Joel Lüthi
@joelluethi.bsky.social
Head of Research and Development of the BioVisionCenter at the University of Zurich
Pinned
Joel Lüthi
@joelluethi.bsky.social
· Nov 17
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 🧵
1/14 🧵
Reposted by Joel Lüthi
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...
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...
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...
embl.wd103.myworkdayjobs.com
February 2, 2026 at 9:38 AM
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...
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...
Reposted by Joel Lüthi
19th #OME Community Meeting, Düsseldorf · 28–30 April 2026
Registration is now open! Join researchers, developers, and imaging facility staff to connect, share experiences, and discuss the future of OME tools.
Details & registration (deadline: 31 March 2026):
gerbi-gmb.de/event/ome-20...
Registration is now open! Join researchers, developers, and imaging facility staff to connect, share experiences, and discuss the future of OME tools.
Details & registration (deadline: 31 March 2026):
gerbi-gmb.de/event/ome-20...
19th OME Community Meeting - German BioImaging
Join us for the 19th Open Microscopy Environment (OME) Community Meeting from 28.-30.4.2026, in the Haus der Universität Düsseldorf. Invited Speakers Carole Goble – Keynote – Jean-Marie Burel Josh Moo...
gerbi-gmb.de
January 22, 2026 at 4:40 PM
19th #OME Community Meeting, Düsseldorf · 28–30 April 2026
Registration is now open! Join researchers, developers, and imaging facility staff to connect, share experiences, and discuss the future of OME tools.
Details & registration (deadline: 31 March 2026):
gerbi-gmb.de/event/ome-20...
Registration is now open! Join researchers, developers, and imaging facility staff to connect, share experiences, and discuss the future of OME tools.
Details & registration (deadline: 31 March 2026):
gerbi-gmb.de/event/ome-20...
Reposted by Joel Lüthi
Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Scientific Workflows Developer
The European Molecular Biology Laboratory (EMBL) is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service teams covering the ...
embl.wd103.myworkdayjobs.com
January 14, 2026 at 9:37 AM
Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Joel Lüthi
Has napari helped your research this year? Why not say thank you to free and open source software by making a small donation? Every bit helps your friendly core team fix bugs and bring new features to life! CZI will match up to $75K in donations! opencollective.com/napari/donate
December 24, 2025 at 2:59 AM
Has napari helped your research this year? Why not say thank you to free and open source software by making a small donation? Every bit helps your friendly core team fix bugs and bring new features to life! CZI will match up to $75K in donations! opencollective.com/napari/donate
Reposted by Joel Lüthi
We're a bit late in ringing in the giving season, but it is indeed upon us. Enjoy our special edition holiday logo ☃️ and, if you can spare a bit and appreciate napari, please donate to our development efforts! 🙏 CZI will match donations up to $75K.
opencollective.com/napari/donate
opencollective.com/napari/donate
December 18, 2025 at 12:03 PM
We're a bit late in ringing in the giving season, but it is indeed upon us. Enjoy our special edition holiday logo ☃️ and, if you can spare a bit and appreciate napari, please donate to our development efforts! 🙏 CZI will match donations up to $75K.
opencollective.com/napari/donate
opencollective.com/napari/donate
Reposted by Joel Lüthi
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
forum.image.sc/t/toward-bet...
Toward better 2D - 3D registration in BigWarp
BigWarp has so far focused on 2D-2D or 3D-3D registration, and not on 2D-3D registration. After a conversation with @Christian_Tischer , we thought some simple UI changes could make the support for 2...
forum.image.sc
November 29, 2025 at 6:03 PM
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
forum.image.sc/t/toward-bet...
Reposted by Joel Lüthi
I am still digesting all the info from the OME-NGFF hackathon last week.
So I decided to make a little UI for some of the code created there (just to play around), which one can easily show to interested colleagues 😜.
CZI --> OME-ZARR with some options ...
By far not perfect but still fun!
So I decided to make a little UI for some of the code created there (just to play around), which one can easily show to interested colleagues 😜.
CZI --> OME-ZARR with some options ...
By far not perfect but still fun!
November 19, 2025 at 5:06 PM
I am still digesting all the info from the OME-NGFF hackathon last week.
So I decided to make a little UI for some of the code created there (just to play around), which one can easily show to interested colleagues 😜.
CZI --> OME-ZARR with some options ...
By far not perfect but still fun!
So I decided to make a little UI for some of the code created there (just to play around), which one can easily show to interested colleagues 😜.
CZI --> OME-ZARR with some options ...
By far not perfect but still fun!
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!
November 20, 2025 at 1:03 PM
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!
Reposted by Joel Lüthi
Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
GitHub - czimaginginstitute/zarr-particle-tools: Particle extraction and reconstruction from OME-Zarr tilt series.
Particle extraction and reconstruction from OME-Zarr tilt series. - czimaginginstitute/zarr-particle-tools
github.com
November 17, 2025 at 10:30 PM
Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Reposted by Joel Lüthi
📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
November 6, 2025 at 6:56 PM
📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
Reposted by Joel Lüthi
Go read Joel's thread on the hackathon last week in Zürich! If you have any level of interest in OME-NGFF, there are so many exciting things happening. I had a great time meeting some of my favorite people in the world - It was equal parts rewarding, fun and exhausting 🙃️
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 🧵
1/14 🧵
November 17, 2025 at 2:10 PM
Go read Joel's thread on the hackathon last week in Zürich! If you have any level of interest in OME-NGFF, there are so many exciting things happening. I had a great time meeting some of my favorite people in the world - It was equal parts rewarding, fun and exhausting 🙃️
Reposted by Joel Lüthi
Very happy to share some more pics! What an amazing week! I am still recovering!
Thank you so much to you all❤️🩹🥲
Thank you so much to you all❤️🩹🥲
November 17, 2025 at 1:56 PM
Very happy to share some more pics! What an amazing week! I am still recovering!
Thank you so much to you all❤️🩹🥲
Thank you so much to you all❤️🩹🥲
Plus more hacking pictures I forgot to attach to the workflows effort 😅
November 17, 2025 at 1:25 PM
Plus more hacking pictures I forgot to attach to the workflows effort 😅
So grateful for this community, and very excited for what’s coming next for OME-Zarr. 🚀
(14/14 🧵)
(14/14 🧵)
November 17, 2025 at 1:24 PM
So grateful for this community, and very excited for what’s coming next for OME-Zarr. 🚀
(14/14 🧵)
(14/14 🧵)
More amazing organisers & helpers!
@tischi.bsky.social @vladimirulman.bsky.social @normanrz.com @perlman.bsky.social @virginieuhlmann.bsky.social @lorenzocerrone.bsky.social @cfusterbarcelo.bsky.social & Valentina Marcelli
(13/14 🧵)
@tischi.bsky.social @vladimirulman.bsky.social @normanrz.com @perlman.bsky.social @virginieuhlmann.bsky.social @lorenzocerrone.bsky.social @cfusterbarcelo.bsky.social & Valentina Marcelli
(13/14 🧵)
November 17, 2025 at 1:24 PM
More amazing organisers & helpers!
@tischi.bsky.social @vladimirulman.bsky.social @normanrz.com @perlman.bsky.social @virginieuhlmann.bsky.social @lorenzocerrone.bsky.social @cfusterbarcelo.bsky.social & Valentina Marcelli
(13/14 🧵)
@tischi.bsky.social @vladimirulman.bsky.social @normanrz.com @perlman.bsky.social @virginieuhlmann.bsky.social @lorenzocerrone.bsky.social @cfusterbarcelo.bsky.social & Valentina Marcelli
(13/14 🧵)
And none of this would have been possible without all the organizers & helpers, who kept things running smoothly. Huge thanks to everyone who made the hackathon happen — you are the reason this community keeps thriving.
@joshmoore.bsky.social @jo-soltwedel.bsky.social
Continued ...
(12/14 🧵)
@joshmoore.bsky.social @jo-soltwedel.bsky.social
Continued ...
(12/14 🧵)
November 17, 2025 at 1:24 PM
And none of this would have been possible without all the organizers & helpers, who kept things running smoothly. Huge thanks to everyone who made the hackathon happen — you are the reason this community keeps thriving.
@joshmoore.bsky.social @jo-soltwedel.bsky.social
Continued ...
(12/14 🧵)
@joshmoore.bsky.social @jo-soltwedel.bsky.social
Continued ...
(12/14 🧵)
This event would not have been possible without the generous support of the University of Zurich and of swissuniversities' Programme Open Science II. Thank you so much for giving us the resources to promote and develop FAIR practices in bioimaging!
(11/14 🧵)
(11/14 🧵)
November 17, 2025 at 1:24 PM
This event would not have been possible without the generous support of the University of Zurich and of swissuniversities' Programme Open Science II. Thank you so much for giving us the resources to promote and develop FAIR practices in bioimaging!
(11/14 🧵)
(11/14 🧵)
Tons of additional work on ZIP-Zarr, Java libraries, capability manifests, conformance testing, Open Seadragon, bug fixing, prototyping, brainstorming and general OME-Zarr spec discussions
(10/14 🧵)
(10/14 🧵)
November 17, 2025 at 1:24 PM
Tons of additional work on ZIP-Zarr, Java libraries, capability manifests, conformance testing, Open Seadragon, bug fixing, prototyping, brainstorming and general OME-Zarr spec discussions
(10/14 🧵)
(10/14 🧵)
So many fixes and additions to the ViZarr viewer to ensure it's a good basis to rely on as an OME-Zarr web viewer going forward
(9/14 🧵)
(9/14 🧵)
November 17, 2025 at 1:24 PM
So many fixes and additions to the ViZarr viewer to ensure it's a good basis to rely on as an OME-Zarr web viewer going forward
(9/14 🧵)
(9/14 🧵)
A great plugin prototype to run Fractal tasks interactively in napari: Making interoperable workflow tasks accessible directly in a viewer
(8/14 🧵)
(8/14 🧵)
November 17, 2025 at 1:24 PM
A great plugin prototype to run Fractal tasks interactively in napari: Making interoperable workflow tasks accessible directly in a viewer
(8/14 🧵)
(8/14 🧵)
Exciting developments to make OME-Zarr even more accessible from FIJI: Keep an eye out for an update site to empower more drag & drop opening of OME-Zarrs in FIJI
(7/14 🧵)
(7/14 🧵)
November 17, 2025 at 1:24 PM
Exciting developments to make OME-Zarr even more accessible from FIJI: Keep an eye out for an update site to empower more drag & drop opening of OME-Zarrs in FIJI
(7/14 🧵)
(7/14 🧵)
Big progress on the Transformations and Collections RFCs: Setting the stage for the next developments in the spec and towards OME-Zarr 1.0
(6/14 🧵)
(6/14 🧵)
November 17, 2025 at 1:24 PM
Big progress on the Transformations and Collections RFCs: Setting the stage for the next developments in the spec and towards OME-Zarr 1.0
(6/14 🧵)
(6/14 🧵)
A major refresh of the OME-NGFF website (ngff.openmicroscopy.org), making it clearer, more accessible, and easier to navigate
(5/14 🧵)
(5/14 🧵)
November 17, 2025 at 1:24 PM
A major refresh of the OME-NGFF website (ngff.openmicroscopy.org), making it clearer, more accessible, and easier to navigate
(5/14 🧵)
(5/14 🧵)
The energy, the generosity, and the collaborative spirit were amazing to see.
A few highlight outcomes of the hackathon (longer form to follow later):
(4/14 🧵)
A few highlight outcomes of the hackathon (longer form to follow later):
(4/14 🧵)
November 17, 2025 at 1:24 PM
The energy, the generosity, and the collaborative spirit were amazing to see.
A few highlight outcomes of the hackathon (longer form to follow later):
(4/14 🧵)
A few highlight outcomes of the hackathon (longer form to follow later):
(4/14 🧵)
50 developers, researchers and image analysis experts from across the OME-Zarr ecosystem came together to prototype, break things, fix things, design new ideas, and have the conversations that only happen when everyone is in the same room (or around the same dinner table).
(3/14 🧵)
(3/14 🧵)
November 17, 2025 at 1:24 PM
50 developers, researchers and image analysis experts from across the OME-Zarr ecosystem came together to prototype, break things, fix things, design new ideas, and have the conversations that only happen when everyone is in the same room (or around the same dinner table).
(3/14 🧵)
(3/14 🧵)