Lightnews — Scholar-powered news

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napari @napari.org · 2d

Join the new plugin sustainability initiative!

Everyone is invited to fill out this interest form: forms.gle/iwX6P4tuooHK...

Follow along with initial discussion on Zulip: napari.zulipchat.com#narrow/chann...

The first zoom meeting will be this coming week: napari.org/stable/commu...

Meeting schedule

We hold regular meetings, the timings of which are available on our public calendar. If you are using napari or interested in how napari could be used in your work, please join one of our regular comm...

napari.org

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

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".

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Aug 11

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

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BrainGlobe @brainglobe.info · Aug 6

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...

Release v2.3.0 · brainglobe/brainglobe-atlasapi

What's Changed Improve core test coverage by @stellaprins in #535 Update dependencies, add docstrings, fix url error handling by @stellaprins in #542 Add tests for atlas_gen annotation_utils by ...

github.com

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BrainGlobe @brainglobe.info · Jul 28

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...

A three-dimensional view of the Kocher lab’s bumblebee brain atlas visualised with brainrender-napari.

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Nicolas Chiaruttini @nkiaru.bsky.social · Jul 24

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:

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Jul 16

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!

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BrainGlobe @brainglobe.info · Jun 10

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...

Different versions of the Common Coordinate Framework: CCFv2 and CCFv3 from the AIBS, as well as the extended and improved CCFv3a-BBP from the Blue Brain Project.

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Sainsbury Wellcome Centre @sainsburywellcome.bsky.social · May 28

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...

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Niko Sirmpilatze @nikosirmpilatze.com · May 19

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.

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Apr 16

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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BrainGlobe @brainglobe.info · Apr 25

Fully funded (including travel and accomodation) BrainGlobe course in London. Applications close June 6th.

Any questions, get in touch.

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Apr 25

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.

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

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.

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Apr 25

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.

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

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.

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

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.

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BrainGlobe @brainglobe.info · Apr 16

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 avaiable.

More details and applications: neuroinformatics.dev/open-softwar...

Open Software Week — NIU

neuroinformatics.dev

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BrainGlobe @brainglobe.info · Apr 16

If you'd like to learn how to use BrainGlobe, we're part of @neuroinformatics.dev's "Open Source Week".

London, UK, August 11-15.

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Apr 16

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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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · Apr 16

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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