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Reposted by Joel Lüthi

Jean-Yves Tinevez @jytinevez.bsky.social · 1d

Job alert!

We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?

See also on the forum:
forum.image.sc/t/research-e...

Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA

Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...

forum.image.sc

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Reposted by Joel Lüthi

Roger Castells @rcastellsg.bsky.social · 3d

We’re looking for an enthusiastic postdoc to join our team. 😊

The project focuses on protein design and cryo-EM applied to cancer research. 🔬🧪

The position is fully funded for 3 years.

Please share 🙏

Job description and application details (deadline: October 11th): www.cnio.es/en/empleo/po...

Postdoctoral Research Assistant for the Biomolecular Design and Structural Nanomedicine Group

DescriptionWe are looking for a Postdoctoral Researcher to join Roger Castells-Graells’ lab at the Spanish National Cancer Research Centre (CNIO). The successful candidate will work on innovative biom...

www.cnio.es

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Reposted by Joel Lüthi

napari @napari.org · 6d

napari 0.6.5 is out! 🚀

Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: napari.org/dev/release/...

Image depicting the napari viewer in grid mode with scale bars and color bars enabled

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Reposted by Joel Lüthi

Siân Culley @superresolusian.bsky.social · 9d

BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...

Bioimage Analysis Specialist | King's College London

www.kcl.ac.uk

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Reposted by Joel Lüthi

Anna Foix @afoix.bsky.social · 15d

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)

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Joel Lüthi @joelluethi.bsky.social · 20d

Want to hack with ~40 motivated developers in the OME-Zarr space this fall in Zurich, November 12 - 14th? The application window for the 2025 OME-NGFF workflows hackathon is closing on September 30th! Apply here to be part of this exciting week about OME-Zarr: forms.gle/849cf2fBk1pJ...

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Ignacio Arganda-Carreras @iarganda.bsky.social · 20d

Day 5️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @embl.org

@tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev

Christian Tischer addresses the online participants of the EMBO Advanced methods in biomage analysis course before starting his tutorial on OME-Zarr.

Christian Tischer gets prepared to start his tutorial on OME-Zarr in front a full classroom.

Christian Tischer gives the first intructions to the onsite and the online participants of the EMBO Advanced methods in biomage analysis course for his tutorial on OME-Zarr.

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Joel Lüthi @joelluethi.bsky.social · 22d

Want to learn more? Check out www.biovisioncenter.uzh.ch/en/events/Op...

Want to sign up for it? Register here: forms.gle/jLzDBGGWnKLt...
(6/6)

Open Bioimaging Practices Meetups

www.biovisioncenter.uzh.ch

Joel Lüthi @joelluethi.bsky.social · 22d

And we'll round off 2025 on November 26th at 4pm with guest presentations by Giliane Rochat about lightsheet processing for OME-Zarrs & Flurin Sturzenegger about the ZMB Fractal task collection. (5/6)

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Joel Lüthi @joelluethi.bsky.social · 22d

We'll have the second meeting on October 28th at 4pm with a guest presentation by @m-albert.bsky.social about multiview-stitcher (github.com/multiview-st...) & dask-image (image.dask.org/en/latest/) (4/6)

GitHub - multiview-stitcher/multiview-stitcher: A toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.

A toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D. - multiview-stitcher/multiview-stitcher

github.com

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Joel Lüthi @joelluethi.bsky.social · 22d

We'll start the season next week on September 24th at 4pm with a guest presentation by @csoneson.bsky.social & @silviabarbiero.bsky.social about the ez_zarr library (see github.com/fmicompbio/e...) (3/6)

GitHub - fmicompbio/ez_zarr: GIve easy, high-level access to ome-zarr fileset

GIve easy, high-level access to ome-zarr fileset. Contribute to fmicompbio/ez_zarr development by creating an account on GitHub.

github.com

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Joel Lüthi @joelluethi.bsky.social · 22d

At each event, we'll present updates on recent work on Fractal, ngio & other OME-Zarr tools at the BioVisionCenter. And guest presenters share their work with OME-Zarrs. All events will be hybrid, but snacks are only available for in-person participants 😉 (2/6)

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Joel Lüthi @joelluethi.bsky.social · 22d

Are you working with OME-Zarrs in Switzerland?
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)

Flyer for the Open Bioimaging Practices Meetups.
1. September 24th at 4pm: Guest presentation by Charlotte Soneson & Silvia Barbiero
2. October 28th at 4pm: Guest presentation by Marvin Albert
3. November 26th at 4pm: Guest presentations by Giliane Rochat & Flurin Sturzenegger

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Joel Lüthi @joelluethi.bsky.social · 26d

100% this! It's nice to set a week aside and do work together then and there. But there always seems to be more to be done afterwards.

Once we understand who really cares about which aspects and what motivates them, it's also much easier to reach out to them again later (& not waste their time)

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Joel Lüthi @joelluethi.bsky.social · 26d

I have also seen collaborations work purely virtually or work virtually for a long time before any in-person meetings. But in most cases, it's easier to get the ball rolling with in-person interaction & it speeds up the collaboration afterwards. (3/3)

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Joel Lüthi @joelluethi.bsky.social · 26d

That's not to say that all community collaboration needs to be in person though! I've seen it continue well virtually after in-person meetups, once people know each other.
I see the in-person meetups as the nucleus & reinforcement of productive virtual collaborations :) (2/3)

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Joel Lüthi @joelluethi.bsky.social · 26d

Hey @elinarahul.bsky.social
In my experience, in-person connection opportunities are key to get people to get to know each other and understand the different perspectives. As such, it's key to have some moments for in-person collaboration. (1/3)

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Reposted by Joel Lüthi

Daniel Krentzel @danielkrentzel.bsky.social · 28d

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)

www.nature.com/articles/s41...

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods

CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...

www.nature.com

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Reposted by Joel Lüthi

Silvia Barbiero @silviabarbiero.bsky.social · Aug 15

We’re excited to share that ez_zarr now supports Zarr v3! 🚀 Huge thanks to @mbstadler.bsky.social & @csoneson.bsky.social who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting 📊
📄 joss.theoj.org/papers/10.2110… (1/3)

ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets

Barbiero et al., (2025). ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. Journal of Open Source Software, 10(109), 7882, https://doi.org/10.21105/joss.07882

joss.theoj.org

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Reposted by Joel Lüthi

GloBIAS @globias.bsky.social · Aug 20

Next one in the #GloBIAS seminar series: Behind the Scenes at SciLifeLab BIIF: Lessons from Managing a National Bioimage Analysis Support Unit. Presented by Anna Klemm, head of BioImage Informatics Infrastructure Unit, Uppsala University, Sweden

Wednesday, 27th of August, 2pm CEST

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Reposted by Joel Lüthi

Virginie Uhlmann @virginieuhlmann.bsky.social · Aug 25

Once is an exception, twice is a trend, thrice is a tradition!

Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!

Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!

Joel Lüthi @joelluethi.bsky.social · Aug 25

We're happy to announce the 2025 International OME-NGFF workshop 🎉

📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025

📍 Location: Zurich, Switzerland

Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...

#bioimaging #openscience #OMENGFF #OMEZarr

(1/x 🧵)

Visual of segmented human induced pluripotent stem cells with the key workshop dates: Symposium on November 10-11, Hackathon on November 12-14th in Zurich Switzerland

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Reposted by Joel Lüthi

Erick Ratamero @erickratamero.com · Aug 25

I'll be there! Giving a talk! and hacking on _something_ for a few days!

Joel Lüthi @joelluethi.bsky.social · Aug 25

We're happy to announce the 2025 International OME-NGFF workshop 🎉

📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025

📍 Location: Zurich, Switzerland

Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...

#bioimaging #openscience #OMENGFF #OMEZarr

(1/x 🧵)

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Joel Lüthi @joelluethi.bsky.social · Aug 25

You are an OME-Zarr developer yourself? Join us at the hackathon! Help push OME-Zarr towards 1.0, work on RFCs to the spec, contribute to tooling in Java or Python or build workflows using OME-Zarrs.

Find out more & apply to the hackathon here: biovisioncenter.notion.site/2025-OME-NGF...

2025 OME-NGFF Workflows Hackathon | Notion

Date: November 12th - 14th, 2025

biovisioncenter.notion.site

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Joel Lüthi @joelluethi.bsky.social · Aug 25

Learn more about OME-NGFF, get hands-on demos & hear how people use OME-Zarrs world-wide at the symposium.

Speakers: Jason Swedlow, Josh Moore, Prisca Liberali, Kedar Narayan, John Bogovic & more.

You can register for the symposium here: www.ema.uzh.ch/de/register/...

2025 International OME-NGFF Symposium

10. November – 11. November 2025 | Careum Auditorium 2

www.ema.uzh.ch

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Joel Lüthi @joelluethi.bsky.social · Aug 25

We're happy to announce the 2025 International OME-NGFF workshop 🎉

📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025

📍 Location: Zurich, Switzerland

Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...

#bioimaging #openscience #OMENGFF #OMEZarr

(1/x 🧵)

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