Anna Klemm
@ahklemm.bsky.social
BioImage Analyst
Head of BioImage Informatics, SciLifeLab
NBIS, Sweden
https://www.scilifelab.se/units/bioimage-informatics/
Head of BioImage Informatics, SciLifeLab
NBIS, Sweden
https://www.scilifelab.se/units/bioimage-informatics/
Reposted by Anna Klemm
Felix Zhou's u-Segment3D is out:
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
November 12, 2025 at 2:41 AM
Felix Zhou's u-Segment3D is out:
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
Reposted by Anna Klemm
🚀Join Helsinki BioImaging as an Image Analysis Specialist🖥️to support cross-disciplinary image analysis projects. If you love coding and are interested in working at the crossroads of computer science and biology, apply by 🗓️ November 15, 2025⤵️
jobs.helsinki.fi/job/Helsinki...
#jobopening
jobs.helsinki.fi/job/Helsinki...
#jobopening
Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging
Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging
jobs.helsinki.fi
October 10, 2025 at 1:58 PM
🚀Join Helsinki BioImaging as an Image Analysis Specialist🖥️to support cross-disciplinary image analysis projects. If you love coding and are interested in working at the crossroads of computer science and biology, apply by 🗓️ November 15, 2025⤵️
jobs.helsinki.fi/job/Helsinki...
#jobopening
jobs.helsinki.fi/job/Helsinki...
#jobopening
Reposted by Anna Klemm
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 Anna Klemm
Great to see Node staff, #i4A training grantee hernanmn.bsky.social & others at the EMBO "Advanced Methods in BioImage Analysis" course! @ahklemm.bsky.social @perrinegil.bsky.social @jytinevez.bsky.social @france-bioimaging.bsky.social @iemcas.bsky.social
More🔽
www.eurobioimaging.eu/news/success...
More🔽
www.eurobioimaging.eu/news/success...
October 2, 2025 at 3:23 PM
Great to see Node staff, #i4A training grantee hernanmn.bsky.social & others at the EMBO "Advanced Methods in BioImage Analysis" course! @ahklemm.bsky.social @perrinegil.bsky.social @jytinevez.bsky.social @france-bioimaging.bsky.social @iemcas.bsky.social
More🔽
www.eurobioimaging.eu/news/success...
More🔽
www.eurobioimaging.eu/news/success...
Reposted by Anna Klemm
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
#HappyFluorescenceFriday!
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
September 23, 2025 at 3:48 PM
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
Reposted by Anna Klemm
Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)?
Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
Next #GloBIAS seminar is coming up: join us on 22nd of September, 4 pm CEST to hear from Jean-Yves Tinevez about: The scientific added value of a core-facility dedicated to Bioimage Analysis services. Want to register? -> www.globias.org/activities/b...
September 18, 2025 at 9:26 AM
Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)?
Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
Reposted by Anna Klemm
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
@tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev
September 18, 2025 at 7:23 AM
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
@tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev
Reposted by Anna Klemm
Let's finish the day with the round table discussion 🗣️💬 fantastically led by @ahklemm.bsky.social and Suganya Sivagurunathan from @scilifelab.se & Uppsala University!
So many interesting comments about reproducible science 🧪 and commercial vs open-source software 👩💻 in image facility projects 🔬
So many interesting comments about reproducible science 🧪 and commercial vs open-source software 👩💻 in image facility projects 🔬
September 17, 2025 at 4:07 PM
Let's finish the day with the round table discussion 🗣️💬 fantastically led by @ahklemm.bsky.social and Suganya Sivagurunathan from @scilifelab.se & Uppsala University!
So many interesting comments about reproducible science 🧪 and commercial vs open-source software 👩💻 in image facility projects 🔬
So many interesting comments about reproducible science 🧪 and commercial vs open-source software 👩💻 in image facility projects 🔬
Reposted by Anna Klemm
What better way of celebrating the end of our 2nd day of training classes than with pizza 🍕, refreshements 🍻 and selfies 🤳! 😜
September 16, 2025 at 6:20 AM
What better way of celebrating the end of our 2nd day of training classes than with pizza 🍕, refreshements 🍻 and selfies 🤳! 😜
Reposted by Anna Klemm
🚨 Wow, that really sounds like an amazing opportunity… If I were a bit younger, I would start preparing my application already… 😮
www.scilifelab.se/news/ready-t...
www.scilifelab.se/news/ready-t...
Ready to shape the future of AI in life science?
The next call for DDLS Fellows is opening soon, offering an outstanding opportunity for ambitious young researchers to establish their own internationally competitive research groups. This round has a...
www.scilifelab.se
September 12, 2025 at 1:46 PM
🚨 Wow, that really sounds like an amazing opportunity… If I were a bit younger, I would start preparing my application already… 😮
www.scilifelab.se/news/ready-t...
www.scilifelab.se/news/ready-t...
Reposted by Anna Klemm
Better ML for cryo-ET starts with better benchmarks.
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods
A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...
doi.org
August 26, 2025 at 2:22 PM
Better ML for cryo-ET starts with better benchmarks.
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
Reposted by Anna Klemm
Thrilled to announce that I'm back in Buenos Aires and open for image & data analysis projects!
My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally.
Check out my portfolio and contact:
acorbat.github.io
My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally.
Check out my portfolio and contact:
acorbat.github.io
iPortfolio Bootstrap Template - Index
acorbat.github.io
August 26, 2025 at 2:54 PM
Thrilled to announce that I'm back in Buenos Aires and open for image & data analysis projects!
My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally.
Check out my portfolio and contact:
acorbat.github.io
My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally.
Check out my portfolio and contact:
acorbat.github.io
Reposted by Anna Klemm
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!
Reposted by Anna Klemm
Next one in the #GloBIAS seminar series: Behind the Scenes at SciLifeLab BIIF: Lessons from Managing a National Bioimage Analysis Support Unit. Presented by Anna Klemm, head of BioImage Informatics Infrastructure Unit, Uppsala University, Sweden
Wednesday, 27th of August, 2pm CEST
Wednesday, 27th of August, 2pm CEST
August 20, 2025 at 3:04 PM
Next one in the #GloBIAS seminar series: Behind the Scenes at SciLifeLab BIIF: Lessons from Managing a National Bioimage Analysis Support Unit. Presented by Anna Klemm, head of BioImage Informatics Infrastructure Unit, Uppsala University, Sweden
Wednesday, 27th of August, 2pm CEST
Wednesday, 27th of August, 2pm CEST
Reposted by Anna Klemm
The #CBIAS2025 abstract deadline is this Sunday, August 31st. Submit your #BioImageAnalysis work, whether it’s a new tool or a biological discovery. #EarlyCareerResearchers, this is for you! Short and flash talk slots are up for grabs.
www.crick.ac.uk/whats-on/cri...
www.crick.ac.uk/whats-on/cri...
August 26, 2025 at 11:12 AM
The #CBIAS2025 abstract deadline is this Sunday, August 31st. Submit your #BioImageAnalysis work, whether it’s a new tool or a biological discovery. #EarlyCareerResearchers, this is for you! Short and flash talk slots are up for grabs.
www.crick.ac.uk/whats-on/cri...
www.crick.ac.uk/whats-on/cri...
Reposted by Anna Klemm
I am stunned!
First edition of the "Bio-Imaging with Shakespeare" LinkedIn Newsletter (buff.ly/8x7Shiq) is out for 15h and already 130 subscribers.
If you are interested in the topic FOLLOW ME on LinkedIn and Bsky and SUBSCRIBE
on LinkedIn buff.ly/cLPh8eZ
#bioimageanalysis #biovoxxel #fiji
First edition of the "Bio-Imaging with Shakespeare" LinkedIn Newsletter (buff.ly/8x7Shiq) is out for 15h and already 130 subscribers.
If you are interested in the topic FOLLOW ME on LinkedIn and Bsky and SUBSCRIBE
on LinkedIn buff.ly/cLPh8eZ
#bioimageanalysis #biovoxxel #fiji
August 13, 2025 at 11:59 PM
I am stunned!
First edition of the "Bio-Imaging with Shakespeare" LinkedIn Newsletter (buff.ly/8x7Shiq) is out for 15h and already 130 subscribers.
If you are interested in the topic FOLLOW ME on LinkedIn and Bsky and SUBSCRIBE
on LinkedIn buff.ly/cLPh8eZ
#bioimageanalysis #biovoxxel #fiji
First edition of the "Bio-Imaging with Shakespeare" LinkedIn Newsletter (buff.ly/8x7Shiq) is out for 15h and already 130 subscribers.
If you are interested in the topic FOLLOW ME on LinkedIn and Bsky and SUBSCRIBE
on LinkedIn buff.ly/cLPh8eZ
#bioimageanalysis #biovoxxel #fiji
Reposted by Anna Klemm
A new extension! Rémy made a wrapper of @albertdm.bsky.social + @maweigert.bsky.social 's Spotiflow (2/3)
forum.image.sc/t/qupath-ext...
forum.image.sc/t/qupath-ext...
QuPath extension Spotiflow is now available
Hello @qupath team & users, We are pleased to announce a new qupath-spotiflow-extension to handle spotiflow in QuPath 🎉 ! This extension reproduces the logic behind the qupath-extension-cellpose to ...
forum.image.sc
August 12, 2025 at 3:10 PM
A new extension! Rémy made a wrapper of @albertdm.bsky.social + @maweigert.bsky.social 's Spotiflow (2/3)
forum.image.sc/t/qupath-ext...
forum.image.sc/t/qupath-ext...
Reposted by Anna Klemm
My tutorial materials & slides about #Reproducible #BioImageAnalysis using Python, Napari, Jupyter and #AI are available #openaccess.
Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩
scads.github.io/embo-lsm-bia...
Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩
scads.github.io/embo-lsm-bia...
August 12, 2025 at 5:57 PM
My tutorial materials & slides about #Reproducible #BioImageAnalysis using Python, Napari, Jupyter and #AI are available #openaccess.
Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩
scads.github.io/embo-lsm-bia...
Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩
scads.github.io/embo-lsm-bia...
Reposted by Anna Klemm
New Imaging Mass Cytometry data in the Image Data Resource (IDR, idr.openmicroscopy.org).
IDR: Image Data Resource
idr.openmicroscopy.org
August 6, 2025 at 4:28 PM
New Imaging Mass Cytometry data in the Image Data Resource (IDR, idr.openmicroscopy.org).
Reposted by Anna Klemm
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!!! 🔥🔥🔥
Reposted by Anna Klemm
Preprint alert! Want to hear more about the coolest new society on the block? You should check out our new preprint discussing @globias.bsky.social ! Hop into 🧵 for a couple quick highlights (1/x):
GloBIAS: strengthening the foundations of BioImage Analysis
There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of b...
arxiv.org
July 10, 2025 at 10:23 PM
Preprint alert! Want to hear more about the coolest new society on the block? You should check out our new preprint discussing @globias.bsky.social ! Hop into 🧵 for a couple quick highlights (1/x):
Reposted by Anna Klemm
Day 2 of #Zidas2025 is happening!
After a lecture from @ahklemm.bsky.social, it's now time for hands on with @ilastik-team.bsky.social by @benediktbest.bsky.social from Anna Kreshuk's lab and some tracking in the afternoon with #Trackmate from @jytinevez.bsky.social !
After a lecture from @ahklemm.bsky.social, it's now time for hands on with @ilastik-team.bsky.social by @benediktbest.bsky.social from Anna Kreshuk's lab and some tracking in the afternoon with #Trackmate from @jytinevez.bsky.social !
July 8, 2025 at 9:22 AM
Day 2 of #Zidas2025 is happening!
After a lecture from @ahklemm.bsky.social, it's now time for hands on with @ilastik-team.bsky.social by @benediktbest.bsky.social from Anna Kreshuk's lab and some tracking in the afternoon with #Trackmate from @jytinevez.bsky.social !
After a lecture from @ahklemm.bsky.social, it's now time for hands on with @ilastik-team.bsky.social by @benediktbest.bsky.social from Anna Kreshuk's lab and some tracking in the afternoon with #Trackmate from @jytinevez.bsky.social !
Reposted by Anna Klemm
Did you ever notice discrepancies in benchmarking of bioinformatics tools? We did too! Setting out to benchmark spatial clustering methods, we encountered major reproducibility issues in previous benchmarks and questionable "ground truths".
More in our preprint: www.biorxiv.org/content/10.1...
More in our preprint: www.biorxiv.org/content/10.1...
Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering
Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcript...
www.biorxiv.org
July 2, 2025 at 12:05 PM
Did you ever notice discrepancies in benchmarking of bioinformatics tools? We did too! Setting out to benchmark spatial clustering methods, we encountered major reproducibility issues in previous benchmarks and questionable "ground truths".
More in our preprint: www.biorxiv.org/content/10.1...
More in our preprint: www.biorxiv.org/content/10.1...
Reposted by Anna Klemm
New tool CellSeg3D, from the group of blu.ski/@epfl-brainmind professor Mackenzie Mathis @trackingactions.bsky.social enables self-supervised 3D cell segmentation in fluorescent microscopy,👇 labeling time & 👆quantitative analysis -
paper: elifesciences.org/articles/99848
news: tinyurl.com/y2hpmbb9
paper: elifesciences.org/articles/99848
news: tinyurl.com/y2hpmbb9
Self-supervised, label-free 3D cell imaging is here
EPFL researchers introduce CellSeg3D, a self-supervised tool for 3D cell segmentation in fluorescence microscopy, eliminating the need for manual labeling and enhancing accessibility for various biolo...
actu.epfl.ch
June 30, 2025 at 6:16 PM
New tool CellSeg3D, from the group of blu.ski/@epfl-brainmind professor Mackenzie Mathis @trackingactions.bsky.social enables self-supervised 3D cell segmentation in fluorescent microscopy,👇 labeling time & 👆quantitative analysis -
paper: elifesciences.org/articles/99848
news: tinyurl.com/y2hpmbb9
paper: elifesciences.org/articles/99848
news: tinyurl.com/y2hpmbb9
Reposted by Anna Klemm
Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology!
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
F-BIAS: Towards a distributed national core facility for bioimage analysis †
Author summary We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territo...
journals.plos.org
June 11, 2025 at 8:29 AM
Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology!
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility