Virginie Uhlmann
@virginieuhlmann.bsky.social
Assistant Professor in Bioimaging and Data Analysis and Director of the BioVisionCenter at UZH; Research Group Leader at EMBL-EBI. Loves image analysis, mountains, and birds.
So nice to see this!!!
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 8:33 PM
So nice to see this!!!
Reposted by Virginie Uhlmann
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 🧵
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.
Reposted by Virginie Uhlmann
📢 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
Seeing our good old AURA-Net from 2021 (doi.org/10.1109/ISBI...) end up 2nd on a 2025 U-Net variants leaderboard was not on my bingo card for this year, but here we are
(source: doi.org/10.48550/arX...)
(source: doi.org/10.48550/arX...)
November 5, 2025 at 1:18 PM
Seeing our good old AURA-Net from 2021 (doi.org/10.1109/ISBI...) end up 2nd on a 2025 U-Net variants leaderboard was not on my bingo card for this year, but here we are
(source: doi.org/10.48550/arX...)
(source: doi.org/10.48550/arX...)
If you ever used napari in your research, take a moment to read this.
Napari, like many other resources in the bioimaging world, is freely available despite the fact that it costs many people much time and efforts to develop and maintain it.
Now you get a chance to give back, don't miss it :)
Napari, like many other resources in the bioimaging world, is freely available despite the fact that it costs many people much time and efforts to develop and maintain it.
Now you get a chance to give back, don't miss it :)
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:
napari.org/island-dispa...
napari.org/island-dispa...
October 22, 2025 at 11:14 AM
If you ever used napari in your research, take a moment to read this.
Napari, like many other resources in the bioimaging world, is freely available despite the fact that it costs many people much time and efforts to develop and maintain it.
Now you get a chance to give back, don't miss it :)
Napari, like many other resources in the bioimaging world, is freely available despite the fact that it costs many people much time and efforts to develop and maintain it.
Now you get a chance to give back, don't miss it :)
Reposted by Virginie Uhlmann
My take: Engineering *is* important. Ideas are cheap. Novelty is overrated. "Hyperparameter tuning" is a cynically dismissive term for something that is in fact the real, difficult problem.
Sometimes I’ll see a paper that implements an idea I’ve had but implements it poorly for engineering reasons. But then it’s hard to write a follow up paper because it’s not “novel” anymore
October 9, 2025 at 2:13 PM
My take: Engineering *is* important. Ideas are cheap. Novelty is overrated. "Hyperparameter tuning" is a cynically dismissive term for something that is in fact the real, difficult problem.
Reposted by Virginie Uhlmann
Thrilled to be speaking at #CBIAS2025! 🥳
CBIAS has been my scientific home since the beginning of my PhD, providing a welcoming space for early-career researchers. This year feels extra special, as I’ll be presenting my work in the final year of my PhD.
Join us if you get the chance! 😃
CBIAS has been my scientific home since the beginning of my PhD, providing a welcoming space for early-career researchers. This year feels extra special, as I’ll be presenting my work in the final year of my PhD.
Join us if you get the chance! 😃
The provisional program for The 6th Crick Bioimage Analysis Symposium (#CBIAS2025) is live!
Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.
Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.
Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
September 23, 2025 at 12:17 PM
Thrilled to be speaking at #CBIAS2025! 🥳
CBIAS has been my scientific home since the beginning of my PhD, providing a welcoming space for early-career researchers. This year feels extra special, as I’ll be presenting my work in the final year of my PhD.
Join us if you get the chance! 😃
CBIAS has been my scientific home since the beginning of my PhD, providing a welcoming space for early-career researchers. This year feels extra special, as I’ll be presenting my work in the final year of my PhD.
Join us if you get the chance! 😃
Reposted by Virginie Uhlmann
The program for the #CBIAS2025 is now live – space is limited, so register now to secure your spot! 24th-25th Nov, Wellcome Trust, London (UK) - see you there!
🔗⬇️
www.crick.ac.uk/whats-on/cri...
🔗⬇️
www.crick.ac.uk/whats-on/cri...
September 23, 2025 at 1:13 PM
The program for the #CBIAS2025 is now live – space is limited, so register now to secure your spot! 24th-25th Nov, Wellcome Trust, London (UK) - see you there!
🔗⬇️
www.crick.ac.uk/whats-on/cri...
🔗⬇️
www.crick.ac.uk/whats-on/cri...
You may have heard me talk about learned shape representations for a long time, but it took @afoix.bsky.social's hard work to bring it to life 🍾 Catch her at @neuripsconf.bsky.social to find out more!!
Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)
📄 arxiv.org/pdf/2507.01009 (1/N)
September 23, 2025 at 8:57 AM
You may have heard me talk about learned shape representations for a long time, but it took @afoix.bsky.social's hard work to bring it to life 🍾 Catch her at @neuripsconf.bsky.social to find out more!!
Reposted by Virginie Uhlmann
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...
September 18, 2025 at 9:42 AM
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...
I am in this picture and I don't like it
Science: only when you write up the manuscript, you realize what you should have done.
September 16, 2025 at 7:27 PM
I am in this picture and I don't like it
Reposted by Virginie Uhlmann
🎉 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
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
September 15, 2025 at 9:57 AM
🎉 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
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
Reposted by Virginie Uhlmann
The abstract submission deadline for #CBIAS2025 has just closed and, for the first time, we have a near perfect gender-balance in our abstract submissions.
In fact, we have slightly more submissions from women than men.
In fact, we have slightly more submissions from women than men.
a man with his arms crossed is smiling and saying noice !
ALT: a man with his arms crossed is smiling and saying noice !
media.tenor.com
September 1, 2025 at 9:44 AM
The abstract submission deadline for #CBIAS2025 has just closed and, for the first time, we have a near perfect gender-balance in our abstract submissions.
In fact, we have slightly more submissions from women than men.
In fact, we have slightly more submissions from women than men.
Reposted by Virginie Uhlmann
I'll be there! Giving a talk! and hacking on _something_ for a few days!
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 9:32 AM
I'll be there! Giving a talk! and hacking on _something_ for a few days!
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!
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!
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 1:50 PM
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!
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!
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!!! 🔥🔥🔥
And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be:
www.youtube.com/watch?v=8t8R...
www.youtube.com/watch?v=8t8R...
Bioimaging | UZH Research Spotlight
YouTube video by Universität Zürich
www.youtube.com
June 24, 2025 at 5:39 PM
And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be:
www.youtube.com/watch?v=8t8R...
www.youtube.com/watch?v=8t8R...
Hey bioimaging folks, join us for the next OME-NGFF Community Call on June 24 at 9:00 CEST and 17:00 CEST!
Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...
Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...
June 3, 2025 at 10:17 AM
Hey bioimaging folks, join us for the next OME-NGFF Community Call on June 24 at 9:00 CEST and 17:00 CEST!
Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...
Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...
Reposted by Virginie Uhlmann
#HappyFluorescenceFriday
#microscopycommunity. @bioimagingna.bsky.social was at OME205 with @openmicroscopy.org this past week with the makers of BioFormats. OME-TIFF, OME-Zarr and OMERO sharing their work and listening to your challenges.
#microscopycommunity. @bioimagingna.bsky.social was at OME205 with @openmicroscopy.org this past week with the makers of BioFormats. OME-TIFF, OME-Zarr and OMERO sharing their work and listening to your challenges.
May 2, 2025 at 4:29 PM
#HappyFluorescenceFriday
#microscopycommunity. @bioimagingna.bsky.social was at OME205 with @openmicroscopy.org this past week with the makers of BioFormats. OME-TIFF, OME-Zarr and OMERO sharing their work and listening to your challenges.
#microscopycommunity. @bioimagingna.bsky.social was at OME205 with @openmicroscopy.org this past week with the makers of BioFormats. OME-TIFF, OME-Zarr and OMERO sharing their work and listening to your challenges.
Reposted by Virginie Uhlmann
🚀 We just released a major Fractal update!
More flexible workflows, dynamic monitoring, and a new history system for better traceability – built to handle Terabytes of high-dimensional microscopy data in #OME-Zarr.
Full announcement post here: fractal-analytics-platform.github.io/news/2025-04...
More flexible workflows, dynamic monitoring, and a new history system for better traceability – built to handle Terabytes of high-dimensional microscopy data in #OME-Zarr.
Full announcement post here: fractal-analytics-platform.github.io/news/2025-04...
April 29, 2025 at 8:23 AM
🚀 We just released a major Fractal update!
More flexible workflows, dynamic monitoring, and a new history system for better traceability – built to handle Terabytes of high-dimensional microscopy data in #OME-Zarr.
Full announcement post here: fractal-analytics-platform.github.io/news/2025-04...
More flexible workflows, dynamic monitoring, and a new history system for better traceability – built to handle Terabytes of high-dimensional microscopy data in #OME-Zarr.
Full announcement post here: fractal-analytics-platform.github.io/news/2025-04...
Reposted by Virginie Uhlmann
How can AI help you to analyze your microscopy images?
Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6!
Applications are due 🚨 April 30 🚨
Read on for more! 👇
www.mbl.edu/education/ad...
Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6!
Applications are due 🚨 April 30 🚨
Read on for more! 👇
www.mbl.edu/education/ad...
AI@MBL: Machine Learning for Microscopy Image Analysis | Marine Biological Laboratory
The goal of this course is to familiarize researchers in the life sciences with state-of-the-art deep learning techniques for microscopy image analysis and to introduce them to tools and frameworks th...
www.mbl.edu
April 18, 2025 at 6:48 PM
How can AI help you to analyze your microscopy images?
Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6!
Applications are due 🚨 April 30 🚨
Read on for more! 👇
www.mbl.edu/education/ad...
Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6!
Applications are due 🚨 April 30 🚨
Read on for more! 👇
www.mbl.edu/education/ad...
Reposted by Virginie Uhlmann
What an incredible first week for Etch A Cell - ImmunoExplorers! 🚀
✨ 688 volunteers have together contributed 23,474 classifications (and counting!), helping us reach 72% completion of our first dataset.
Join the effort here: 🔗 www.zooniverse.org/projects/h-s...
Thank you 🙌 #CitizenScience
✨ 688 volunteers have together contributed 23,474 classifications (and counting!), helping us reach 72% completion of our first dataset.
Join the effort here: 🔗 www.zooniverse.org/projects/h-s...
Thank you 🙌 #CitizenScience
March 27, 2025 at 11:17 AM
What an incredible first week for Etch A Cell - ImmunoExplorers! 🚀
✨ 688 volunteers have together contributed 23,474 classifications (and counting!), helping us reach 72% completion of our first dataset.
Join the effort here: 🔗 www.zooniverse.org/projects/h-s...
Thank you 🙌 #CitizenScience
✨ 688 volunteers have together contributed 23,474 classifications (and counting!), helping us reach 72% completion of our first dataset.
Join the effort here: 🔗 www.zooniverse.org/projects/h-s...
Thank you 🙌 #CitizenScience
Reposted by Virginie Uhlmann
Be a part of groundbreaking research!
🔬 Help us study immune cells & fight transplant rejection:
www.zooniverse.org/projects/h-s...
Together, we can make a difference! 💪 #CitizenScience #KidneyHealth #Zooniverse
(6/6) ✅
🔬 Help us study immune cells & fight transplant rejection:
www.zooniverse.org/projects/h-s...
Together, we can make a difference! 💪 #CitizenScience #KidneyHealth #Zooniverse
(6/6) ✅
March 19, 2025 at 10:41 AM
Be a part of groundbreaking research!
🔬 Help us study immune cells & fight transplant rejection:
www.zooniverse.org/projects/h-s...
Together, we can make a difference! 💪 #CitizenScience #KidneyHealth #Zooniverse
(6/6) ✅
🔬 Help us study immune cells & fight transplant rejection:
www.zooniverse.org/projects/h-s...
Together, we can make a difference! 💪 #CitizenScience #KidneyHealth #Zooniverse
(6/6) ✅
Share this with everyone you know and help us hunt the immune cells!!!
There's a lot we still don’t know about immune cells in rejection:
❓ Which immune cells are there?
❓ Are they activated?
❓ What are they doing?
🧵 (3/6)
❓ Which immune cells are there?
❓ Are they activated?
❓ What are they doing?
🧵 (3/6)
March 19, 2025 at 3:23 PM
Share this with everyone you know and help us hunt the immune cells!!!