@globias.bsky.social 2026 conference is ongoing with heavy focus on AI.
Is AI there to help is? Is it there to replace us? Where will will be in a few years? Are we turning in AI servants?
#bioimageAnalysis
Is AI there to help is? Is it there to replace us? Where will will be in a few years? Are we turning in AI servants?
#bioimageAnalysis
November 11, 2026 at 1:24 PM
@globias.bsky.social 2026 conference is ongoing with heavy focus on AI.
Is AI there to help is? Is it there to replace us? Where will will be in a few years? Are we turning in AI servants?
#bioimageAnalysis
Is AI there to help is? Is it there to replace us? Where will will be in a few years? Are we turning in AI servants?
#bioimageAnalysis
👉 In Fiji: Help › Update… › Manage update sites › BiaPy
🔗 biapyx.github.io
📄 BiaPy paper: doi.org/10.1038/s415...
🙌 Thanks to all collaborators that made BiaPy possible 😍
#BiaPy #Fiji #ImageJ #BioimageAnalysis #Microscopy #DeepLearning #BioImageModelZoo #nnUNet #Cellpose #OpenSource
🔗 biapyx.github.io
📄 BiaPy paper: doi.org/10.1038/s415...
🙌 Thanks to all collaborators that made BiaPy possible 😍
#BiaPy #Fiji #ImageJ #BioimageAnalysis #Microscopy #DeepLearning #BioImageModelZoo #nnUNet #Cellpose #OpenSource
githubforumscemailtwittersignal
BiaPy is an open source Python library for building bioimage analysis pipelines
biapyx.github.io
November 11, 2026 at 3:32 PM
👉 In Fiji: Help › Update… › Manage update sites › BiaPy
🔗 biapyx.github.io
📄 BiaPy paper: doi.org/10.1038/s415...
🙌 Thanks to all collaborators that made BiaPy possible 😍
#BiaPy #Fiji #ImageJ #BioimageAnalysis #Microscopy #DeepLearning #BioImageModelZoo #nnUNet #Cellpose #OpenSource
🔗 biapyx.github.io
📄 BiaPy paper: doi.org/10.1038/s415...
🙌 Thanks to all collaborators that made BiaPy possible 😍
#BiaPy #Fiji #ImageJ #BioimageAnalysis #Microscopy #DeepLearning #BioImageModelZoo #nnUNet #Cellpose #OpenSource
New review article by our colleague Carl-Magnus Svensson!
The article explores how AI is increasingly being used to support the analysis and understanding of fungal infections in research and diagnostics.
Congratulations, Carl!
doi.org/10.1177/2049...
#BioimageAnalysis #FungalInfections
The article explores how AI is increasingly being used to support the analysis and understanding of fungal infections in research and diagnostics.
Congratulations, Carl!
doi.org/10.1177/2049...
#BioimageAnalysis #FungalInfections
Sage Journals: Discover world-class research
Subscription and open access journals from Sage, the world's leading independent academic publisher.
doi.org
November 10, 2026 at 10:31 AM
New review article by our colleague Carl-Magnus Svensson!
The article explores how AI is increasingly being used to support the analysis and understanding of fungal infections in research and diagnostics.
Congratulations, Carl!
doi.org/10.1177/2049...
#BioimageAnalysis #FungalInfections
The article explores how AI is increasingly being used to support the analysis and understanding of fungal infections in research and diagnostics.
Congratulations, Carl!
doi.org/10.1177/2049...
#BioimageAnalysis #FungalInfections
AI models learned cellular features from ~1.77 million Cell Painting images and improved benchmark retrieval over CellProfiler. Better image representations still need biological interpretation. 🔬
#BioimageAnalysis
Nature Methods ·
doi.org/10.1038/s415...
#BioimageAnalysis
Nature Methods ·
doi.org/10.1038/s415...
Advancing morphological profiling with self-supervised learning through comparative insights into representation learning of cellular perturbations - Nature Methods
This Article presents a large-scale analysis of self-supervised learning methods for high-content morphological profiling.
doi.org
November 1, 2026 at 7:22 AM
AI models learned cellular features from ~1.77 million Cell Painting images and improved benchmark retrieval over CellProfiler. Better image representations still need biological interpretation. 🔬
#BioimageAnalysis
Nature Methods ·
doi.org/10.1038/s415...
#BioimageAnalysis
Nature Methods ·
doi.org/10.1038/s415...
Thanks to all authors and the HPC teams at the Crick, VIB/VSC and Liverpool. If you run an imaging facility, we hope this helps you decide whether, and how, to take the step. Comments welcome! 7/9
#bioimaging #HPC #bioimageanalysis #corefacilities
#bioimaging #HPC #bioimageanalysis #corefacilities
October 30, 2026 at 11:01 AM
Thanks to all authors and the HPC teams at the Crick, VIB/VSC and Liverpool. If you run an imaging facility, we hope this helps you decide whether, and how, to take the step. Comments welcome! 7/9
#bioimaging #HPC #bioimageanalysis #corefacilities
#bioimaging #HPC #bioimageanalysis #corefacilities
Code, step-by-step beginner guide and documentation (Python notebook and a Matlab version): github.com/Marien-kaefe...
Feedback and questions welcome!
#bioimageanalysis #bioimaging #cardiacresearch #opensource #microscopy
Feedback and questions welcome!
#bioimageanalysis #bioimaging #cardiacresearch #opensource #microscopy
GitHub - Marien-kaefer/BeatRatePy
Contribute to Marien-kaefer/BeatRatePy development by creating an account on GitHub.
github.com
October 29, 2026 at 9:54 AM
Code, step-by-step beginner guide and documentation (Python notebook and a Matlab version): github.com/Marien-kaefe...
Feedback and questions welcome!
#bioimageanalysis #bioimaging #cardiacresearch #opensource #microscopy
Feedback and questions welcome!
#bioimageanalysis #bioimaging #cardiacresearch #opensource #microscopy
Proud to sponsor #CBIAS2026! 🔬📊
The @crick.ac.uk BioImage Analysis Symposium program is live (Nov 23–24, hybrid).
🔗 https://f.mtr.cool/vk4hi8lyp2
#BioImageAnalysis #CoreFacilities
The @crick.ac.uk BioImage Analysis Symposium program is live (Nov 23–24, hybrid).
🔗 https://f.mtr.cool/vk4hi8lyp2
#BioImageAnalysis #CoreFacilities
Crick BioImage Analysis Symposium 2026
f.mtr.cool
October 22, 2026 at 9:04 AM
Proud to sponsor #CBIAS2026! 🔬📊
The @crick.ac.uk BioImage Analysis Symposium program is live (Nov 23–24, hybrid).
🔗 https://f.mtr.cool/vk4hi8lyp2
#BioImageAnalysis #CoreFacilities
The @crick.ac.uk BioImage Analysis Symposium program is live (Nov 23–24, hybrid).
🔗 https://f.mtr.cool/vk4hi8lyp2
#BioImageAnalysis #CoreFacilities
Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2027 course!
Bioimage Analysis Beginnings Bootcamp
Thank you for your interest in our bootcamp. Details are below. Applications are due by November 16th.
This course is designed to teach bioimage analysis decision-making principles (how do I decide ...
broad.io
October 20, 2026 at 3:41 PM
Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2027 course!
New application note: napari-TurboBox ⚡📦, a napari plugin for 3D bounding-box annotation. Edit a box in one slice and follow it live in the orthogonal views: ~2 ms per mouse move even with 10⁴ boxes, 79× faster than napari-bbox.
📄 arxiv.org/abs/2610.22413
#napari #BioimageAnalysis #Annotation
📄 arxiv.org/abs/2610.22413
#napari #BioimageAnalysis #Annotation
October 20, 2026 at 10:44 AM
New application note: napari-TurboBox ⚡📦, a napari plugin for 3D bounding-box annotation. Edit a box in one slice and follow it live in the orthogonal views: ~2 ms per mouse move even with 10⁴ boxes, 79× faster than napari-bbox.
📄 arxiv.org/abs/2610.22413
#napari #BioimageAnalysis #Annotation
📄 arxiv.org/abs/2610.22413
#napari #BioimageAnalysis #Annotation
The hidden test set came from different embryos than the training data, and the final leaderboard reshuffled a lot: 2nd place climbed 26 spots, 6th climbed 88.
Generalising across embryos is the real challenge, and it's the one that matters in the lab. #BioImageAnalysis
Generalising across embryos is the real challenge, and it's the one that matters in the lab. #BioImageAnalysis
October 6, 2026 at 2:13 AM
The hidden test set came from different embryos than the training data, and the final leaderboard reshuffled a lot: 2nd place climbed 26 spots, 6th climbed 88.
Generalising across embryos is the real challenge, and it's the one that matters in the lab. #BioImageAnalysis
Generalising across embryos is the real challenge, and it's the one that matters in the lab. #BioImageAnalysis
Intentional mentorship builds stronger, more supportive scientific communities.
Huge thanks to @latambioimaging.bsky.social for hosting this event, and to Hernan Grecco & Maria Victoria Repetto for their invaluable guidance in designing it! 🙌
#Mentorship #BioimageAnalysis #AcademicMobility
Huge thanks to @latambioimaging.bsky.social for hosting this event, and to Hernan Grecco & Maria Victoria Repetto for their invaluable guidance in designing it! 🙌
#Mentorship #BioimageAnalysis #AcademicMobility
September 22, 2026 at 7:59 PM
Intentional mentorship builds stronger, more supportive scientific communities.
Huge thanks to @latambioimaging.bsky.social for hosting this event, and to Hernan Grecco & Maria Victoria Repetto for their invaluable guidance in designing it! 🙌
#Mentorship #BioimageAnalysis #AcademicMobility
Huge thanks to @latambioimaging.bsky.social for hosting this event, and to Hernan Grecco & Maria Victoria Repetto for their invaluable guidance in designing it! 🙌
#Mentorship #BioimageAnalysis #AcademicMobility
Drowning in Image data? Know there’s a better way to analyse it, but don’t know where to start?
📣 UK-BIAS to the rescue!
👩💻🧑💻👨💻We’re the first dedicated #BioImageAnalysis service in the UK-node of @eurobioimaging.bsky.social bringing together specialists from ten UK institutions. 👩💻🧑💻👨💻
📣 UK-BIAS to the rescue!
👩💻🧑💻👨💻We’re the first dedicated #BioImageAnalysis service in the UK-node of @eurobioimaging.bsky.social bringing together specialists from ten UK institutions. 👩💻🧑💻👨💻
September 17, 2026 at 3:10 PM
Drowning in Image data? Know there’s a better way to analyse it, but don’t know where to start?
📣 UK-BIAS to the rescue!
👩💻🧑💻👨💻We’re the first dedicated #BioImageAnalysis service in the UK-node of @eurobioimaging.bsky.social bringing together specialists from ten UK institutions. 👩💻🧑💻👨💻
📣 UK-BIAS to the rescue!
👩💻🧑💻👨💻We’re the first dedicated #BioImageAnalysis service in the UK-node of @eurobioimaging.bsky.social bringing together specialists from ten UK institutions. 👩💻🧑💻👨💻
🚨 Job Alert 🚨🔬🧪👩💻🖥️ Are you interested in #BioimageAnalysis #ComputerVision #AI #ML methods for the #LifeSciences? Do you want to work on #DigitalPathology of tissues, cells, organelles? Check out this #PostDoc opportunity in a collaboration with Jens Rittscher from @oxengsci.bsky.social @ox.ac.uk
Research assistant / Post-doctoral fellow image analysis - Center for Stroke Research DM.16.25
full-time | 21.02.2025 | Campus Charité Mitte
karriere.charite.de
February 7, 2025 at 8:47 AM
🚨 Job Alert 🚨🔬🧪👩💻🖥️ Are you interested in #BioimageAnalysis #ComputerVision #AI #ML methods for the #LifeSciences? Do you want to work on #DigitalPathology of tissues, cells, organelles? Check out this #PostDoc opportunity in a collaboration with Jens Rittscher from @oxengsci.bsky.social @ox.ac.uk
Phindr3D doesn’t require segmentation of cells to learn #3D features from the microscopy image data set. #MachineLearning #BioImageAnalysis
November 22, 2024 at 7:50 PM
Phindr3D doesn’t require segmentation of cells to learn #3D features from the microscopy image data set. #MachineLearning #BioImageAnalysis
Phindr3D uses unsupervised data-driven feature learning which enables computationally facile classification, clustering and data visualization. Unbiased quantitative phenotypic #BioImageAnalysis of #3D #microscopy images in #HighContentScreening is a fundamental challenge.
November 22, 2024 at 7:50 PM
Phindr3D uses unsupervised data-driven feature learning which enables computationally facile classification, clustering and data visualization. Unbiased quantitative phenotypic #BioImageAnalysis of #3D #microscopy images in #HighContentScreening is a fundamental challenge.
Job - Alert 🧬
🎓 MASTERS INTERN (M/F/D): MACHINE LEARNING AND BIOIMAGE ANALYSIS
Deadline: 2025-03-31
Location: Germany, Dortmund, Nordrhein Westfalen
www.academiceurope.com/job/?id=7080
#hiring #MastersInternship #BioimageAnalysis #computerscience #statistics #BiomedicalSciences #Mathematics
🎓 MASTERS INTERN (M/F/D): MACHINE LEARNING AND BIOIMAGE ANALYSIS
Deadline: 2025-03-31
Location: Germany, Dortmund, Nordrhein Westfalen
www.academiceurope.com/job/?id=7080
#hiring #MastersInternship #BioimageAnalysis #computerscience #statistics #BiomedicalSciences #Mathematics
Academic Europe - Masters Intern (m/f/d): Machine learning and bioimage analysis
www.academiceurope.com
March 5, 2025 at 7:36 AM
Job - Alert 🧬
🎓 MASTERS INTERN (M/F/D): MACHINE LEARNING AND BIOIMAGE ANALYSIS
Deadline: 2025-03-31
Location: Germany, Dortmund, Nordrhein Westfalen
www.academiceurope.com/job/?id=7080
#hiring #MastersInternship #BioimageAnalysis #computerscience #statistics #BiomedicalSciences #Mathematics
🎓 MASTERS INTERN (M/F/D): MACHINE LEARNING AND BIOIMAGE ANALYSIS
Deadline: 2025-03-31
Location: Germany, Dortmund, Nordrhein Westfalen
www.academiceurope.com/job/?id=7080
#hiring #MastersInternship #BioimageAnalysis #computerscience #statistics #BiomedicalSciences #Mathematics
Special thanks to our imaging facilities in Adelaide, collaborators interstate and abroad and the developers and advisors of open source AI tools, and team behind ilastik, LABkit and CellPose whose contributions are driving innovation in #Bioimageanalysis #EndMalaria #NCRISimpact #AIinScience
February 4, 2025 at 10:42 PM
Special thanks to our imaging facilities in Adelaide, collaborators interstate and abroad and the developers and advisors of open source AI tools, and team behind ilastik, LABkit and CellPose whose contributions are driving innovation in #Bioimageanalysis #EndMalaria #NCRISimpact #AIinScience
[TRAINING] Apply for the new EMBO Course📢
Practical courses on advanced #bioimageanalysis, including image analysis workflows, data management, deep-learning...
For early-career/image analysis scientists
📅 Sep 14–19, 2025
🌍 On site or online
📌Apply by June 4
🔗Link in coms
Practical courses on advanced #bioimageanalysis, including image analysis workflows, data management, deep-learning...
For early-career/image analysis scientists
📅 Sep 14–19, 2025
🌍 On site or online
📌Apply by June 4
🔗Link in coms
May 6, 2025 at 9:31 AM
[TRAINING] Apply for the new EMBO Course📢
Practical courses on advanced #bioimageanalysis, including image analysis workflows, data management, deep-learning...
For early-career/image analysis scientists
📅 Sep 14–19, 2025
🌍 On site or online
📌Apply by June 4
🔗Link in coms
Practical courses on advanced #bioimageanalysis, including image analysis workflows, data management, deep-learning...
For early-career/image analysis scientists
📅 Sep 14–19, 2025
🌍 On site or online
📌Apply by June 4
🔗Link in coms
[NEWS] Last week, FBI was proud to attend the IEEE annual congress, #ISBI2025, in Houston
Our Challenge Officer, Dorian Kauffmann, presented the results of "Fuse My Cells" Challenge, the 2nd ed. of this deep-learning competition in #BioimageAnalysis
He was joined by the winner: Marek Wodzinski 👏
Our Challenge Officer, Dorian Kauffmann, presented the results of "Fuse My Cells" Challenge, the 2nd ed. of this deep-learning competition in #BioimageAnalysis
He was joined by the winner: Marek Wodzinski 👏
April 24, 2025 at 2:45 PM
[NEWS] Last week, FBI was proud to attend the IEEE annual congress, #ISBI2025, in Houston
Our Challenge Officer, Dorian Kauffmann, presented the results of "Fuse My Cells" Challenge, the 2nd ed. of this deep-learning competition in #BioimageAnalysis
He was joined by the winner: Marek Wodzinski 👏
Our Challenge Officer, Dorian Kauffmann, presented the results of "Fuse My Cells" Challenge, the 2nd ed. of this deep-learning competition in #BioimageAnalysis
He was joined by the winner: Marek Wodzinski 👏
I gave two seminars at @embl.org Heidelberg these days: One about using LLMs via #biabob for #BioImageAnalysis and one about how LLMs impact BioImage #DataScience
Thanks EMBL for having me!
Materials #openaccess 🧑🏫🖥️🔓
zenodo.org/records/1705...
zenodo.org/records/1710...
scads.github.io/llm-bia-2025
Thanks EMBL for having me!
Materials #openaccess 🧑🏫🖥️🔓
zenodo.org/records/1705...
zenodo.org/records/1710...
scads.github.io/llm-bia-2025
September 16, 2025 at 7:02 PM
I gave two seminars at @embl.org Heidelberg these days: One about using LLMs via #biabob for #BioImageAnalysis and one about how LLMs impact BioImage #DataScience
Thanks EMBL for having me!
Materials #openaccess 🧑🏫🖥️🔓
zenodo.org/records/1705...
zenodo.org/records/1710...
scads.github.io/llm-bia-2025
Thanks EMBL for having me!
Materials #openaccess 🧑🏫🖥️🔓
zenodo.org/records/1705...
zenodo.org/records/1710...
scads.github.io/llm-bia-2025
Check out this masterpiece of systematic #BioImageAnalysis 🤩
August 30, 2025 at 9:34 AM
Check out this masterpiece of systematic #BioImageAnalysis 🤩
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...
Are you a #BioImageAnalysis pro? Challenge your skills by playing #BIAbubbles! 🎉
Find the right workflows and reproduce the result! 🔬🖥️🕹️
And if you have challenging BIA tasks, new level contributions are welcome! 😀
github.com/haesleinhuep...
Find the right workflows and reproduce the result! 🔬🖥️🕹️
And if you have challenging BIA tasks, new level contributions are welcome! 😀
github.com/haesleinhuep...
April 25, 2025 at 7:28 PM
Are you a #BioImageAnalysis pro? Challenge your skills by playing #BIAbubbles! 🎉
Find the right workflows and reproduce the result! 🔬🖥️🕹️
And if you have challenging BIA tasks, new level contributions are welcome! 😀
github.com/haesleinhuep...
Find the right workflows and reproduce the result! 🔬🖥️🕹️
And if you have challenging BIA tasks, new level contributions are welcome! 😀
github.com/haesleinhuep...
My slides about "Learning and Training #BioImageAnalysis in the Age of AI" presented at the @globias.bsky.social @carpentries.carpentries.org workshop are available #openaccess. Big thanks for hosting us @istaustria-iof.bsky.social ! 🔬🖥️🤖
zenodo.org/records/1516...
zenodo.org/records/1516...
April 7, 2025 at 7:16 PM
My slides about "Learning and Training #BioImageAnalysis in the Age of AI" presented at the @globias.bsky.social @carpentries.carpentries.org workshop are available #openaccess. Big thanks for hosting us @istaustria-iof.bsky.social ! 🔬🖥️🤖
zenodo.org/records/1516...
zenodo.org/records/1516...
The claude 3.5 sonnet "new" model (versioning 🤦) currently leads the #BioImageAnalysis #CodeGen benchmark, o1-mini is on place 4, o1 was to expensive to try. You find details in the github repo:
github.com/haesleinhuep...
github.com/haesleinhuep...
December 21, 2024 at 7:24 AM
The claude 3.5 sonnet "new" model (versioning 🤦) currently leads the #BioImageAnalysis #CodeGen benchmark, o1-mini is on place 4, o1 was to expensive to try. You find details in the github repo:
github.com/haesleinhuep...
github.com/haesleinhuep...