👉 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
Hi Octavio. Bioimage analysis roles in microbiology tend to be scattered across lab sites and society pages. We track them on a single microbiology board: https://suitch.co/jobs/microbiology?via=bluesky-reply
November 10, 2026 at 8:48 AM
Hi Octavio. Bioimage analysis roles in microbiology tend to be scattered across lab sites and society pages. We track them on a single microbiology board: https://suitch.co/jobs/microbiology?via=bluesky-reply
🚀 One more thing! The Fiji plugin builds on the latest BiaPy releases (v3.7.2 & v3.7.3), bringing a new shared Wizard, improved data checks, Fiji integration and 2D/3D object tracking. We've been so busy these past weeks that we haven't properly announced them! 😅
github.com/BiaPyX/BiaPy...
github.com/BiaPyX/BiaPy...
Releases · BiaPyX/BiaPy
Open source Python library for building bioimage analysis pipelines - Releases · BiaPyX/BiaPy
github.com
November 11, 2026 at 3:37 PM
🚀 One more thing! The Fiji plugin builds on the latest BiaPy releases (v3.7.2 & v3.7.3), bringing a new shared Wizard, improved data checks, Fiji integration and 2D/3D object tracking. We've been so busy these past weeks that we haven't properly announced them! 😅
github.com/BiaPyX/BiaPy...
github.com/BiaPyX/BiaPy...
🎉The Journal of Microscopy is happy to announce the publication of a new special issue - GloBIAS!
The Guest Editors of this new issue are delighted to share their work, concentrating on the topic of reproducibility in bioimage analysis.
Read the full issue here: tinyurl.com/2s44h864
The Guest Editors of this new issue are delighted to share their work, concentrating on the topic of reproducibility in bioimage analysis.
Read the full issue here: tinyurl.com/2s44h864
November 10, 2026 at 11:08 AM
🎉The Journal of Microscopy is happy to announce the publication of a new special issue - GloBIAS!
The Guest Editors of this new issue are delighted to share their work, concentrating on the topic of reproducibility in bioimage analysis.
Read the full issue here: tinyurl.com/2s44h864
The Guest Editors of this new issue are delighted to share their work, concentrating on the topic of reproducibility in bioimage analysis.
Read the full issue here: tinyurl.com/2s44h864
🤖 Use pretrained models from the #BioImage Model Zoo 🦒
🛠️ Run models like #Cellpose-SAM directly on your images, or fine-tune them on your own data with no extra setup.
The plugin only lists the models that fit your task 🤗
🛠️ Run models like #Cellpose-SAM directly on your images, or fine-tune them on your own data with no extra setup.
The plugin only lists the models that fit your task 🤗
November 11, 2026 at 3:32 PM
🤖 Use pretrained models from the #BioImage Model Zoo 🦒
🛠️ Run models like #Cellpose-SAM directly on your images, or fine-tune them on your own data with no extra setup.
The plugin only lists the models that fit your task 🤗
🛠️ Run models like #Cellpose-SAM directly on your images, or fine-tune them on your own data with no extra setup.
The plugin only lists the models that fit your task 🤗
You need powerful resources for your bioimage analysis, but you don’t have them locally?
Visit our website to learn more about the Bioimage ANalysis Desktop Service BAND. Cloud-based, accessible, no need for local software installation.
👉 nfdi4bioimage.de/en/services/...
Visit our website to learn more about the Bioimage ANalysis Desktop Service BAND. Cloud-based, accessible, no need for local software installation.
👉 nfdi4bioimage.de/en/services/...
November 6, 2026 at 12:08 PM
You need powerful resources for your bioimage analysis, but you don’t have them locally?
Visit our website to learn more about the Bioimage ANalysis Desktop Service BAND. Cloud-based, accessible, no need for local software installation.
👉 nfdi4bioimage.de/en/services/...
Visit our website to learn more about the Bioimage ANalysis Desktop Service BAND. Cloud-based, accessible, no need for local software installation.
👉 nfdi4bioimage.de/en/services/...
Image credits:
3D: IDR idr0062, Blin et al. 2019, CC BY 4.0
Slide: CMU-1, OpenSlide test data, CC0
Plate: BBBC013v1 by Ilya Ravkin, Broad Bioimage Benchmark Collection, CC BY 3.0. Masks and phenotypes are ours.
Sources and citations: find-nuclei.github.io/docs/sample-...
3D: IDR idr0062, Blin et al. 2019, CC BY 4.0
Slide: CMU-1, OpenSlide test data, CC0
Plate: BBBC013v1 by Ilya Ravkin, Broad Bioimage Benchmark Collection, CC BY 3.0. Masks and phenotypes are ours.
Sources and citations: find-nuclei.github.io/docs/sample-...
November 8, 2026 at 5:04 PM
Image credits:
3D: IDR idr0062, Blin et al. 2019, CC BY 4.0
Slide: CMU-1, OpenSlide test data, CC0
Plate: BBBC013v1 by Ilya Ravkin, Broad Bioimage Benchmark Collection, CC BY 3.0. Masks and phenotypes are ours.
Sources and citations: find-nuclei.github.io/docs/sample-...
3D: IDR idr0062, Blin et al. 2019, CC BY 4.0
Slide: CMU-1, OpenSlide test data, CC0
Plate: BBBC013v1 by Ilya Ravkin, Broad Bioimage Benchmark Collection, CC BY 3.0. Masks and phenotypes are ours.
Sources and citations: find-nuclei.github.io/docs/sample-...
What kind of AI bioimage analysis models are out there? Join our webinar to hear Fynn Beuttenmüller of @embl.org present "AI models for biological imaging" and learn more about the tools and resources from the bioimage.io 🦒
🗓️ Nov 6 @ 10 am CET
Register⤵️
www.eurobioimaging.eu/events/ai-de...
🗓️ Nov 6 @ 10 am CET
Register⤵️
www.eurobioimaging.eu/events/ai-de...
November 5, 2026 at 1:05 PM
What kind of AI bioimage analysis models are out there? Join our webinar to hear Fynn Beuttenmüller of @embl.org present "AI models for biological imaging" and learn more about the tools and resources from the bioimage.io 🦒
🗓️ Nov 6 @ 10 am CET
Register⤵️
www.eurobioimaging.eu/events/ai-de...
🗓️ Nov 6 @ 10 am CET
Register⤵️
www.eurobioimaging.eu/events/ai-de...
The paper says the data is public: 400 slides, up to 3 GB each. You only want to look at one.
Skip the download. Paste the slide's address into your browser. From TCGA, CAMELYON16, IDR, BioImage Archive, Cell Painting Gallery or Zenodo.
www.find-nuclei.com/blog/public-...
#OpenScience #bioimaging
Skip the download. Paste the slide's address into your browser. From TCGA, CAMELYON16, IDR, BioImage Archive, Cell Painting Gallery or Zenodo.
www.find-nuclei.com/blog/public-...
#OpenScience #bioimaging
November 11, 2026 at 1:15 PM
The paper says the data is public: 400 slides, up to 3 GB each. You only want to look at one.
Skip the download. Paste the slide's address into your browser. From TCGA, CAMELYON16, IDR, BioImage Archive, Cell Painting Gallery or Zenodo.
www.find-nuclei.com/blog/public-...
#OpenScience #bioimaging
Skip the download. Paste the slide's address into your browser. From TCGA, CAMELYON16, IDR, BioImage Archive, Cell Painting Gallery or Zenodo.
www.find-nuclei.com/blog/public-...
#OpenScience #bioimaging
Our extended meta-analysis on bioimage software adoption in microscopy is out! We've added Image Pro to our analysis tools, included NIH Image and Adobe Photoshop as reference entries, and extended the historical timeline back to 1995.
doi.org/10.64898/2026.10.21.760457
doi.org/10.64898/2026.10.21.760457
November 2, 2026 at 3:14 PM
Our extended meta-analysis on bioimage software adoption in microscopy is out! We've added Image Pro to our analysis tools, included NIH Image and Adobe Photoshop as reference entries, and extended the historical timeline back to 1995.
doi.org/10.64898/2026.10.21.760457
doi.org/10.64898/2026.10.21.760457
Join the next L-BIIG meeting!
13 Nov 2026 | 12:00-13:00 GMT
Morgan Gridley (UCL) – Airyscan imaging of synapses
Ben Reilly O'Donnell (Imperial College London) – Dynamic multimodal imaging combining SICM microscopy with mechanical stretch of adult rat cardiomyocytes
🔗 www.ucl.ac.uk/research-inn...
13 Nov 2026 | 12:00-13:00 GMT
Morgan Gridley (UCL) – Airyscan imaging of synapses
Ben Reilly O'Donnell (Imperial College London) – Dynamic multimodal imaging combining SICM microscopy with mechanical stretch of adult rat cardiomyocytes
🔗 www.ucl.ac.uk/research-inn...
London BioImage Interest Group
The London BioImage Interest Group (L-BIIG) connects researchers and technical specialists working on biological image acquisition and analysis across London institutions.
www.ucl.ac.uk
November 2, 2026 at 7:57 AM
Join the next L-BIIG meeting!
13 Nov 2026 | 12:00-13:00 GMT
Morgan Gridley (UCL) – Airyscan imaging of synapses
Ben Reilly O'Donnell (Imperial College London) – Dynamic multimodal imaging combining SICM microscopy with mechanical stretch of adult rat cardiomyocytes
🔗 www.ucl.ac.uk/research-inn...
13 Nov 2026 | 12:00-13:00 GMT
Morgan Gridley (UCL) – Airyscan imaging of synapses
Ben Reilly O'Donnell (Imperial College London) – Dynamic multimodal imaging combining SICM microscopy with mechanical stretch of adult rat cardiomyocytes
🔗 www.ucl.ac.uk/research-inn...
It’s already November 😱, and even though you might not see flowering Thale cress at this time of year – or Benth in our part of the world – you still have access all year round to some colorful microscopic images of their tiniest components, because these have been published in the BioImage Archive.
November 3, 2026 at 2:23 PM
It’s already November 😱, and even though you might not see flowering Thale cress at this time of year – or Benth in our part of the world – you still have access all year round to some colorful microscopic images of their tiniest components, because these have been published in the BioImage Archive.
My talents are wasted in bioimage analysis. I should be doing rocket science. At least according to the ball tracking, my drive went up but never came down. I can only assume it's currently still in orbit.
November 1, 2026 at 4:14 AM
My talents are wasted in bioimage analysis. I should be doing rocket science. At least according to the ball tracking, my drive went up but never came down. I can only assume it's currently still in orbit.
(6/6) 🎉 That's BiaPy v3.7.1!
From cell segmentation to denoising and massive 3D volumes, we hope this release makes your bioimage analysis workflows easier.
📦 github.com/BiaPyX/BiaPy...
⭐ Try it and share your feedback!
From cell segmentation to denoising and massive 3D volumes, we hope this release makes your bioimage analysis workflows easier.
📦 github.com/BiaPyX/BiaPy...
⭐ Try it and share your feedback!
ALT:
static.klipy.com
October 30, 2026 at 6:14 PM
(6/6) 🎉 That's BiaPy v3.7.1!
From cell segmentation to denoising and massive 3D volumes, we hope this release makes your bioimage analysis workflows easier.
📦 github.com/BiaPyX/BiaPy...
⭐ Try it and share your feedback!
From cell segmentation to denoising and massive 3D volumes, we hope this release makes your bioimage analysis workflows easier.
📦 github.com/BiaPyX/BiaPy...
⭐ Try it and share your feedback!
Might as well just put my feet up and count down the days to retirement
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CopilotJ: a conversational multi-agent system for intelligent and efficient bioimage analysis - Nature Methods
Nature Methods - CopilotJ: a conversational multi-agent system for intelligent and efficient bioimage analysis
www.nature.com
October 30, 2026 at 9:08 AM
Might as well just put my feet up and count down the days to retirement
www.nature.com/articles/s41...
www.nature.com/articles/s41...
(5/6) 🔧 Not every improvement needs to be shiny!
We've also improved BioImage Model Zoo 🦒 compatibility, parallel data loading 📂, training visualisations 📊 and image-to-image workflows 🔄.
Plus, plenty of bug fixes! 🐞
We've also improved BioImage Model Zoo 🦒 compatibility, parallel data loading 📂, training visualisations 📊 and image-to-image workflows 🔄.
Plus, plenty of bug fixes! 🐞
October 30, 2026 at 6:14 PM
(5/6) 🔧 Not every improvement needs to be shiny!
We've also improved BioImage Model Zoo 🦒 compatibility, parallel data loading 📂, training visualisations 📊 and image-to-image workflows 🔄.
Plus, plenty of bug fixes! 🐞
We've also improved BioImage Model Zoo 🦒 compatibility, parallel data loading 📂, training visualisations 📊 and image-to-image workflows 🔄.
Plus, plenty of bug fixes! 🐞
Bioimage analysis is outgrowing laptops and workstations: bigger datasets, AI models, GPUs, runs that take hours.
HPC can help, but many researchers and facility staff think it is only for coding experts. Tackling that misconception is the goal of this paper. 2/9
HPC can help, but many researchers and facility staff think it is only for coding experts. Tackling that misconception is the goal of this paper. 2/9
October 30, 2026 at 11:01 AM
Bioimage analysis is outgrowing laptops and workstations: bigger datasets, AI models, GPUs, runs that take hours.
HPC can help, but many researchers and facility staff think it is only for coding experts. Tackling that misconception is the goal of this paper. 2/9
HPC can help, but many researchers and facility staff think it is only for coding experts. Tackling that misconception is the goal of this paper. 2/9
🚨📢🚨📢🚨📢💻💻🔬New paper in the @jofmicroscopy.bsky.social Journal of Microscopy: "Is HPC for you?" 🖥️
A collective perspective on adopting high-performance computing for bioimage analysis in imaging facilities, from teams at the Crick, VIB and Liverpool.
doi.org/10.1111/jmi....
🧵 1/9
A collective perspective on adopting high-performance computing for bioimage analysis in imaging facilities, from teams at the Crick, VIB and Liverpool.
doi.org/10.1111/jmi....
🧵 1/9
October 30, 2026 at 11:01 AM
🚨📢🚨📢🚨📢💻💻🔬New paper in the @jofmicroscopy.bsky.social Journal of Microscopy: "Is HPC for you?" 🖥️
A collective perspective on adopting high-performance computing for bioimage analysis in imaging facilities, from teams at the Crick, VIB and Liverpool.
doi.org/10.1111/jmi....
🧵 1/9
A collective perspective on adopting high-performance computing for bioimage analysis in imaging facilities, from teams at the Crick, VIB and Liverpool.
doi.org/10.1111/jmi....
🧵 1/9
Checkout our new preprint 🔬! An eye-opening analysis detailing the adoption of bioimage-analysis tools in microscopy, curated with Bruno Saraiva and @henriqueslab.bsky.social – a thread 🧵:
preprint: doi.org/10.64898/2026.10.21.760457
github: github.com/HenriquesLab/mapping-bioimage-software
preprint: doi.org/10.64898/2026.10.21.760457
github: github.com/HenriquesLab/mapping-bioimage-software
October 27, 2026 at 9:12 AM
Checkout our new preprint 🔬! An eye-opening analysis detailing the adoption of bioimage-analysis tools in microscopy, curated with Bruno Saraiva and @henriqueslab.bsky.social – a thread 🧵:
preprint: doi.org/10.64898/2026.10.21.760457
github: github.com/HenriquesLab/mapping-bioimage-software
preprint: doi.org/10.64898/2026.10.21.760457
github: github.com/HenriquesLab/mapping-bioimage-software
🔧 Self-supervised models beating CellProfiler in compound retrieval raises questions about the value of domain-specific feature engineering in bioimage analysis.
October 29, 2026 at 4:39 PM
🔧 Self-supervised models beating CellProfiler in compound retrieval raises questions about the value of domain-specific feature engineering in bioimage analysis.
🔬📈 We analysed #microscopy papers to track #bioimage analysis use. ImageJ+Fiji dominate, but others are gaining ground. Researchers undercite them and provide too little detail to reproduce analyses. By Tayla and Bruno, with @guijacquemet.bsky.social lab
📄 doi.org/10.64898/2026.10.21.760457
📄 doi.org/10.64898/2026.10.21.760457
October 27, 2026 at 2:17 PM
🔬📈 We analysed #microscopy papers to track #bioimage analysis use. ImageJ+Fiji dominate, but others are gaining ground. Researchers undercite them and provide too little detail to reproduce analyses. By Tayla and Bruno, with @guijacquemet.bsky.social lab
📄 doi.org/10.64898/2026.10.21.760457
📄 doi.org/10.64898/2026.10.21.760457
With @inesmcunha.bsky.social, @caronjacobs.bsky.social and @guijacquemet.bsky.social, we performed an LLM-supported deep-dive into 15 years of bioimage-analysis software adoption—which tools dominate, how adoption varies by field, and how deep-learning integrates into established workflows. (2/5)
October 27, 2026 at 9:12 AM
With @inesmcunha.bsky.social, @caronjacobs.bsky.social and @guijacquemet.bsky.social, we performed an LLM-supported deep-dive into 15 years of bioimage-analysis software adoption—which tools dominate, how adoption varies by field, and how deep-learning integrates into established workflows. (2/5)
With @inesmcunha.bsky.social, @caronjacobs.bsky.social and @guijacquemet.bsky.social, we performed an LLM-supported deep-dive into 15 years of bioimage-analysis software adoption—which tools dominate, how adoption varies by field, and how deep-learning integrates into established workflows (2/5)
October 27, 2026 at 9:02 AM
With @inesmcunha.bsky.social, @caronjacobs.bsky.social and @guijacquemet.bsky.social, we performed an LLM-supported deep-dive into 15 years of bioimage-analysis software adoption—which tools dominate, how adoption varies by field, and how deep-learning integrates into established workflows (2/5)
Mapping bioimage-analysis software adoption in microscopy https://www.biorxiv.org/content/10.64898/2026.10.21.760457v1
October 26, 2026 at 10:47 PM
Mapping bioimage-analysis software adoption in microscopy https://www.biorxiv.org/content/10.64898/2026.10.21.760457v1