Ricardo Henriques@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
2,919 Photos and videos
🔬🚀 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.

1
7
27
1,977
🚨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
6
9
338
👉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
1
4
5
498
#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🤩
1
2
2
235
🔬🚀 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.

1
7
27
1,977
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.

1
2
3
336
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.
1
2
211
Ricardo Henriques retweeted
Weisong Zhao@weisong_zhao
Sep 2
Great to see our #RIED work featured on the cover of the September 3 issue of @Nature !
Weisong Zhao@weisong_zhao
Aug 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)
3
9
55
3,438
Ricardo Henriques retweeted
Richard Sever@cshperspectives
Aug 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]
3
12
1,098
Ricardo Henriques retweeted
Weisong Zhao@weisong_zhao
Aug 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)
6
61
260
49,293
🚀📷 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…
12
36
2,029
Bonjour Curie!
RT-SuperES
@RTsuperES
Jul 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
2
599
Timely callout to #RxivMaker. With rxiv-maker you write in Markdown and the tool generates the LaTeX, so author comments and to-do notes never reach the source files you upload to arXiv. Built it for easy writing with amazing formatting, avoiding this leak is welcome side effect
nature
@Nature
Jul 10
Passwords, GPS coordinates and private conversations have all been found in the metadata and source files of millions of preprint submissions go.nature.com/4gv5Ffx
2
1
1,130
Ricardo Henriques retweeted
Euro-BioImaging ERIC@EuroBioImaging
Jun 23
Working with single molecule localisation microscopy? 🔬 Submit your abstract for #SMLMS2026, hosted in by SciLifeLab, KTH and Stockholm University, with contributions from our Swedish NMI Node colleagues! 🗓️ August 26-28 in Stockholm 🇸🇪 More⤵️ smlms.org/
7
12
593
Ricardo Henriques retweeted
Euro-BioImaging ERIC@EuroBioImaging
Jun 16
#EuroBioImaging Team members are excited to be at #ELMI this week in Coimbra, Portugal, organised by our @PPBioImaging Node. This evening, Luisa Cortes opened the conference on behalf of the organising committee. Looking forward to an exciting programme! 🔬
3
9
426
SMLM people, ASSEMBLE!! 🔬 The single-molecule crowd heads to Stockholm, 26-28 Aug, for #SMLMS2026. MINFLUX, DNA-PAINT, blinking dyes, the whole gang. Cracking line-up, registration's open. Come join us 👉
Euro-BioImaging ERIC@EuroBioImaging
Jun 16
Interested in single molecule localisation microscopy? 🔬 Don't miss #SMLMS2026, hosted in by SciLifeLab, KTH and Stockholm University, with contributions from our Swedish NMI Node colleagues! 🗓️ August 26-28 in Stockholm 🇸🇪 More⤵️ smlms.org/
1
5
17
1,813
Ricardo Henriques retweeted
Euro-BioImaging ERIC@EuroBioImaging
Jun 16
Interested in single molecule localisation microscopy? 🔬 Don't miss #SMLMS2026, hosted in by SciLifeLab, KTH and Stockholm University, with contributions from our Swedish NMI Node colleagues! 🗓️ August 26-28 in Stockholm 🇸🇪 More⤵️ smlms.org/
6
10
2,310
Ricardo Henriques retweeted
RT-SuperES
@RTsuperES
Jun 17
Can your microscope resolve the structure you want to study before you run the experiment? New #bioRxiv preprint: VLab4Mic predicts structural resolvability in #SuperResolution microscopy, helping choose modality and probe. Great work from @HenriquesLab. @RTsuperES ; @EUeic @JDamianMtzR biorxiv.org/content/10.64898…

VLab4Mic: prediction of structural resolvability in super-resolution microscopy

Determining whether a microscopy experiment can resolve a specific feature of a protein assembly remains difficult because researchers must balance imaging modality, labelling strategy, and probe...

biorxiv.org
1
2
3
526
🔬🚀 Updated #VLab4Mic preprint. Rebuilt the clathrin models from full-length triskelions, dome+flat lattice toy simulations share a common motif. Wanna see how it looks across microscopy methods? (Thank you for the advice Stephane Vassilopoulos) biorxiv.org/content/10.64898…
1
6
21
2,333
Ricardo Henriques retweeted
juliette.griffie@GriffieJuliette
Jun 17
🔬🌟 Join us for SMLMS2026 in Stockholm! 🔬🌟 We’re excited to welcome the advanced light microscopy community to Stockholm August 26–28 2026. Check out our fantastic speaker line-up and register here: smlms.org 🚨Only 2 weeks left for abstract submission 🚨
4
4
802
Ricardo Henriques retweeted
juliette.griffie@GriffieJuliette
Jun 16
And it is out!!!🚨 Very excited to be sharing SMLMFlow. It has been a fantastic journey with @sebjbauer and a great opportunity to work with old friends😜Daniel Sage and Ruby Peters.
Sebastian Bauer@sebjbauer
Jun 16
I am thrilled to share SMLMFlow: my first research paper for my PhD! 🥳 📰 Preprint: biorxiv.org/content/10.64898… 🧵👇 1/5
3
7
655
Load more