Ricardo Henriques
@henriqueslab.bsky.social
@AIOpticalBioLab.bsky.social. Group Leader #ITQB & H. Prof #UCL. #Nanoscopy & #AI for #LifeSciences. #SRRF sensei. #ERCCoG, #EMBO member. Dad. Opinions my own
- henriqueslab.org -
- henriqueslab.org -
📯👨🚀 Calling all #bioimage analysis aficionados. #EZInput is out! We wanted to bring #ImageJ’s capacity to record settings to the #Python ecosystem 🐍. It is a declarative library for generating UIs that just work. Done with @guijacquemet.bsky.social lab
arxiv.org/abs/2601.08859 #ScientificComputing
arxiv.org/abs/2601.08859 #ScientificComputing
January 15, 2026 at 11:36 AM
📯👨🚀 Calling all #bioimage analysis aficionados. #EZInput is out! We wanted to bring #ImageJ’s capacity to record settings to the #Python ecosystem 🐍. It is a declarative library for generating UIs that just work. Done with @guijacquemet.bsky.social lab
arxiv.org/abs/2601.08859 #ScientificComputing
arxiv.org/abs/2601.08859 #ScientificComputing
Check out rxiv-maker.henriqueslab.org/examples/sho... to have a look at the preprints already using #RxivMaker
December 19, 2025 at 11:20 AM
Check out rxiv-maker.henriqueslab.org/examples/sho... to have a look at the preprints already using #RxivMaker
🚀📰 End-of-year news for #RxivMaker =). Now it generates both #pdf and #docx from #markdown. Docx makes it easier to collaborate on a document for non-markdown users, making it simple to loop between docx and #RxivMaker to a professional-looking #preprint
Preprint updated: arxiv.org/abs/2508.00836
Preprint updated: arxiv.org/abs/2508.00836
December 19, 2025 at 11:20 AM
🚀📰 End-of-year news for #RxivMaker =). Now it generates both #pdf and #docx from #markdown. Docx makes it easier to collaborate on a document for non-markdown users, making it simple to loop between docx and #RxivMaker to a professional-looking #preprint
Preprint updated: arxiv.org/abs/2508.00836
Preprint updated: arxiv.org/abs/2508.00836
🧬 @itqbnova.bsky.social has 15 BRIDGE fellowships for Master's graduates pursuing PhDs!
We have a spot: "Decoding the morphological language of infection using AI". Build AI to map how viruses hijack cells & bacteria survive antibiotics.
Deadline: 05/01/2026
www.itqb.unl.pt/education/br...
We have a spot: "Decoding the morphological language of infection using AI". Build AI to map how viruses hijack cells & bacteria survive antibiotics.
Deadline: 05/01/2026
www.itqb.unl.pt/education/br...
December 19, 2025 at 9:54 AM
🧬 @itqbnova.bsky.social has 15 BRIDGE fellowships for Master's graduates pursuing PhDs!
We have a spot: "Decoding the morphological language of infection using AI". Build AI to map how viruses hijack cells & bacteria survive antibiotics.
Deadline: 05/01/2026
www.itqb.unl.pt/education/br...
We have a spot: "Decoding the morphological language of infection using AI". Build AI to map how viruses hijack cells & bacteria survive antibiotics.
Deadline: 05/01/2026
www.itqb.unl.pt/education/br...
Going through my UCL-times photos, this little one came up
December 15, 2025 at 5:49 PM
Going through my UCL-times photos, this little one came up
🚨🔬🤖🚀 #PhotoFiTT is out! With @guijacquemet.bsky.social's & @microbematos.bsky.social's labs, we launched a new phototoxicity measurement for live microscopy using cell clocks⏱️. By rockstars @mariodelr.bsky.social @gomez-mariscal.bsky.social et al! AI-powered + label-free
doi.org/10.1038/s414...
doi.org/10.1038/s414...
December 15, 2025 at 3:22 PM
🚨🔬🤖🚀 #PhotoFiTT is out! With @guijacquemet.bsky.social's & @microbematos.bsky.social's labs, we launched a new phototoxicity measurement for live microscopy using cell clocks⏱️. By rockstars @mariodelr.bsky.social @gomez-mariscal.bsky.social et al! AI-powered + label-free
doi.org/10.1038/s414...
doi.org/10.1038/s414...
🔬🤖 ICYMI: impressive preprint from @owenlabuob.bsky.social tackling a major bottleneck – how to systematically compare super-resolution microscopy across experiments. Novel ML framework embeds single-molecule data for cross-sample analysis. Integrated with nano-org database✨ doi.org/10.1101/2025...
November 3, 2025 at 5:57 PM
🔬🤖 ICYMI: impressive preprint from @owenlabuob.bsky.social tackling a major bottleneck – how to systematically compare super-resolution microscopy across experiments. Novel ML framework embeds single-molecule data for cross-sample analysis. Integrated with nano-org database✨ doi.org/10.1101/2025...
Using #LLMs for science👨💻💬? We have a fun tool for you: introducing #folder2md4llms. It converts an entire folder of docs/code/pdfs/pptx into a single markdown file that you can upload to your chatbot of choice. We use it to talk with our publications database or code repos
github.com/HenriquesLab...
github.com/HenriquesLab...
October 28, 2025 at 5:22 PM
Using #LLMs for science👨💻💬? We have a fun tool for you: introducing #folder2md4llms. It converts an entire folder of docs/code/pdfs/pptx into a single markdown file that you can upload to your chatbot of choice. We use it to talk with our publications database or code repos
github.com/HenriquesLab...
github.com/HenriquesLab...
🦠🔬🤖🧑💻 #mAIcrobe interface preview, a platform for #DeepLearning enabled bacterial image-based phenotyping. Check it out
💻: github.com/HenriquesLab...
📄: www.biorxiv.org/content/10.1...
💻: github.com/HenriquesLab...
📄: www.biorxiv.org/content/10.1...
October 27, 2025 at 12:08 PM
🦠🔬🤖🧑💻 #mAIcrobe interface preview, a platform for #DeepLearning enabled bacterial image-based phenotyping. Check it out
💻: github.com/HenriquesLab...
📄: www.biorxiv.org/content/10.1...
💻: github.com/HenriquesLab...
📄: www.biorxiv.org/content/10.1...
Cool news about #RxivMaker. Adding lots of new features 🏃. An rxiv-markdown manuscript can now have embedded code that helps keep all your data updated (e.g. inserting number of samples by reading data like .xls). Both #RxivMaker and #mAIcrobe preprints are written with it
arxiv.org/abs/2508.00836
arxiv.org/abs/2508.00836
October 23, 2025 at 10:26 AM
Cool news about #RxivMaker. Adding lots of new features 🏃. An rxiv-markdown manuscript can now have embedded code that helps keep all your data updated (e.g. inserting number of samples by reading data like .xls). Both #RxivMaker and #mAIcrobe preprints are written with it
arxiv.org/abs/2508.00836
arxiv.org/abs/2508.00836
🦠🔬🤖🧑💻 #mAIcrobe is out! With @pinholab.bsky.social's lab, we launched an open-source framework for high-throughput bacterial image analysis. By rockstars A. Brito & B. Saraiva et al, making #DeepLearning for phenotyping accessible! Easy to use, plus model training
📜 www.biorxiv.org/content/10.1...
📜 www.biorxiv.org/content/10.1...
October 22, 2025 at 11:10 AM
🦠🔬🤖🧑💻 #mAIcrobe is out! With @pinholab.bsky.social's lab, we launched an open-source framework for high-throughput bacterial image analysis. By rockstars A. Brito & B. Saraiva et al, making #DeepLearning for phenotyping accessible! Easy to use, plus model training
📜 www.biorxiv.org/content/10.1...
📜 www.biorxiv.org/content/10.1...
🚀🔬 Announcing #IMS2026 at @itqbnova.bsky.social! We're assembling a #LifeSciences #Microscopy symposium packed with ✨ speakers and 🧑🔬 workshops. All about imaging cells with photons, electrons and AI! If you love microscopy, you need to be here. Join us on March 19!
ims2026.itqbnovacommunity.org
ims2026.itqbnovacommunity.org
October 21, 2025 at 2:25 PM
🚀🔬 Announcing #IMS2026 at @itqbnova.bsky.social! We're assembling a #LifeSciences #Microscopy symposium packed with ✨ speakers and 🧑🔬 workshops. All about imaging cells with photons, electrons and AI! If you love microscopy, you need to be here. Join us on March 19!
ims2026.itqbnovacommunity.org
ims2026.itqbnovacommunity.org
LLM-agent never skips leg day
September 8, 2025 at 7:03 PM
LLM-agent never skips leg day
📝 #RxivMaker updated to v1.3.0, new:
🔍 PDF change tracking - see manuscript diffs directly in PDF
🚀 Docker engine in Google Colab & Github Actions = 5x faster installation
🐱 Repo: github.com/HenriquesLab...
📰: zenodo.org/records/1591...
🔍 PDF change tracking - see manuscript diffs directly in PDF
🚀 Docker engine in Google Colab & Github Actions = 5x faster installation
🐱 Repo: github.com/HenriquesLab...
📰: zenodo.org/records/1591...
July 15, 2025 at 11:03 AM
📝 #RxivMaker updated to v1.3.0, new:
🔍 PDF change tracking - see manuscript diffs directly in PDF
🚀 Docker engine in Google Colab & Github Actions = 5x faster installation
🐱 Repo: github.com/HenriquesLab...
📰: zenodo.org/records/1591...
🔍 PDF change tracking - see manuscript diffs directly in PDF
🚀 Docker engine in Google Colab & Github Actions = 5x faster installation
🐱 Repo: github.com/HenriquesLab...
📰: zenodo.org/records/1591...
🚨Join us! We're soon opening 3 postdoctoral positions in #AIDrivenBiology. Seeking biologists (especially microbiology and infection biology), computer scientists, and microscopy developers. Ideal candidates are those eager to use or develop next-gen tech for cell biology. Get in touch (DM/email)
July 10, 2025 at 8:34 AM
🚨Join us! We're soon opening 3 postdoctoral positions in #AIDrivenBiology. Seeking biologists (especially microbiology and infection biology), computer scientists, and microscopy developers. Ideal candidates are those eager to use or develop next-gen tech for cell biology. Get in touch (DM/email)
Scientific coders 🧑🔬🧑💻
#RxivMaker v1.2 now has a #VSCode extension to manage citations and for syntax highlighting of #RxivMarkdown
💽: github.com/HenriquesLab...
📰: doi.org/10.5281/zeno...
#RxivMaker v1.2 now has a #VSCode extension to manage citations and for syntax highlighting of #RxivMarkdown
💽: github.com/HenriquesLab...
📰: doi.org/10.5281/zeno...
July 9, 2025 at 7:29 AM
Scientific coders 🧑🔬🧑💻
#RxivMaker v1.2 now has a #VSCode extension to manage citations and for syntax highlighting of #RxivMarkdown
💽: github.com/HenriquesLab...
📰: doi.org/10.5281/zeno...
#RxivMaker v1.2 now has a #VSCode extension to manage citations and for syntax highlighting of #RxivMarkdown
💽: github.com/HenriquesLab...
📰: doi.org/10.5281/zeno...
#RxivMaker updated to v1.1.0: now supports R auto-generated figures and lots of bug fixes
Details in: github.com/HenriquesLab...
Details in: github.com/HenriquesLab...
July 4, 2025 at 10:37 AM
#RxivMaker updated to v1.1.0: now supports R auto-generated figures and lots of bug fixes
Details in: github.com/HenriquesLab...
Details in: github.com/HenriquesLab...
Hi Bianca, we've added support for generating R figures. Thank you for suggesting it =). If you get a chance to give it a try in the future, let us know how it worked out
July 4, 2025 at 10:33 AM
Hi Bianca, we've added support for generating R figures. Thank you for suggesting it =). If you get a chance to give it a try in the future, let us know how it worked out
It's here! ✨
The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF
➡️ Open link: rdcu.be/euvEw
The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF
➡️ Open link: rdcu.be/euvEw
July 3, 2025 at 8:44 AM
It's here! ✨
The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF
➡️ Open link: rdcu.be/euvEw
The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF
➡️ Open link: rdcu.be/euvEw
We follow this up by detecting HIV viral morphogenesis 🦠✨ in live-cell fluorescence images. Leveraging the brilliant expertise of João Mamede’s team
July 2, 2025 at 7:19 AM
We follow this up by detecting HIV viral morphogenesis 🦠✨ in live-cell fluorescence images. Leveraging the brilliant expertise of João Mamede’s team
The new #SReD paper is packed with eye-opening demos! We demonstrate how SReD accurately detects spectrin ring patterns in neurons🧠, pinpointing instances where rings are disrupted. Possible through the deep system expertise from @christlet.bsky.social and team!
July 2, 2025 at 7:15 AM
The new #SReD paper is packed with eye-opening demos! We demonstrate how SReD accurately detects spectrin ring patterns in neurons🧠, pinpointing instances where rings are disrupted. Possible through the deep system expertise from @christlet.bsky.social and team!
🔬👨💻📰 #SReD is out!
Automated structural detection for #ImageJ & #FIJI, from nano to macro ✨🐘. No training data, no bias - texture analysis with GPU acceleration!⚡️
Brainchild of @afonsomendes92.bsky.social and adventure w @christlet.bsky.social lab + friends.
Check: www.nature.com/articles/s41...
Automated structural detection for #ImageJ & #FIJI, from nano to macro ✨🐘. No training data, no bias - texture analysis with GPU acceleration!⚡️
Brainchild of @afonsomendes92.bsky.social and adventure w @christlet.bsky.social lab + friends.
Check: www.nature.com/articles/s41...
July 2, 2025 at 7:09 AM
🔬👨💻📰 #SReD is out!
Automated structural detection for #ImageJ & #FIJI, from nano to macro ✨🐘. No training data, no bias - texture analysis with GPU acceleration!⚡️
Brainchild of @afonsomendes92.bsky.social and adventure w @christlet.bsky.social lab + friends.
Check: www.nature.com/articles/s41...
Automated structural detection for #ImageJ & #FIJI, from nano to macro ✨🐘. No training data, no bias - texture analysis with GPU acceleration!⚡️
Brainchild of @afonsomendes92.bsky.social and adventure w @christlet.bsky.social lab + friends.
Check: www.nature.com/articles/s41...