@HenriquesLab

@AIOpticalBioLab. Group Leader @itqbnova & H. Prof @LMCB_UCL. #Nanoscopy & #AI for #LifeSciences. #SRRF sensei. #ERCCoG, #EMBO member. Dad. Opinions my own

 Lisbon and London
henriqueslab.org
Joined August 2009
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🔬🚀 New paper out: mAIcrobe, our open-source #napari plugin for high-throughput bacterial image analysis. Segmentation, morphological profiling and cell cycle classification, all in one place 👇 doi.org/10.1038/s44488-026-0…
Screenshot of the published article page: title mAIcrobe, an open-source framework for high-throughput bacterial image analysis, the seven authors, and the abstract.

ALT Screenshot of the published article page: title mAIcrobe, an open-source framework for high-throughput bacterial image analysis, the seven authors, and the abstract.

Diagram of the mAIcrobe workflow. Acquisition feeds into segmentation with StarDist, Cellpose and community models, then morphological profiling and a three-class cell cycle classifier, ending in a feature-space scatter plot with three separated clusters.

ALT Diagram of the mAIcrobe workflow. Acquisition feeds into segmentation with StarDist, Cellpose and community models, then morphological profiling and a three-class cell cycle classifier, ending in a feature-space scatter plot with three separated clusters.

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Our two ERC-funded PhD-track fellowships close Tuesday 27 October. Physicists, engineers and computer scientists: one call is yours, building a smart microscope that catches infection live and images it at 20 nm. Start in December at ITQB NOVA. henriqueslab.org/pages/recru…

Recruitment

Open positions in the HenriquesLab

henriqueslab.org
Ricardo Henriques@HenriquesLabOct 14
🔬🚀 A head start on your PhD! Two ERC-funded fellowships for Master's graduates at ITQB NOVA, Lisbon: seven months in our lab (Dec 2026 to Jun 2027) to start your research and build a strong 2027 FCT PhD application with us. Apply by 27 Oct 👇 henriqueslab.org/pages/recru…
Poster split by a diagonal: a fluorescent human cell in cyan and magenta on the left, a laser bench with green, cyan and red light on the right. Start your PhD with us: two fellowships for Master's graduates at ITQB NOVA, 065/BI/2026 (biology) and 066/BI/2026 (engineering). Apply by 27 October.

ALT Poster split by a diagonal: a fluorescent human cell in cyan and magenta on the left, a laser bench with green, cyan and red light on the right. Start your PhD with us: two fellowships for Master's graduates at ITQB NOVA, 065/BI/2026 (biology) and 066/BI/2026 (engineering). Apply by 27 October.

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Ricardo Henriques retweeted
J Cell Science@J_Cell_SciOct 19
In their Tools & Resources article, Bruno Saraiva, Guillaume Jacquemet, Ricardo Henriques @HenriquesLab and team introduce Rxiv-Maker, their automated template engine for streamlined scientific publications. journals.biologists.com/jcs/…
System architecture of Rxiv-Maker. Rxiv-Maker integrates Markdown content, YAML metadata, executable scripts and bibliographies through a processing engine that combines local execution with LaTeX PDF compilation or Word (.docx) generation.

ALT System architecture of Rxiv-Maker. Rxiv-Maker integrates Markdown content, YAML metadata, executable scripts and bibliographies through a processing engine that combines local execution with LaTeX PDF compilation or Word (.docx) generation.

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🔬🚀 A head start on your PhD! Two ERC-funded fellowships for Master's graduates at ITQB NOVA, Lisbon: seven months in our lab (Dec 2026 to Jun 2027) to start your research and build a strong 2027 FCT PhD application with us. Apply by 27 Oct 👇 henriqueslab.org/pages/recru…
Poster split by a diagonal: a fluorescent human cell in cyan and magenta on the left, a laser bench with green, cyan and red light on the right. Start your PhD with us: two fellowships for Master's graduates at ITQB NOVA, 065/BI/2026 (biology) and 066/BI/2026 (engineering). Apply by 27 October.

ALT Poster split by a diagonal: a fluorescent human cell in cyan and magenta on the left, a laser bench with green, cyan and red light on the right. Start your PhD with us: two fellowships for Master's graduates at ITQB NOVA, 065/BI/2026 (biology) and 066/BI/2026 (engineering). Apply by 27 October.

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⚙️ Physicists, engineers, computer scientists (066/BI/2026): build a smart microscope that spots infection events live with neural networks, fixes the cell at that moment with NanoJ-Fluidics and images it at about 20 nm. euraxess.ec.europa.eu/jobs/4…
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You need a Master's by 30 Nov 2026 (final mark ≥14/20), good English and a wish to do a PhD. Please share with anyone finishing a Master's this year 🙌
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🚀 Rxiv-Maker is now peer-reviewed and open access! Write in Markdown, get a typeset PDF or an editable Word file, with figures, citations and cross-references numbered for you. Led by @Bruno_MSaraiva with Guillaume Jacquemet's lab 🔬 doi.org/10.1242/jcs.265183
Top of the first page of the published article 'Rxiv-Maker – an automated template engine for streamlined scientific publications' by Bruno M. Saraiva, Rita Carlota, António D. Brito, Iván Hidalgo-Cenalmor, Guillaume Jacquemet and Ricardo Henriques, showing the title, authors and abstract.

ALT Top of the first page of the published article 'Rxiv-Maker – an automated template engine for streamlined scientific publications' by Bruno M. Saraiva, Rita Carlota, António D. Brito, Iván Hidalgo-Cenalmor, Guillaume Jacquemet and Ricardo Henriques, showing the title, authors and abstract.

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The manuscript can carry its own Python or R code, so figures and reported values are rebuilt from the data at every compile and the text stays in step with the analysis. One command also packages it for arXiv or bioRxiv 👇 rxiv-maker.henriqueslab.org
Rxiv-Maker architecture. Markdown content, Python scripts, R scripts, BibTeX references and YAML metadata feed the Rxiv-Maker processing engine, which builds a LaTeX document and figures, then outputs a publication-ready PDF and an editable Word file.

ALT Rxiv-Maker architecture. Markdown content, Python scripts, R scripts, BibTeX references and YAML metadata feed the Rxiv-Maker processing engine, which builds a LaTeX document and figures, then outputs a publication-ready PDF and an editable Word file.

A Python code block embedded in a Rxiv-Maker manuscript. It loads monthly arXiv submission counts and computes the totals and year span that the manuscript text then quotes, so the numbers update whenever the data change.

ALT A Python code block embedded in a Rxiv-Maker manuscript. It loads monthly arXiv submission counts and computes the totals and year span that the manuscript text then quotes, so the numbers update whenever the data change.

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Thank you to Rita Carlota, @Antonio_DBrito and @IvanHCenalmor, and to everyone who has already written preprints with it and sent us feedback =) Give it a go: pipx install rxiv-maker
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🚨I have open PhD positions to join my new lab at #NIMSB🚀!! nimsb.unl.pt/join-us/ 🌟I'm looking for motivated candidates, eager to join a multidisciplinary team + study the intracellular dynamics driving cancer cell migration with advanced computational methods & microscopy👾
🤖 Made with AI
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👉We show that #DLaccuracy depends on #imageresolution, with each architecture having an optimum, usually at a lower resolution. For imaging, this can lead to 🔬Higher throughput 💾Lower storage ⚡Faster inference 🌱More sustainable computing 🧫 Potentially, reduced photodamage
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#ReScale4DL is very close to my🫀Among the 1st ideas shaped with @HenriquesLab in my early days in his lab, it became a unique opportunity for me to link mathematical concepts to experimental imaging. It also turned out to be my last postdoc story and the 1st publication as PI🤩
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Led by @Antonio_DBrito and @Bruno_MSaraiva, with Dominik Alwardt, Beatriz de P. Mariz, Sérgio Filipe and Mariana Pinho at @ITQBNOVA. StarDist, Cellpose and U-Net segmentation, plus a classifier you can retrain on your own species =)
Four panels. A schematic pairs a microscope with a model, then three split micrographs show raw image beside colour-coded segmentation masks: Staphylococcus aureus by SIM with StarDist, Streptococcus pneumoniae by phase contrast with U-Net, and Bacillus subtilis by widefield with U-Net.

ALT Four panels. A schematic pairs a microscope with a model, then three split micrographs show raw image beside colour-coded segmentation masks: Staphylococcus aureus by SIM with StarDist, Streptococcus pneumoniae by phase contrast with U-Net, and Bacillus subtilis by widefield with U-Net.

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We put it to work on antibiotic phenotyping in E. coli and on cell cycle defects in S. aureus DnaA mutants. It grew out of eHooke, our old S. aureus pipeline, now opened up to rods, cocci and whatever else you image. pypi.org/project/napari-mAIc…
Four fluorescence micrographs of Escherichia coli in red and blue, each cell marked with a coloured cross showing its predicted class. Panels labelled Control, Mecillinam, Nalidixic acid and Control, with cell shape differing between treatments.

ALT Four fluorescence micrographs of Escherichia coli in red and blue, each cell marked with a coloured cross showing its predicted class. Panels labelled Control, Mecillinam, Nalidixic acid and Control, with cell shape differing between treatments.

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Ricardo Henriques retweeted
Weisong Zhao@weisong_zhaoSep 2
Great to see our #RIED work featured on the cover of the September 3 issue of @Nature !
Weisong Zhao@weisong_zhaoAug 12
Out at @nature just now! nature.com/articles/s41586-0… We present #RIED, a new paradigm for excitation-free super-resolution microscopy. We establish chemical super-resolution microscopy using electrochemiluminescence (ECL), chemiluminescence (CL), and bioluminescence (BL). (1/n)
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Ricardo Henriques retweeted
Richard Sever@cshperspectivesAug 13
bioRxiv/medRxiv have been dealing with endless bot attacks recently (plus the usual DDOS stuff, etc). Tricky to address without impacting genuine users. Apologies. We're working with our hosting service on solutions & think we're getting there [he shouts in his red queen costume]
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Ricardo Henriques retweeted
Weisong Zhao@weisong_zhaoAug 12
Out at @nature just now! nature.com/articles/s41586-0… We present #RIED, a new paradigm for excitation-free super-resolution microscopy. We establish chemical super-resolution microscopy using electrochemiluminescence (ECL), chemiluminescence (CL), and bioluminescence (BL). (1/n)
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🚀📷 What can cell shape, signal and movement tell us about a cell's future? #DeepLearning now predicts cell fate from #Microscopy. Work with Rita,@_mariod, @inesmcunha, Juliette + Guillaume👇 preprints.org/manuscript/202…
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Bonjour Curie!
RT-SuperES
@RTsuperESJul 10
This week the RT-SuperES consortium met in Paris for our annual meeting. Good science, honest discussion, and clear next steps for the final year: bringing imaging, ML, fluidics and super-resolution into one adaptive workflow. #RTSuperES #AdaptiveMicroscopy #EICPathfinder @abbelight @meshorer1 @GAlmouzni @HenriquesLab @ilastik_team @S_LevequeFort
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