Josh Moore

Winter-themed graphic titled “Winter Data Wonder #11.” A dark blue text panel framed by snow and icicles reads: “NFDI4BIOIMAGE shows how even a 100-GB microscopy dataset can be accessed directly on a smartphone — thanks to data streaming with the cloud-compatible OME-Zarr format.” Light blue snowy background with falling snow dots and a small snow-covered tree in the lower right corner.

❄️Winter Data Wonder #11

NFDI4BIOIMAGE shows how cloud-compatible data streaming makes large image datasets directly viewable in the browser — enabling mobile, flexible work with microscopy data.

🔗 Read more:
nfdi4bioimage.de/news/news-de...

Contributed by @nfdi4bioimage.bsky.social

Research Software Engineer - Spatial-omics The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...

We are hiring a Research Software Engineer to enhance and maintain the SpatialData framework.

We will work together with colleagues at EMBL, DKFZ, GSK, and across the scverse community.

🔗 Deadline: 15/02/2026
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...

#ELMI2026 will take place in Coimbra, Portugal 🇵🇹from June 16-19 hosted by @ppbioimaging.bsky.social colleagues. Submit your abstracts for oral presentations by January 18!
More information & registration🔽
ppbi.pt/wordpress/in...

#NFDBIOIMAGEfromAtoZ - O for OMERO.

What do @nfdi4bioimage.bsky.social and the @openmicroscopy.org have in common? Both aim to improve the management, documentation, and sharing of bioimage data.

👉 Find out more about #OMERO: www.openmicroscopy.org/omero/

Photo of Marius Politze of MatWerk looking sheepish in front of a truly scary slide, titled "Detailed View of the Arch(itecture)", which shows house diagram with many, many floors each representing one tool or service in use within the consortium.

Shock slide of the first @nfdi.de workshop on #OverallArchitecture" 🤯 Marius Politze of #MatWerk sharing the breadth & depth of tools & services in use.

OME-Zarr is the answer. The question was: How do we enable interactive visualisation, FAIR sharing & image analysis at the TB scale?

Lorenzo Cerrone demoing visualizing HCS plates stored as OME-Zarr

Joel presenting Fractal

CytoData 2025 audience

It's been great to present OME-Zarrs & Fractal for interoperable bioimage analysis at the 2025 @cytodata.bsky.social conference in Berlin today. Thanks a lot to the organizers & especially Christopher Schmied for having us!

Hackathon participants group picture

We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data.
1/14 🧵

Greetings from NFDI4Bioimage Task Area Leader Björn Grüning at the #EOSCSymposium2025, which is taking place from November 3 to 5 at Brussels. At the conference, Björn Grüning presents the #Galaxy use case, which is one of the first #EOSC candidate use cases.

👉 gxy.io/eosc25

Picture: Nicolas Lobet

📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...

📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!

Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬

📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...

YouTube video by Blender Microscopy Nodes: handling large biological volumes — Blender Conference 2025

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

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.

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

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...

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

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)

🎉 Our paper “MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis” is out in @natmethods.nature.com!
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata

🚀 Registration is open for BioHackathon Germany 2025! Join us 1–5 Dec in Walsrode for hands-on projects, networking, and innovation in #bioinformatics. 🧬🤝
🏨 Anders Hotel Walsrode | 🍽️ Social events | ✈️ Easy travel
🔗 Seats limited—register now! www.denbi.de/de-nbi-event...
#Hackathon

Julia Thönnißen from @fz-juelich.de demonstrates how large-scale 3D imaging data from neuroscience research can be handled & analyzed without the need for data duplication. Leveraging #OME-Zarr, the #tiamat tool developed at FZJ enables seamless work at scale. @nfdi4bioimage.bsky.social #CoRDI2025

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

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)

Are you using Zarr (or want to know more)? Join us in #Rome for Zarr Adopter Days on Oct 16-17! This is a great chance to learn from implementers, get hands-on support & collaborate w/ the @stacspec.bsky.social sprint folks. Register now to save your spot! zarr-summit-2025.netlify.app

2025 OME-NGFF Workflows Hackathon | Notion Date: November 12th - 14th, 2025

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...

Screenshot of OMERO.web showing OME-Zarr import page

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

How to make bioimage analysis workflows #FAIR? Riccardo Massei shows how to use efficient RDM & analysis pipelines in #Galaxy. As a @nfdi4bioimage.bsky.social Data Steward, Riccardo supports the community with expertise in data handling for high-content screening, image analysis & more. #CoRDI2025

Find Robert Wagner on the ground floor level or C.A.R.L at the #CoRDI2025 conference to learn how #OMERO helps with #FAIR data management in the field of low-temperature plasma science. @inpgreifswald.bsky.social @nfdi4bioimage.bsky.social

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

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!

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

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 🧵)

Zarr is hiring again! Build scalable bioimaging solutions, collaborate globally, and join the Friedrich Miescher Institute for Biomedical Research as a Computational Scientist or Research Software Engineer
www.fmi.ch/education-ca...

🧪Job opening at Janelia @hhmijanelia.bsky.social Integrative Imaging platform for a bioimage analyst. Please repost.

This plays on repeat in my head. (So I might as well share.)

#OME #Bio-Formats #Memes

Our project BioFAIR: Towards FAIR Practices in Bioimaging has been selected for funding through the swissuniversities Open Science II Programme (www.swissuniversities.ch/en/topics/op...)!

More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥

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!