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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 5d

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 5d

A new version of fancylog is released (v0.6.0). In this version, the “program” variable passed to the logger has been deprecated in favour of “package”.

This is a breaking change, and support for “program” will be removed in v0.7.0.

github.com/neuroinforma...

Release v0.6.0 · neuroinformatics-unit/fancylog

What's Changed rename program to package by @AlexandroBerumen in #60 New Contributors @AlexandroBerumen made their first contribution in #60 Full Changelog: v0.5.2...v0.6.0

github.com

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 19d

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...

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Reposted by SWC/GCNU Neuroinformatics Unit

Niko Sirmpilatze @nikosirmpilatze.com · 20d

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.

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 21d

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.

DrLachie @drlachie.bsky.social · 22d

Check out the PyCon Au talk from my team member: @ishratz25.bsky.social on the challenges and solutions(?) of cell counting in whole-brain light sheet images! Also give her a follow, she's new here.
www.youtube.com/watch?v=ccLn...

"Big Brains, Small Targets: Whole-Brain Image Analysis with Python" - Ishrat Zaman (PyCon AU 2025)

YouTube video by PyCon AU

www.youtube.com

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Reposted by SWC/GCNU Neuroinformatics Unit

BrainGlobe @brainglobe.info · 23d

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...

Coronal sections of the DeMBA from anterior to posterior at five ages. Each section shows the STPT template on the left side and the transformed Allen Mouse Brain CCFv3 segmentations on the right side.

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 23d

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

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Reposted by SWC/GCNU Neuroinformatics Unit

BrainGlobe @brainglobe.info · 23d

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...

Software built by the community — BrainGlobe

brainglobe.info

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 23d

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

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Reposted by SWC/GCNU Neuroinformatics Unit

BrainGlobe @brainglobe.info · 26d

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...

Coronal and lateral views of the mouse brain, visualized using the napari viewer

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 26d

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.

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Reposted by SWC/GCNU Neuroinformatics Unit

Marco Dalla Vecchia @marcodv.bsky.social · Aug 25

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!

Marco Dalla Vecchia @marcodv.bsky.social · Aug 16

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

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 15

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

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Reposted by SWC/GCNU Neuroinformatics Unit

Rebecca Lowes @rebeccalowes.bsky.social · Aug 18

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

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 13

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

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Reposted by SWC/GCNU Neuroinformatics Unit

Niko Sirmpilatze @nikosirmpilatze.com · Aug 18

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/

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Reposted by SWC/GCNU Neuroinformatics Unit

Marco Dalla Vecchia @marcodv.bsky.social · Aug 16

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

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 15

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

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 15

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

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 15

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

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 14

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

#niu_osw

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 14

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

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 14

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

Big Imaging Data

neuroinformatics.dev

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Reposted by SWC/GCNU Neuroinformatics Unit

Marco Dalla Vecchia @marcodv.bsky.social · Aug 14

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!

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 13

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

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Reposted by SWC/GCNU Neuroinformatics Unit

Fabrizio Musacchio @fabmusacchio.bsky.social · Aug 12

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

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 13

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

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 13

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

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 12

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

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