Software engineer and neuroscientist. Head research engineer at UCL SWC/GCNU. Open source developer, lead @neuroinformatics & @brainglobe.
Runner and cyclist. Sandwich enthusiast.
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: https://brainglobe.info/blog/CCFv3BBP.html
Original paper: https://doi.org/10.1162/imag_a_00565
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.
Version 0.7.0 of movement released!
This version adds support for loading and saving pose data in Neurodata Without Borders (NWB) format, using the ndx-pose extension.
We hope this will make it easier to use movement within larger data analysis pipelines.
Join us for the @neuroinformatics 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:
https://neuroinformatics.dev/open-software-week/
Tracking the Flight: Exploring a Computational Framework for Analyzing Escape Responses in Plains Zebra (Equus quagga)
Isla Duporge, Sofia Minano, Nikoloz Sirmpilatze, Igor Tatarnikov, Scott Wolf, Adam L. Tyson, Daniel Rubenstein
https://arxiv.org/abs/2505.16882 https://arxiv.org/pdf/2505.16882 https://arxiv.org/html/2505.16882
arXiv:2505.16882v1 Announce Type: new
Abstract: Ethological research increasingly benefits from the growing affordability and accessibility of drones, which enable the capture of high-resolution footage of animal movement at fine spatial and temporal scales. However, analyzing such footage presents the technical challenge of separating animal movement from drone motion. While non-trivial, computer vision techniques such as image registration and Structure-from-Motion (SfM) offer practical solutions. For conservationists, open-source tools that are user-friendly, require minimal setup, and deliver timely results are especially valuable for efficient data interpretation. This study evaluates three approaches: a bioimaging-based registration technique, an SfM pipeline, and a hybrid interpolation method. We apply these to a recorded escape event involving 44 plains zebras, captured in a single drone video. Using the best-performing method, we extract individual trajectories and identify key behavioral patterns: increased alignment (polarization) during escape, a brief widening of spacing just before stopping, and tighter coordination near the group's center. These insights highlight the method's effectiveness and its potential to scale to larger datasets, contributing to broader investigations of collective animal behavior.
Reminder to register for our @neuroinformatics "Open Software Week" this August in London, for some hands-on training and hacking on open-source Python tools for analysing animal motion, whole-brain microscopy (with @brainglobe), or big imaging data.
Spaces are limited but registration and food are "free as in beer". We'll be able to provide travel stipends for several participants, thanks to generous support from @SoftwareSaved @SWC_Neuro @ResearchSoftEng and AIBIO UK.
https://neuroinformatics.dev/open-software-week
#neuroscience #python #opensource
https://mastodon.online/@neuroinformatics/114348660994777557
We’ve received additional funding for our "Open Software Week", so we expect to be able to fully fund the travel and accomodation for most participants outside of London.
Full details:
https://neuroinformatics.dev/open-software-week
Fully funded (including travel and accomodation) BrainGlobe course in London. Applications close June 6th.
Any questions, get in touch.
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.
https://neuroinformatics.dev/open-software-week
Get in touch with any qu's.
As part of this week-long event, I will be hosting a 2-day “Animals in Motion” workshop in London, with the generous support of @SoftwareSaved.
It’s for anyone who wants to get hands-on experience with using open-source software to track animals from video footage and analyse their motion.
Attendance is free of charge, but spots are limited. A small number of travel stipends are available. More info at https://neuroinformatics.dev/open-software-week/
#neuroscience #behavior #ethology #neuroethology #python
From: @neuroinformatics
https://mastodon.online/@neuroinformatics/114348660994777557
Please come join us in London in August!
A free week-long workshop including training in neuroscience tools and contributing to open-source software.
No cost and travel stipends available.
Full details: https://neuroinformatics.dev/open-software-week
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.
https://neuroinformatics.dev/open-software-week
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If you'd like to learn how to use BrainGlobe, we're part of @neuroinformatics's "Open Source Week" at @SWC_Neuro!
There will be a two-day hands-on BrainGlobe course with a focus on whole-brain image data analysis and visualisation, along with a series of satellite events and a hackday!
Attendance is free and travel stipends are available.
Full details and application:
👨🏫 SSI Fellows Alessandro Felder and @niksirbi will be mentoring at the upcoming Google Summer of Code (GSoC) as part of the @neuroinformatics team. Find out more at https://www.software.ac.uk/news/ssi-fellows-google-summer-code
movement v0.5.0 is now out. Includes a new ROI plotting method and an additional example.
Full details:
https://movement.neuroinformatics.dev
A new high-resolution 3D brain atlas for the Eurasian blackcap is now available via @brainglobe This new, open-source map will support research into magnetoreception, migration, and navigation 🧭
Blog ⤵️
https://www.sainsburywellcome.org/web/blog/mapping-migratory-bird-brain
Preprint⤵️
https://www.biorxiv.org/content/10.1101/2025.03.04.641293v1
A non-model organism “renaissance” has been discussed, 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!
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: https://brainglobe.info/documentation/brainglobe-workflows/brainmapper
Two new versions of movement (0.3.0 & 0.4.0) released last week!
Highlights include:
- A new general rolling_filter() function that allows you to compute rolling window mean/median/min/max.
- GUI improvements, including the ability to load tracked bounding boxes.
Full documentation:
https://movement.neuroinformatics.dev
