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will-j-moore.bsky.social @will-j-moore.bsky.social · 1d

Very nice! Your Affine Transform blog post is really neat and just what I needed right now 👍 for #OME-Zarr RFC-5. I also want to try out marimo and Web Assembly 😍

Marco Dalla Vecchia @marcodv.bsky.social · 2d

I'm happy to release into the wild my new professional and personal website marcodallavecchia.gitlab.io/web/

I finally found some time to reorganize ideas and redo the framework with @quarto.org

You can read my first blog post on the website here!
marcodallavecchia.gitlab.io/web/blog/web...

Personal & Professional Website – marcodallavecchia/web

my corner of the web

marcodallavecchia.gitlab.io

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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 · 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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Sofya Garushyants @garushyants.bsky.social · 23d

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 22d

What to do if you have extraordinary size data but no extraordinary local memory? 😱

At the @grcib2025.bsky.social, @joshmoore.bsky.social addressed this issue in the talk “When Data Doesn’t Fit – A Bioimaging Story from Files to FAIR”.

👉 Interested? zenodo.org/records/1708...

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aybukey.bsky.social @aybukey.bsky.social · Aug 27

Honoured to be featured - and even prouder of what the @bioimagearchive.bsky.social team is building together for the life sciences community.

EMBL-EBI @ebi.embl.org · Aug 27

Meet Aybuke Kupcu Yoldas 🇹🇷🇬🇧 our BioImage Archive Data Project Leader.

Aybuke swapped telescopes for microscopes and stars ⭐ for cells a few years ago, when she pivoted from astrophysics to bioimaging.

She now helps make bioimages easy to access and reuse.

www.ebi.ac.uk/about/news/p...

We are EMBL: Aybuke Kupcu Yoldas on trading stars for cells

Aybuke Kupcu Yoldas, Senior Imaging Bioinformatician at EMBL-EBI, talks about the Bioimage Archive and her journey from astrophysics to biology

www.ebi.ac.uk

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will-j-moore.bsky.social @will-j-moore.bsky.social · Sep 8

From #ome-ngff-validator you can open open #OME-Zarr images in a bunch of viewers, and neuroglancer's rendering of multi-channel images just got a lot nicer: ome.github.io/ome-ngff-val... - See github.com/google/neuro...

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Erick Ratamero @erickratamero.com · Aug 30

new blog post: in which I talk (briefly) about getting a new job and moving back to Europe, getting a VPS, and self-hosting my code and my personal website. pages.erickratamero.com/personal-web...

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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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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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will-j-moore.bsky.social @will-j-moore.bsky.social · Aug 29

Currently working on #OMERO web-based import of public #OME-Zarr images github.com/ome/omero-we...

Screenshot of OMERO.web showing OME-Zarr import page

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · Aug 27

Poster Session at #CoRDI2025. Here is @joshmoore.bsky.social presenting how cloud-ready next-generation file formats like #OME-Zarr enable federated repositories with large N-dimensional arrays at peta-scale.
#OME-NGFF @nfdi4bioimage.bsky.social
Find the poster on C.A.R.L level 2 @rwth.bsky.social

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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · Aug 25

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods!
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...

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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 🧵)

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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BioImaging North America @bioimagingna.bsky.social · Jun 18

#microscopycommunity- do you use BioFormats, OMERO, OME-TIFF, OME-Zarr or are you interested in open source and microscopy? Then you should check out the recordings from OME2025!

buff.ly/fgUxoQf
@openmicroscopy.org
@gerbi-gmb.de‬.
@jacksonlab.bsky.social‬
@mblscience.bsky.social

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · Aug 7

🌟 #MeetOurDataSteward: #3: Riccardo Massei #DataSteward at NFDI4Bioimage and researcher @ufz.de. He makes high-content screening data FAIR and cloud-ready using #OMERO, #Python, #Galaxy, and #Jupyter. Questions? Get in touch!

👉https://nfdi4bioimage.de/about-us/data-stewardship-team/massei/

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trevor manz @manzt.sh · Aug 7

if interested in creating anywidgets of your own, our tutorial was finally shared to youtube:

www.youtube.com/watch?v=frEo...

Abdennur, Lekschas, & Manz - Bring your __repr__’s to life with anywidget | SciPy 2024

YouTube video by SciPy

www.youtube.com

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OME @openmicroscopy.org · Aug 6

For a list of the OME-Zarr images in idr0170, see github.com/IDR/idr0170-... where the metadata can be viewed in BioFile Finder (bff.allencell.org) - use Chrome!

GitHub - IDR/idr0170-rose-mibitof

Contribute to IDR/idr0170-rose-mibitof development by creating an account on GitHub.

github.com

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Juan Nunez-Iglesias @jni.codes · Aug 1

It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇

Australian Museum Eureka Prizes @eurekaprizes.bsky.social · Jul 30

@napari.org @jni.codes is a finalist in the @ardc.edu.au Eureka Prize for Excellence in Research Software.

Learn more: youtu.be/0g_MkTa_NwQ

#EurekaPrizes

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OME @openmicroscopy.org · Jul 25

New landing pages have landed for every study in the Image Data Resource (IDR)!
Now, you can easily see clear details of the study - including how to download the data!
To access the landing page for a study, just click on its thumbnail from the homepage (idr.openmicroscopy.org).

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Johannes Soltwedel @jo-soltwedel.bsky.social · Jul 18

As good as a time as any to announce: After a great time at @poldresden.bsky.social I'm looking forward to starting my new position at @gerbi-gmb.de as a software developer for @openmicroscopy.org 🔬😀!

Scalable #RDM solutions in the ome-zarr-verse, here we come!

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Uri Manor @manorlaboratory.bsky.social · Jul 11

undark.org/2025/07/11/i...

Interview: How a Hearing-Loss Grant Got Cut in the Fight Over DEI

“It felt like the floor dropped out,” researcher Uri Manor said after the sudden suspension of his lab’s award.

undark.org

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · Jun 26

#TiM2023 and #TiM2025 data is now publicly available!
Find the data collected and annotated at the Trends in Microscopy conference in an OMERO-based framework introduced by I3D:bio '23 and extended in '25, supported by the @nfdi4bioimage.bsky.social data stewards.
👉 nfdi4bioimage.de/news/news-de...

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Johannes Soltwedel @jo-soltwedel.bsky.social · Jun 17

FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging

Let's have a look 👇🧪💻🔬

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · Jun 10

Michele Bortolomeazzi, Christian Schmidt and Jan-Philipp Mallm at @nfdi4bioimage.bsky.social have developed a new OMERO-web plugin: OMERO-vitessce. It enables the visualization of datasets hosted in #OMERO with the #Vitessce multimodal data viewer.
Find the poster here:
👉 zenodo.org/records/1483...

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