Author | Lightnews

David Stansby @dstansby.bsky.social · 1d

Thanks for the feedback! The code was previously licensed under BSD-3, and I've just added a CC-BY 4.0 license for the content, so you're free to use, share, and remix as long as there's attribution

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David Stansby @dstansby.bsky.social · 2d

Written by myself @uclengineering.bsky.social and colleagues at @ucl-arc.bsky.social , we're hoping this provides a useful primer on how to use the modern OME-Zarr data format to handle big bioimaging data.

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David Stansby @dstansby.bsky.social · 2d

Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".

ome-zarr-book.readthedocs.io

An Introduction to OME-Zarr for Big Bioimaging Data

ome-zarr-book.readthedocs.io

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Reposted by David Stansby

Data & Society @datasociety.bsky.social · 7d

As LLMs manufacture a form of scholarship, presentation doesn’t mean what it used to. D&S's Ranjit Singh looks at how this threatens the open-access research repository arXiv, how its founder is fighting to sustain its credibility, & what researchers can do to help. datasociety.net/points/on-ar...

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Reposted by David Stansby

Crick BioImage Analysis Symposium @cbias.bsky.social · 13d

A month to go! Will you be at #CBIAS2025?

The program is almost ready, and we look forward to welcoming you in London to discuss all things #BioImageAnalysis, from tool development, to biomedical applications and community building.

Register now! 🔗⬇️

www.crick.ac.uk/whats-on/cri...

Crick BioImage Analysis Symposium 2025

www.crick.ac.uk

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David Stansby @dstansby.bsky.social · 15d

Over at `ome-zarr-models` we're working on implementing support for the new coordinate systems too - here's an example of a transformation graph from multiple tiled images that can be transformed into a common "world" coordinate system. 🟥 ➡️ 🌎

A coordinate transformation graph. Each coordinate system is denoted by a circle, and arrows between systems denote coordinate transformations. Four images named tile_0, tile_1, tile_2, tile_3 have transformations to a "physical" system, and then to a common "world" system.

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David Stansby @dstansby.bsky.social · 27d

My first paper as a journal editor! 🎉😊

Journal of Open Source Software @joss-openjournals.bsky.social · 27d

Just published in JOSS: 'VSMOD: A Vessel Segmentation and MODelization plugin for 3D Slicer' https://doi.org/10.21105/joss.08563

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David Stansby @dstansby.bsky.social · Sep 11

I can recommend inkscape.org

Inkscape - Draw Freely. | Inkscape

Inkscape is professional vector graphics software which runs on Linux, macOS and Windows desktop computers.

inkscape.org

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David Stansby @dstansby.bsky.social · Sep 1

For a long time I've been wondering what RSEs can do to help uphold and support the basic human rights of Palestinians 🇵🇸 - today I've launched gitlab.com/rsesforpales... to collect and discuss actions we can take as a community.

RSEsForPalestine / RSEsForPalestine · GitLab

GitLab.com

gitlab.com

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Reposted by David Stansby

Malorie @malorienilson.com · Aug 30

Just a heads up to anyone using Firefox:

Text reads: Mozilla, in its finite wisdom, embedded LLM bots into recent versions of Firefox for the vitally-important purpose of... naming tab groups. Now, some users are noticing CPU and power usage spikes caused by a background process called Inference.

Ugh. Reminder again for Firefox users to visit your about:config page, search for the browser.ml.chat.enabled key, and set that to false:

Displayed is a screenshot of Firefox showing the config search bar with the listed search. The word "false" is circled in red.

Text continues: If yours says true then double-click it until it reads false.
Doing that turns off the Al chatbot features in Firefox, but also the stupid new LLM tab-naming feature that's rolling out.

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Reposted by David Stansby

Will Jennings @willjennings.bsky.social · Jul 27

The BBC News website has pages & pages of coverage related to farmers protesting inheritance tax, including events where only a few hundred turn out.

In London yesterday 100,000 people marched for trans rights, and nothing.

Imagine if it was 100,000 anti immigrant activists, they'd cover that.

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Reposted by David Stansby

napari @napari.fosstodon.org.ap.brid.gy · Jul 23

🚀 Big news! The napari hub has been reimplemented and is now community-run! :tada: It's still the go-to place for finding and sharing napari plugins, but the website is now snappier and lighter-weight. Check it out 👉 www.napari-hub.org

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Reposted by David Stansby

$profrachelgan.bsky.social$

Prof Rachel Oliver @profrachelgan.bsky.social · May 14

"Gender neutral toilets are available on floor 1 and 15 of our London office." I am somehow reminded of the bit in "Hidden Figures" where the brilliant Black mathematician is forced to run across campus on her break to get to a bathroom she is allowed to use...

Jolyon Maugham KC @goodlawproject.org · May 14

Given the below, we're especially interested in hearing urgently from any affected staff members at the Financial Conduct Authority. More details in how to contact us in the next message.

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Reposted by David Stansby

Zia Weise @ziaweise.bsky.social · Apr 23

Drought conditions in Europe in the first half of April. Getting worse

[Source: joint-research-centre.ec.europa.eu/european-and...

Map of Europe showing worsening drought across central, eastern and parts of northern Europe, the UK and the Benelux, plus increasingly severe conditions in southeastern Europe

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Reposted by David Stansby

LunaLuvgood2020 @lunaluvgood2020.bsky.social · Apr 20

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Emily Hunt @emily.space · Apr 16

The UK supreme court just single-handedly overturned most trans rights in the UK today.

Very disturbingly, the ruling also opens a clear pathway for TERFs to completely push trans people out of public life.

This one ruling pushes trans rights in the UK back at least 25 years. It's horrible

Jess O'Thomson @jessothomson.co.uk · Apr 16

My analysis of today's UK Supreme Court judgment.

The UK Supreme Court Rules That Trans Women Aren't Women Under the Equality Act 2010

www.wearequeeraf.com/uk-supreme-c...

UK Supreme Court Rules That Trans Women Aren’t Women under the Equality Act 2010

The legal definition of a woman in the UK now excludes trans people: This is what it means for Trans+ rights in the country

www.wearequeeraf.com

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Reposted by David Stansby

Higher Education Policy Institute @hepi-news.bsky.social · Apr 9

New Post: OfS free-speech absolutism allows abuse, harassment, and bullying www.hepi.ac.uk/2025/04/09/o...

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Reposted by David Stansby

scientific-python.org @scientific-python.org · Apr 3

Hello world! 👋

🔥 The Scientific Python community is building tools to power our ecosystem and support contributors and maintainers!

🚀 Discover our projects and learn how you can get involved by following us on GitHub:

🔗 github.com/scientific-python

Scientific Python

Community developed, community owned. Scientific Python has 43 repositories available. Follow their code on GitHub.

github.com

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Reposted by David Stansby

British Antarctic Survey 🐧 @bas.ac.uk · Mar 25

Year-end scramble getting you down? ⏳

Applications for lots of our Antarctic #jobs are closing in the next week. They include vehicles manager at Halley, and Radio Operator and IT Engineer at Rothera Research Station.

These are jobs unlike any other, in one of the most beautiful places on Earth ⬇️

Seriously remote work, in Antarctica. The photo is of Halley Research Station, stretching into the distance on a flat white polar landscape, with the label 'Today's Office'

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Reposted by David Stansby

Chelsea G. Summers @chelseagsummers.bsky.social · Mar 19

So on March 9, a French scientist, on a visa to attend a conference in Houston, was denied entry to the US and subsequently expelled because his phone had messages decrying scientific policies put forward by the Trump administration: www.lemonde.fr/internationa...

Etats-Unis : un chercheur français refoulé pour avoir exprimé « une opinion personnelle sur la politique menée par l’administration Trump »

Le ministre de la recherche français a dit sa « préoccupation », mercredi, après cette décision des autorités américaines. Le chercheur du CNRS aurait subi un contrôle aléatoire à son arrivée, avant q...

www.lemonde.fr

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Joel Lüthi @joelluethi.bsky.social · Mar 11

🚀 We’re very excited to share our latest preprint on OME-Zarr! 🚀

Our report on the 2024 OME-NGFF Workflows Hackathon is a deep dive into the status of OME-Zarr and the great work that happened last November at the BioVisionCenter in Zurich.

🔗 Read the preprint: osf.io/preprints/bi...

🧵 (1/15)

OSF

osf.io

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Reposted by David Stansby

Zack Labe @zacklabe.com · Mar 3

While all of this is happening to our scientific agencies, the current extent of sea ice globally remains at record low levels...

More visuals at zacklabe.com/global-sea-i...

Line graph time series of 2025's daily global sea ice extent in red shading compared to each year from 1979 to 2024 using shades of purple to white for each line. There is substantial interannual and daily variability. Seasonal cycles are visible. Note: the poles are affected by very different Earth system processes/seasonality. I am using 5-day running mean data.

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Reposted by David Stansby

Adam Serwer @adamserwer.bsky.social · Feb 25

What drives me crazy about the anti-DEI rhetoric is everyone wants to be judged on merit. But you can't be judged on merit if you can't even get in the door because you don't fit some prejudiced definition of who is capable and who isn't

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David Stansby @dstansby.bsky.social · Feb 19

Well it was bound to happen, but @chanzuckerberg.bsky.social have finally stopped championing equitable oppurtunities - DEI page was online last week but now it's been wiped:

web.archive.org/web/20250212...

Building a more just, inclusive and equitable future

Learn about CZI’s commitment to diversity, equity, inclusion and accessibility, and how we’re investing in advancing racial equity

web.archive.org

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Reposted by David Stansby

Susan Gasser @susanmgasser.bsky.social · Feb 19

It’s sickening how weak-kneed every foundation in US is. Where are your principles?

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