SWC/GCNU Neuroinformatics Unit
@neuroinformatics
Research Software Engineering team at the Sainsbury Wellcome Centre and Gatsby Computational Neuroscience Unit, UCL. We build open source software for neuroscience and machine learning. Posts by @adamltyson.com
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
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
The last day of the first week is underway! Everyone is busy working on their collaboration projects. #NIU_OSSS_26
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
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
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
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
Day 2 finished with a fantastic guest lecture by Kenneth Harris on spurious correlations in neuroscience. #NIU_OSSS_26
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
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
Day 1 of our summer school ended with a symposium. Lots of fantastic science, from a vast array of fields. #NIU_OSSS_26
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
Large Array Data starts with a practical to explore the limits of working with data in memory. #NIU_OSSS_26
Animals in Motion starts with Sofía Miñano with a deep learning primer for computer vision. #NIU_OSSS_26
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
The Neuroinformatics Unit is going to #FENS2026. Come and chat to us if you're interested in open source neuroscience software!
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
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...
Introducing driftplots—a tool for creating customisable, interactive drift maps from Kilosort or @spikeinterface.bsky.social output. Read more: driftplots.neuroinformatics.dev
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...
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...
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
Find out more about movement at movement.neuroinformatics.dev
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...
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
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
Do you want to spend the summer being paid to contribute to open source neuroscience software? We are taking part in Google Summer of Code again, offering paid, remote placements to work on one of our tools. Open to (nearly) everyone worldwide. More details: neuroinformatics.dev/get-involved...
Applications to our summer school have been extended for two weeks! If you want to learn about open-source tools for neuroscience, please join us in London this August. Deadline Feb 15th. Full details: neuroinformatics.dev/open-softwar...
Great new guest blog post by Pille Wetterauer and @jyoti-bhogal.bsky.social about their summer school project to extract a pose estimation skeleton for C. elegans. neuroinformatics.dev/blog/worms_o...
Alongside this new version, Carlo Castoldi wrote a blogpost outlining the changes to how movement calculates displacement. movement.neuroinformatics.dev/latest/blog/...