fund the travel and accomodation for most participants outside of London.

Applications to our "Open Software Week" close on June 6th. Apply now for a week of training, community building and hacking on open-source neuroscience software tools. Stipends available for travel/accomodation etc. neuroinformatics.dev/open-softwar... Get in touch with any qu's.

If you'd like to learn how to use BrainGlobe, we're part of @neuroinformatics.dev's "Open Source Week". London, UK, August 11-15.

We're excited to announce the Neuroinformatics Unit Open Source Week, August 11-15 2025 in London, UK. Bringing together researchers and developers of open-source software for training, community-building and hacking. No cost and travel stipends available. neuroinformatics.dev/open-softwar... 1/

The second is about @brainglobe.info. This course is designed for researchers and students interested in learning about open-source tools for analysing and visualising whole-brain microscopy data. 3/

New version of brainglobe-heatmap (v0.6.0) released, with automated region annotations. github.com/brainglobe/b...

A new high-resolution 3D brain atlas for the Eurasian blackcap is now available via @brainglobe.info. This new, open-source map will support research into magnetoreception, migration, and navigation 🧭 Blog ⤵️ www.sainsburywellcome.org/web/blog/map... Preprint⤵️ www.biorxiv.org/content/10.1...

There may be a non-model organism “renaissance”, but these fields also need experimental tools. Our new blog describes our work building brain atlases for novel species. Get in touch if you're interested in making an atlas for the species you study! brainglobe.info/blog/unchart...

New version of brainglobe-workflows released (v1.4.1)! Includes a fix for a brainmapper bug in which the analysis results for users with 3D tiffs was incorrect. Full documentation: brainglobe.info/documentatio...

New preprint! We built a 3D brain atlas for the migratory and magnetoreceptive Eurasian blackcap. The atlas is available in @brainglobe.info, and is hopefully the first of many! Full details: brainglobe.info/blackcap Preprint: www.biorxiv.org/content/10.1... Short thread:

We're branching out. Rather than just packaging existing atlases, we've started creating new ones! Get in touch if you're interested in collaborating to create a new high-quality brain atlas. brainglobe.info/contact.html

BrainGlobe has a new atlas, for the dwarf cuttlefish (Sepia bandensis). Thanks to UCL student Jung Woo Kim for packaging this atlas! For more details about this (and the rest of BrainGlobe), please see the blog: brainglobe.info/blog/cuttlef... Original paper: doi.org/10.1016/j.cu...

BrainGlobe has a new (c)atlas, for the domestic cat, Felis catus. 🐱 For more details about this (and the rest of BrainGlobe), please see the blog: brainglobe.info/blog/cat-atl...

Excited to announce that we will be taking part in the Google Summer of Code this year! If you'd like to get paid to contribute to BrainGlobe, please get in touch. Applications will be accepted via @neuroinformatics.dev. Full details here: neuroinformatics.dev/get-involved...

Excited to announce that we will be taking part in the Google Summer of Code this year! If you'd like to get paid to contribute to open-source neuroscience software, please get in touch. Full details here: neuroinformatics.dev/get-involved...

Nice package to load BrainGlobe atlases into Blender - "BlenderBrain". github.com/ArtemKirsano...

BrainGlobe has three new mouse brain atlases including: - Multimodal (LSFM & MRI) developmental atlas from Yongsoo Kim's lab - Multimodal (LSFM & MRI) adult atlas from Gubra - High-resolution Australian mouse brain atlas (MRI) See the blog for more details: brainglobe.info/blog/mouse-a...

New version of brainglobe-space released (v1.0.3). Includes small changes including updating supported Python versions. Full details: github.com/brainglobe/b...

New version of morphapi released (v0.3.1) with a minor bug fix. Full details: github.com/brainglobe/m...

New release of the BrainGlobe Atlas API (v2.1.0). Some small changes, and support for custom offline atlases. Full details: github.com/brainglobe/b...

New release of brainglobe-heatmap (v0.5.5) which contains a small bug fix. Full details: github.com/brainglobe/b...

New cellfinder version release (v1.4.1) which contains a small bug fix. Full details: github.com/brainglobe/c...

Excellent paper that makes great use of a not very well-known BrainGlobe tool to make many of the figures, brainglobe-heatmap: brainglobe.info/documentatio...

BrainGlobe has a new atlas, the first non-human primate, the gray mouse lemur (Microcebus murinus). For more details about this (and the rest of BrainGlobe), please see the blog: brainglobe.info/blog/mouse-l...

BrainGlobe has a new atlas, the prairie vole! For more details see the blog: brainglobe.info/blog/prairie... Original paper: doi.org/10.7554/eLif...

BrainGlobe has a new atlas, the Axolotl (Ambystoma mexicanum)! For more details see the blog: brainglobe.info/blog/axolotl... Original paper: doi.org/10.1038/s415...

Nice tutorial on how to combine BrainGlobe and BiaPy to detect cells in whole brain microscopy images. We're always interested in ways to make our software interoperable with other tools. biapy.readthedocs.io/en/latest/tu...

BrainGlobe now includes an atlas with barrel column annotations from Bolaños-­Puchet & Teska et al. Full details on the blog: brainglobe.info/blog/barrel-... Thanks to Axel Bisi for bringing this to BrainGlobe! Original paper: doi.org/10.1162/imag...

We've just released the "brainmapper" widget allowing analysis of cellular distributions in whole-brain microscopy images entirely within napari. Full details available on the blog: brainglobe.info/blog/brainma...

We've added a new atlas - the blind Mexican cavefish, Astyanax mexicanus. More details on the blog: brainglobe.info/blog/cavefis...

Nice piece about our team featured on the Sainsbury Wellcome Centre Blog. www.sainsburywellcome.org/web/blog/neu...