@joshmoore.bsky.social
Technical Director – @gerbi-gmb.de | Standardizing open bioimaging data infrastructure TA1 lead for @nfdi4bioimage.bsky.social #OSS Maintainer for @openmicroscopy.org and @zarr.dev
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.
26.11.2025 14:50 — 👍 3 🔁 0 💬 0 📌 0
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!
20.11.2025 13:02 — 👍 15 🔁 5 💬 0 📌 0
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
📣 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...
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
19.09.2025 07:35 — 👍 67 🔁 19 💬 4 📌 2
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...
18.09.2025 09:42 — 👍 11 🔁 11 💬 0 📌 0
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
28.08.2025 08:57 — 👍 8 🔁 1 💬 0 📌 0
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
19.08.2025 18:39 — 👍 6 🔁 4 💬 0 📌 0
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...
29.08.2025 07:11 — 👍 3 🔁 1 💬 0 📌 0
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
27.08.2025 08:15 — 👍 10 🔁 2 💬 0 📌 0
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
27.08.2025 08:00 — 👍 9 🔁 3 💬 0 📌 0
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.
13.02.2025 00:17 — 👍 12 🔁 11 💬 0 📌 1This 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!
The deadline to submit proposals for BioHackathon Germany 2025 is approaching! Submit your project idea by July 15! More information is available here: www.denbi.de/de-nbi-event...
02.07.2025 13:58 — 👍 2 🔁 2 💬 0 📌 0
#OLSPub as an alternative to #PubMed:
Infrastructure made in Europe
The recording of our information event ‚Resilient and independent life science research infrastructure‘ is now online and can be watched here:
youtu.be/2vSkx07VyeM
Such good news for European data management 🇪🇺
16.06.2025 14:57 — 👍 7 🔁 0 💬 0 📌 0
🌐 Junior Web Developer / Scientific Prototyper
🛠️ Job Alert: Web Developer / Scientific Prototyper (up to 100%, fully remote, based in EU)
We’re looking for a creative web developer to build engaging tools and interactive demos for the imaging community.
