Johannes Soltwedel
@jo-soltwedel.bsky.social
Post-doc in Bio-image analysis @PoL, TU Dresden, Physicist, Python code-jockey, train enthusiast.
Reposted by Johannes Soltwedel
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
Reposted by Johannes Soltwedel
Can we please discuss accessibility at conferences?
When organizers and schedules assume that everyone can walk fast and climb stairs, people with mobility issues (visible or invisible) might feel excluded.
/
When organizers and schedules assume that everyone can walk fast and climb stairs, people with mobility issues (visible or invisible) might feel excluded.
/
November 20, 2025 at 8:08 AM
Can we please discuss accessibility at conferences?
When organizers and schedules assume that everyone can walk fast and climb stairs, people with mobility issues (visible or invisible) might feel excluded.
/
When organizers and schedules assume that everyone can walk fast and climb stairs, people with mobility issues (visible or invisible) might feel excluded.
/
Reposted by Johannes Soltwedel
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 1:24 PM
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 Johannes Soltwedel
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".
ome-zarr-book.readthedocs.io
ome-zarr-book.readthedocs.io
An Introduction to OME-Zarr for Big Bioimaging Data
ome-zarr-book.readthedocs.io
November 4, 2025 at 3:33 PM
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".
ome-zarr-book.readthedocs.io
ome-zarr-book.readthedocs.io
Hopping on the ✨ 🚅 to Dresden after a week of #OME_NGFF_Hackathon. Looking forward till next time 😃
November 14, 2025 at 7:08 PM
Hopping on the ✨ 🚅 to Dresden after a week of #OME_NGFF_Hackathon. Looking forward till next time 😃
Reposted by Johannes Soltwedel
We wrapped up the symposium part of our 2025 International OME-NGFF workshop on Tuesday. What a phenomenal two days! I'm humbled by the incredible positive energy, talent, and enthusiasm that filled this event.
November 13, 2025 at 5:08 PM
We wrapped up the symposium part of our 2025 International OME-NGFF workshop on Tuesday. What a phenomenal two days! I'm humbled by the incredible positive energy, talent, and enthusiasm that filled this event.
Happy Hackers @ #OME_NGFF_Hackathon
November 13, 2025 at 11:06 PM
Happy Hackers @ #OME_NGFF_Hackathon
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
November 12, 2025 at 5:00 PM
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
Reposted by Johannes Soltwedel
OME-NGFF Hackathon in Zürich just started! We're organizing ourselves to dig into various topics during the next few days. Let's shape the future of microscopy image data standards together. #OME-NGFF_Hackathon #GerBI
November 12, 2025 at 10:27 AM
OME-NGFF Hackathon in Zürich just started! We're organizing ourselves to dig into various topics during the next few days. Let's shape the future of microscopy image data standards together. #OME-NGFF_Hackathon #GerBI
Reposted by Johannes Soltwedel
Co-organized by @nfdi4bioimage.bsky.social through @joshmoore.bsky.social & Christian Tischer, we're happy to see the #OME_NGFF_Hackathon 2024 in full swing! Exciting work bringing forward #OMEZarr for #FAIR bioimage data management. Shout out to the host BioVisionCenter!
@gerbi.bsky.social #NFDI
@gerbi.bsky.social #NFDI
This week, we're hosting the #OME_NGFF_Hackathon 2024 at the BioVisionCenter at the University of Zurich. We're bringing together 40 motivated researchers and specialist for #OMEZarr workflows, #OMEZarr Python tools & #OMEZarr Java tools. (1/3)
November 21, 2024 at 11:20 AM
Co-organized by @nfdi4bioimage.bsky.social through @joshmoore.bsky.social & Christian Tischer, we're happy to see the #OME_NGFF_Hackathon 2024 in full swing! Exciting work bringing forward #OMEZarr for #FAIR bioimage data management. Shout out to the host BioVisionCenter!
@gerbi.bsky.social #NFDI
@gerbi.bsky.social #NFDI
Reposted by Johannes Soltwedel
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...
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
October 7, 2025 at 12:39 PM
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...
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...
Reposted by Johannes Soltwedel
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 🧵)
📅 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 🧵)
August 25, 2025 at 9:07 AM
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 🧵)
📅 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 🧵)
Reposted by Johannes Soltwedel
🚀 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
🏨 Anders Hotel Walsrode | 🍽️ Social events | ✈️ Easy travel
🔗 Seats limited—register now! www.denbi.de/de-nbi-event...
#Hackathon
September 3, 2025 at 8:55 AM
🚀 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
🏨 Anders Hotel Walsrode | 🍽️ Social events | ✈️ Easy travel
🔗 Seats limited—register now! www.denbi.de/de-nbi-event...
#Hackathon
So it seems like #LinkedIn also wants to start using your personal data to train #AI models 🙄 Opt-out here:
www.linkedin.com/mypreference...
www.linkedin.com/mypreference...
LinkedIn Login, Sign in | LinkedIn
Login to LinkedIn to keep in touch with people you know, share ideas, and build your career.
www.linkedin.com
September 22, 2025 at 12:57 PM
So it seems like #LinkedIn also wants to start using your personal data to train #AI models 🙄 Opt-out here:
www.linkedin.com/mypreference...
www.linkedin.com/mypreference...
Reposted by Johannes Soltwedel
The new Thermal Trace app from #C3S and #ECMWF is here! 80+ years of thermal stress data based on “feels-like” temperatures for any location worldwide, now at your fingertips. Fast, intuitive, interactive – and free! Read our article for the full details and head to the app. 🔗
bit.ly/46ZMllL
bit.ly/46ZMllL
August 20, 2025 at 8:10 AM
The new Thermal Trace app from #C3S and #ECMWF is here! 80+ years of thermal stress data based on “feels-like” temperatures for any location worldwide, now at your fingertips. Fast, intuitive, interactive – and free! Read our article for the full details and head to the app. 🔗
bit.ly/46ZMllL
bit.ly/46ZMllL
Whenever I feel down, I have a 👀 at the download statistics of that #opensource data-repository I and my team at OncoRay (Dresden) compiled during my PhD at @tudresden.bsky.social @hzdr.bsky.social.
😌
rodare.hzdr.de/record/3131
😌
rodare.hzdr.de/record/3131
August 7, 2025 at 8:54 AM
Whenever I feel down, I have a 👀 at the download statistics of that #opensource data-repository I and my team at OncoRay (Dresden) compiled during my PhD at @tudresden.bsky.social @hzdr.bsky.social.
😌
rodare.hzdr.de/record/3131
😌
rodare.hzdr.de/record/3131
Reposted by Johannes Soltwedel
🎉 Amazing NEWS for #ImageAnalysis & #LifeSciences folks!
The ultimate #imageanalysis #hattrick is here 🧠🔬✨
www.biovoxxel.de/individual-w...
Read the 🧵👇
All necessary info and links at the end !
#bioimaging #learning #science #lifescience #microscopy #fiji #imagej #machinelearning #deeplearning
The ultimate #imageanalysis #hattrick is here 🧠🔬✨
www.biovoxxel.de/individual-w...
Read the 🧵👇
All necessary info and links at the end !
#bioimaging #learning #science #lifescience #microscopy #fiji #imagej #machinelearning #deeplearning
July 21, 2025 at 7:49 PM
🎉 Amazing NEWS for #ImageAnalysis & #LifeSciences folks!
The ultimate #imageanalysis #hattrick is here 🧠🔬✨
www.biovoxxel.de/individual-w...
Read the 🧵👇
All necessary info and links at the end !
#bioimaging #learning #science #lifescience #microscopy #fiji #imagej #machinelearning #deeplearning
The ultimate #imageanalysis #hattrick is here 🧠🔬✨
www.biovoxxel.de/individual-w...
Read the 🧵👇
All necessary info and links at the end !
#bioimaging #learning #science #lifescience #microscopy #fiji #imagej #machinelearning #deeplearning
Reposted by Johannes Soltwedel
Great to see @alexhego.bsky.social share instructions on a DL pixel‑classification problem we worked on at image.sc. If you’re working on a challenging 3D DL semantic‑segmentation problem and need more options than most tools provide, check out this repository. github.com/AlexHego/DL-...
GitHub - AlexHego/DL-pixel-classification
Contribute to AlexHego/DL-pixel-classification development by creating an account on GitHub.
github.com
July 21, 2025 at 6:41 PM
Great to see @alexhego.bsky.social share instructions on a DL pixel‑classification problem we worked on at image.sc. If you’re working on a challenging 3D DL semantic‑segmentation problem and need more options than most tools provide, check out this repository. github.com/AlexHego/DL-...
Suitable @poldresden.bsky.social farewell cake for a #bioimage analyst? 🥮🤤
July 21, 2025 at 8:46 PM
Suitable @poldresden.bsky.social farewell cake for a #bioimage analyst? 🥮🤤
Reposted by Johannes Soltwedel
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!!! 🔥🔥🔥
More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥
Funded Projects - swissuniversities
www.swissuniversities.ch
July 21, 2025 at 7:29 AM
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!!! 🔥🔥🔥
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!
Scalable #RDM solutions in the ome-zarr-verse, here we come!
July 18, 2025 at 10:43 AM
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!
Scalable #RDM solutions in the ome-zarr-verse, here we come!
Reposted by Johannes Soltwedel
#EUProject | #BioImaging & AI
➡️ BioImage Model Zoo by @ai4life.bsky.social is a platform for #AI models in biological imaging
➡️ To find out about the training courses and tools available to help you use the platform correctly for your area of study, visit: www.embrc.eu/project/ai4life/
🌊🧪🦑
➡️ BioImage Model Zoo by @ai4life.bsky.social is a platform for #AI models in biological imaging
➡️ To find out about the training courses and tools available to help you use the platform correctly for your area of study, visit: www.embrc.eu/project/ai4life/
🌊🧪🦑
July 16, 2025 at 1:48 PM
#EUProject | #BioImaging & AI
➡️ BioImage Model Zoo by @ai4life.bsky.social is a platform for #AI models in biological imaging
➡️ To find out about the training courses and tools available to help you use the platform correctly for your area of study, visit: www.embrc.eu/project/ai4life/
🌊🧪🦑
➡️ BioImage Model Zoo by @ai4life.bsky.social is a platform for #AI models in biological imaging
➡️ To find out about the training courses and tools available to help you use the platform correctly for your area of study, visit: www.embrc.eu/project/ai4life/
🌊🧪🦑
Reposted by Johannes Soltwedel
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...
www.fmi.ch/education-ca...
July 16, 2025 at 6:26 PM
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...
www.fmi.ch/education-ca...
#bioimage 🔬 data #visualization and #exploration in @napari.org with the napari-clusters-plotter (0.10.0) becoming yet a bit more versatile: Select objects & put them into new layers for processing, introspection or whatever. Works for all layers, of course! #bioimageanalysis
@mazoc.bsky.social
@mazoc.bsky.social
July 16, 2025 at 2:09 PM
#bioimage 🔬 data #visualization and #exploration in @napari.org with the napari-clusters-plotter (0.10.0) becoming yet a bit more versatile: Select objects & put them into new layers for processing, introspection or whatever. Works for all layers, of course! #bioimageanalysis
@mazoc.bsky.social
@mazoc.bsky.social
Reposted by Johannes Soltwedel
Are you looking for an exciting position at the intersection of super-resolution microscopy and AI? Then check out the PhD and PostDoc position we offer for a joint project with the Group of Stephan Hell at MPI Göttingen. Please share with anyone interested, read on for links and details.
July 7, 2025 at 11:46 AM
Are you looking for an exciting position at the intersection of super-resolution microscopy and AI? Then check out the PhD and PostDoc position we offer for a joint project with the Group of Stephan Hell at MPI Göttingen. Please share with anyone interested, read on for links and details.