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 -
🔬🤖 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...
So... have a read of our #preprint about #preprints, which makes more #preprints! Kudos to amazing Bruno Saraiva and @guijacquemet.bsky.social, who teamed up to create #RxivMaker and made it awesome
June 27, 2025 at 1:22 PM
So... have a read of our #preprint about #preprints, which makes more #preprints! Kudos to amazing Bruno Saraiva and @guijacquemet.bsky.social, who teamed up to create #RxivMaker and made it awesome
Got 2 minutes to spare and a Google account? Give it a go in Google Colab or fork the repo – everything's been designed to be super easy, with no specialist knowledge needed
Colab: colab.research.google.com/github/Henri...
Github: github.com/HenriquesLab...
Colab: colab.research.google.com/github/Henri...
Github: github.com/HenriquesLab...
June 27, 2025 at 1:06 PM
Got 2 minutes to spare and a Google account? Give it a go in Google Colab or fork the repo – everything's been designed to be super easy, with no specialist knowledge needed
Colab: colab.research.google.com/github/Henri...
Github: github.com/HenriquesLab...
Colab: colab.research.google.com/github/Henri...
Github: github.com/HenriquesLab...
For those of you who use our HenriquesLab #bioRxiv template on @overleaf.com (🙏), the PDFs will look familiar. We enhanced the template with a fully automated, reproducible workflow, building on the style you love
Btw, Overleaf is awesome; we've done nearly-all preprints there. You should use it!
Btw, Overleaf is awesome; we've done nearly-all preprints there. You should use it!
June 27, 2025 at 1:00 PM
For those of you who use our HenriquesLab #bioRxiv template on @overleaf.com (🙏), the PDFs will look familiar. We enhanced the template with a fully automated, reproducible workflow, building on the style you love
Btw, Overleaf is awesome; we've done nearly-all preprints there. You should use it!
Btw, Overleaf is awesome; we've done nearly-all preprints there. You should use it!
Under the #RxivMaker hood:
- 🦾 You Write, It Builds: Write #Markdown and engine autogenerates #LaTeX PDF
- 📊 Dynamic Figures: Generate figures with #Python or #Mermaid that automatically update when data changes
- 🤖 Zero-Install: Runs on #GoogleColab or builds with #GitHub Actions, no local setup
- 🦾 You Write, It Builds: Write #Markdown and engine autogenerates #LaTeX PDF
- 📊 Dynamic Figures: Generate figures with #Python or #Mermaid that automatically update when data changes
- 🤖 Zero-Install: Runs on #GoogleColab or builds with #GitHub Actions, no local setup
June 27, 2025 at 12:48 PM
Under the #RxivMaker hood:
- 🦾 You Write, It Builds: Write #Markdown and engine autogenerates #LaTeX PDF
- 📊 Dynamic Figures: Generate figures with #Python or #Mermaid that automatically update when data changes
- 🤖 Zero-Install: Runs on #GoogleColab or builds with #GitHub Actions, no local setup
- 🦾 You Write, It Builds: Write #Markdown and engine autogenerates #LaTeX PDF
- 📊 Dynamic Figures: Generate figures with #Python or #Mermaid that automatically update when data changes
- 🤖 Zero-Install: Runs on #GoogleColab or builds with #GitHub Actions, no local setup
🧑🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
June 27, 2025 at 12:34 PM
🧑🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
We've been cooking something pretty cool with @guijacquemet.bsky.social, standby for some news in a bit
June 27, 2025 at 11:35 AM
We've been cooking something pretty cool with @guijacquemet.bsky.social, standby for some news in a bit