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...

I enjoyed chatting with Peter about my @softwaresaved.bsky.social fellowship. Tune in for the backstory behind animals-in-motion.neuroinformatics.dev and @neuroinformatics.dev 's "Open Software Week". PS: Code for Thought is a great podcast to follow if you’re into research software.

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...

This summer we took part in Google Summer of Code (GSoC) for the first time. In this guest blog, GSoC participant Shrey Singh talks about working on the datashuttle project. neuroinformatics.dev/blog/datashu...

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!

First day of work back in @istaustria-iof.bsky.social after 2 weeks exchange with the guys at @neuroinformatics.dev. Still processing all the ideas and new information in my brain, I hope to be able to write them down and make something concrete out of all of it very soon!

Last week I took part in the @neuroinformatics.dev Open Software Week in London. There were great workshops on collaborative coding and deep learning methods for motion tracking. Big thanks to all the organisers, I'd love to be back next year! #niu_osw

Had a blast teaching "Animals in Motion" last week, together with my @neuroinformatics.dev colleagues. All course materials, including hands-on coding exercises, are freely available as an online book: 🔗 animals-in-motion.neuroinformatics.dev/latest/

What an experience, great people, great material and great environment. Thanks for making this possible and I hope this becomes a well established yearly tradition @neuroinformatics.dev

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 final day of Open Software Week is the Hackday! Participants are working on applying existing tools to new data, further developing NIU software and improving documentation. #niu_osw

Day 4 of Open Software Week continues with both the "Big Imaging Data" track, and a workshop on "Collaborative Coding with Git". #niu_osw

Open Software Week continues with a careers clinic with a panel discussion from diverse Research Technology Professionals with a background in life sciences. Panellists are Mayo Faulkner, Vicki Yorke-Edwards, Batool Almarzouq, Laura Porta & Jonas Hartmann. #niu_osw

Day 4 of Open Software Week begins with the "Big Imaging Data" track. Participants will learn how to handle big microscopy data with open-source software and build connections between the imaging and software engineering community. Today's material: neuroinformatics.dev/slides-big-i... #niu_osw

Day 3 of open software week #OSW by @neuroinformatics.dev! Super cool demos and time to dig deep into 2D and 3D visualizations of the mapped atlas with cells, segmented structures, and annotations. You can even make movies or html exports! Looking forward to the big data track next!

Just discovered 🧠 #NeuroBlueprint: a lightweight, standardized project structure for organizing neuroscience data. Simple, #BIDS inspired, and automatable. Designed to make #collaboration and #reproducibility in #neuroscience easier✌️ 🌍 https://neuroblueprint.neuroinformatics.dev#NeuroBlueprint

On the "Animals in Motion" track, students are learning how to use the Python package, movement, to analyse pose tracks. Today's course materials: animals-in-motion.neuroinformatics.dev/latest/04-mo... #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

The Animals in Motion track started with a survey of participants to understand the field they work in, and the models they study. Lots of different fields want to track animals! #niu_osw

Open Software Week is only possible due to the generous funding of @sainsburywellcome.bsky.social, @society-rse.org, softwaresaved.bsky.social and @aibio-uk.bsky.social. Thank you! #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

I'm headed to London where in the next two weeks I'll learn from the amazing people at @neuroinformatics.dev! I'm super excited for the open software week #OSW to learn all about large image data handling, @brainglobe.info and much more!

Version 0.5.0 of fancylog released! This version adds more comprensive logging of the local Python environment, including the versions of all installed packages. To update: "pip install fancylog -U" Release notes: github.com/neuroinforma...

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...

Version 0.9.0 of movement released! This version adds a new feature to compute kinetic energy features, and adds a gallery of examples in the API documentation. To update: "pip install movement -U" Release notes: github.com/neuroinforma...

SWC Senior Research Software Engineer Laura Porta is co-organising a free event for carers, people living with dementia and artists. 📍Community Sauna Baths, London E9 📅6 Aug Info and register ⤵️ lu.ma/dqvjka90

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...

New blog post: derotation is a Python package for correcting motion artifacts in rotating multiphoton movies. It applies line-by-line correction, estimates the center of rotation, and integrates with downstream tools like Suite2p. Read more: neuroinformatics.dev/blog/derotat...

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!

Version 0.8.0 of movement released! This version comes with support for bounding boxes in the napari plugin. Release notes: github.com/neuroinforma...

Open Software Week outcome emails will be sent over the next two weeks. Please make sure to check your spam if you've applied.

🐾 Exciting news from the Behaviour Forum: Meet movement, a powerful Python package for animal behavior research! 🚀 Developed with the community in mind, it’s here to simplify body movement analysis. Let’s dive in! 👇 #AnimalBehavior #OpenSource #Python

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...

Version 0.7.1 of movement released! In addition to import/export from SLEAP, DLC, LightningPose, Anipose, VIA & NWB, movement now has a native format for saving data. Saving to netCDF allows you to preserve the complete state of your analysis, including all variables, coordinates, and attributes.

One week left to apply to our "Open Software Week". Join us for a week of training, community building and hacking on open-source neuroscience software tools. Includes animal behaviour, neuroanatomy and large data handling. Travel stipends available. neuroinformatics.dev/open-softwar...

Version 0.7.0 of movement released! This version adds support for loading and saving pose data in Neurodata Without Borders (@nwb.org) format, using the ndx-pose extension. We hope this will make it easier to use movement within larger data analysis pipelines. movement.neuroinformatics.dev

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...

Isla Duporge, Sofia Minano, Nikoloz Sirmpilatze, Igor Tatarnikov, Scott Wolf, Adam L. Tyson, Daniel Rubenstein Tracking the Flight: Exploring a Computational Framework for Analyzing Escape Responses in Plains Zebra (Equus quagga) https://arxiv.org/abs/2505.16882

To answer a common question about our Open Software Week, the event (and travel stipends) are open to everyone, there are no limits as to who can 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.

🟢 Applications are now open for two SSI Fellows' events: Niko Sirmpilatze's "Animals in Motion" and Alessandro Felder's "Big Imaging Data". These events will take place during the NIU Open Software Week running between Monday 11 and Friday 15 August in London. www.software.ac.uk/news/ssi-fel...

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.

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/