SWC/GCNU Neuroinformatics Unit
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neuroinformatics.dev
SWC/GCNU Neuroinformatics Unit
@neuroinformatics.dev
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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.

https://neuroinformatics.dev

Posts by @adamltyson.com
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neuroinformatics.dev
Alongside this new version, Carlo Castoldi wrote a blogpost outlining the changes to how movement calculates displacement.

movement.neuroinformatics.dev/latest/blog/...
Diagram of the previous, and updated implementation of displacement calculations.
November 10, 2025 at 7:24 AM
neuroinformatics.dev
movement v0.11.0 released!

v0.11.0 includes an update on how movement computes displacement vectors and adds support for 3D DLC files.

movement can now also be installed in one line with pip/uv.

More details: github.com/neuroinforma...
An overview of the movement data processing pipeline, from data loading, filtering, viualisation and analysis.
November 10, 2025 at 7:20 AM
neuroinformatics.dev
Save the date! The Open Software Summer School returns August 17-28 2026 in London, U.K.

There will be four separate tracks on animal behaviour, extracellular electrophysiology, anatomy and handling large data.

Applications open Dec 1st.

More details:
neuroinformatics.dev/open-softwar...
The schedule of the open source summer school, showing the four tracks of Animals in Motion, Large array data, BrainGlobe & Extracellular Electrophysiology
October 31, 2025 at 3:25 PM
neuroinformatics.dev
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...
September 19, 2025 at 3:06 PM
neuroinformatics.dev
In our next guest blog, GSoC participant Saarah Hussain talks about her summer working on @brainglobe.info.

neuroinformatics.dev/blog/gsoc_20...
Screenshot of the brainglobe-registration tool Saarah worked on during Google Summer of Code
September 15, 2025 at 1:36 PM
neuroinformatics.dev
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...
The Google Summer of Code and Neuroinformatics logos together
September 15, 2025 at 9:14 AM
neuroinformatics.dev
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!
Some of the summer school participants, gathered after the summer school hackday.
September 12, 2025 at 9:36 AM
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
August 15, 2025 at 8:12 PM
neuroinformatics.dev
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
August 15, 2025 at 9:59 AM
neuroinformatics.dev
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
August 13, 2025 at 10:00 AM
neuroinformatics.dev
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
August 13, 2025 at 9:51 AM
neuroinformatics.dev
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
August 12, 2025 at 3:53 PM
neuroinformatics.dev
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
August 12, 2025 at 11:12 AM
neuroinformatics.dev
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
Open Software Week schedule, showing the three main tracks "Animals in Motion", "BrainGlobe' and"Big Imaging Data".
August 12, 2025 at 7:23 AM
neuroinformatics.dev
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
Open software week attendees in the lecture theatre at the Sainsbury Wellcome Centre, at an "Introduction to Python" workshop
August 11, 2025 at 3:22 PM
neuroinformatics.dev
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...
Image showing a rotated multiphoton image of some cells being derotated by the derotation software.
July 24, 2025 at 3:41 PM
neuroinformatics.dev
Datashuttle automatically creates and validates formatted folder trees for data storage. It also provides data transfer between machines.

Thanks to standardization, it is easy to transfer specific subsets of data (e.g., only the test sessions):

See datashuttle.neuroinformatics.dev for more
July 16, 2025 at 2:34 PM
neuroinformatics.dev
A lack of standardization can cause major headaches. Have you ever spent hours trying to make sense of how a colleague (or your past self) organized a dataset?

Datashuttle implements the NeuroBlueprint format to align projects across researchers

neuroblueprint.neuroinformatics.dev
July 16, 2025 at 2:34 PM
neuroinformatics.dev
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!
July 16, 2025 at 2:34 PM
neuroinformatics.dev
More importantly, this is the first movement release with our new logo!
movement logo, showing the word "movement" within stylised pose tracks
July 8, 2025 at 4:19 PM
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...
Screenshot showing bounding box visualisation in the movement napari plugin.
July 8, 2025 at 4:19 PM
neuroinformatics.dev
More information about input/output is here: movement.neuroinformatics.dev/user_guide/i...

Supported formats below:
June 6, 2025 at 3:39 PM
neuroinformatics.dev
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...
May 30, 2025 at 10:59 AM
neuroinformatics.dev
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.
April 23, 2025 at 8:55 AM
neuroinformatics.dev
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...

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April 16, 2025 at 4:49 PM