The provisional program for The 6th Crick Bioimage Analysis Symposium (#CBIAS2025) is live! Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions. Space is limited - register now! www.crick.ac.uk/whats-on/cri...

updated version of our paper on bayesian modelling for whole-brain cell count data: elifesciences.org/reviewed-pre.... People spend 1-2 years collecting these kinds of gene-expression/anatomy/IEG data... what's another 1-2 months learning + applying Bayes to get more stats bang for your buck 😍

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...

Thrilled to share the first story from my postdoc! 🎉 A wonderful experiment + simulations collaboration. In the Drosophila wing, we find that 3D cell shapes affect signalling range and fine-tune developmental patterning www.biorxiv.org/content/10.1... Thread below ⬇️

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...

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...

Want to enhance your image analysis skills with napari? We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data. 🕒 Applications close on 15 September. Learn more and apply 👇 www.crick.ac.uk/whats-on/cbi...

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!

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...

BIIG seminars are back! 🎉 12-1pm on 12th September: - Kaixiang Shuai (LMCB, UCL): Creating the first Drosophila imaginal wing disc atlas - Aikta Sharma (UCL Mechanical Engineering): Predicting Osteoarthritis in the Tibial Epiphysis with Synchrotron X-ray CT and Digital Volume Correlation

Last few days to submit an abstract for #CBIAS2025 (deadline 31/08)! We invite submissions on all topics related to #bioimageanalysis, from new software tools to discoveries made using existing methods. Early career researchers are especially encouraged to submit! www.crick.ac.uk/whats-on/cri...

ONLY 11 MORE DAYS TO SUBMIT AN ABSTRACT FOR #CBIAS2025!!!

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

Courtney @courtneyl7a7.bsky.social has written a lovely piece on this wonderful community initiative we’ve been running for 5 years at UCL - have a read! And follow @biig-ucl.bsky.social !

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

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

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 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...

Very well deserved. The development of @napari.org is the model we follow with @brainglobe.info & @neuroinformatics.dev.

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...

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!

Special early bird rate registrations for #CBIAS2025 are closing soon, on July 20th! Register early to get your discounted ticket for this year's edition, happening at the Wellcome Trust in London on November 24th and 25th www.crick.ac.uk/whats-on/cri...

More importantly, this is the first movement release with our new logo!

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

🐾 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

🚀 We are excited to share that bombcell is now available in Python! 🐍 Automatically sort your units into good/MUA/noise/non-somatic using quality metrics and interpretable & adjustable classification thresholds. pip install and play around with our toy dataset: 🔗 github.com/Julie-Fabre/...

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

Great chance to join an excellent new lab.

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...

Had a blast at #ASABSpring2025, presenting movement and meeting many enthusiastic early career researchers. If you're into tracking animal movements in videos, do apply for the "Animals in Motion" workshop I'm organising in London this August: neuroinformatics.dev/open-softwar...

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.

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. neuroinformatics.dev/open-softwar... Get in touch with any qu's.

As part of this event, I will be running a 2-day hand-on workshop, for folks that want to use open-source software to study "Animals in Motion". Thanks to the generous support of @softwaresaved.bsky.social & @sainsburywellcome.bsky.social More info at neuroinformatics.dev/open-software-week

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: neuroinformatics.dev/open-softwar...

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/