iiinova — where your digital self keeps evolving

Ricardo Henriques @henriqueslab.bsky.social · 05/10/2026

Yey for light and all the crazy ways it interacts with cells

Reposted by Ricardo Henriques

Christophe 🔬 Leterrier @christlet.bsky.social · 24/09/2026

I think I'm going to lose it being lectured on microscopy image presentation integrity by the winner of the Small Artificial World in Motion competition

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Hao Yin @haoyin.bsky.social · 25/09/2026

Cilia - AI champion show🏆 Credit: GPT6-Astra Inspired by @christlet.bsky.social

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Ricardo Henriques @henriqueslab.bsky.social · 23/09/2026

Okish, although my soul.md is empty since the last grant rejection

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Ricardo Henriques @henriqueslab.bsky.social · 23/09/2026

People pushing "fake it until you make it" to 11

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Ricardo Henriques @henriqueslab.bsky.social · 23/09/2026

Which one gets me prizes more easily?

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Ricardo Henriques @henriqueslab.bsky.social · 23/09/2026

Hey guys, should I buy a microscope or a computer is now just enough l?

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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026

What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar

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Ricardo Henriques @henriqueslab.bsky.social · 23/09/2026

Just woke up to that blood bath today, was completely unaware before

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Christophe 🔬 Leterrier @christlet.bsky.social · 22/09/2026

This is the updated part. Looks like the movie is an AI-generated fluorescence image from a non-labeled acquisition technique. No indication that the Small World jury and organizers have requested and verified the raw data (as mentioned as a possibility in the competition rules)

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Ricardo Henriques @henriqueslab.bsky.social · 23/09/2026

Miss you too Kevin, you never rejected me ❤️❤️ (... I think)

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Rita Strack @ritastrack.bsky.social · 23/09/2026

It was so great to spend time together again!!

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Ricardo Henriques @henriqueslab.bsky.social · 22/09/2026

Just back from the Nature Conference on next-gen fluorescence microscopy @tsinghuauniversity.bsky.social. Awesomely organized! Amazing people to hang out with (we missed you @ritastrack.bsky.social )

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David Tomaz, PhD @dctomaz.bsky.social · 21/09/2026

🔬 VLab4Mic explores this in silico, connecting molecular models with super-resolution experiment design. #Microscopy #SuperResolution #VLab4Mic @aiopticalbiolab.bsky.social

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Ricardo Henriques @henriqueslab.bsky.social · 19/09/2026

Esti's first paper as a PI and last in our lab ❤️. Rock on!

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Reposted by Ricardo Henriques

Sachin Kotak @spindlebehavior.bsky.social · 15/09/2026

Can light build centrosome-like activity? 💡🔬 Yes! We introduce LISA (Light-Induced Spindle Assembly), now in @emboreports.org. By clustering Aurora A with optogenetics, we build centrosome-like activity that nucleates microtubules and rescues spindle defects after centrosome loss. shorturl.at/9h3VQ

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Ricardo Henriques @henriqueslab.bsky.social · 16/09/2026

But how will you breathe underwater?

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Ricardo Henriques @henriqueslab.bsky.social · 15/09/2026

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-mAIcrobe

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

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Ricardo Henriques @henriqueslab.bsky.social · 15/09/2026

Led by António Brito and Bruno Saraiva, with Dominik Alwardt, Beatriz de P. Mariz, Sérgio Filipe and @pinholab.bsky.social, at @itqbnova.bsky.social. Built on @napari.org: StarDist, Cellpose and U-Net, plus a retrainable classifier =)

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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Ricardo Henriques @henriqueslab.bsky.social · 15/09/2026

🔬🚀 Out now in Communications AI & Computing: 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/s44488-026-00022-y

Screenshot of the published article page. Software, Open access, published 15 September 2026. Title: mAIcrobe, an open-source framework for high-throughput bacterial image analysis. Authors: António D. Brito, Dominik Alwardt, Beatriz de P. Mariz, Sérgio R. Filipe, Mariana G. Pinho, Bruno M. Saraiva and Ricardo Henriques. Communications AI & Computing 1, article number 16 (2026), followed by the abstract.

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

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Helen Matthews @helenkmatthews.bsky.social · 22/07/2026

Excellent review of an emerging field in microscopy

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RT-SuperES @rt-superes.bsky.social · 22/07/2026

Can a cell’s shape and movement reveal what it will do next? A new Henriques Lab review explores how AI uses time-lapse microscopy to predict cell fate, while asking whether models predict the future or detect changes already underway. www.preprints.org/manuscript/2...

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Alfred Millett-Sikking @amsikking.bsky.social · 20/07/2026

Ultrafast 3D imaging just got faster! Introducing: "Instant dual-view Snouty (iDV-Snouty) light-sheet microscopy" -> Double the data rate of a Snouty microscope by adding a 2nd view! Use the extra view for a variety of imaging modes! Article here: amsikking.github.io/idv-snouty_l...

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Reposted by Ricardo Henriques

MwahahahahahadScientist @mads100tist.bsky.social · 21/07/2026

May I suggest Yinan's paper for the "scarce labeled datasets" bottleneck (basically, using tracking to infere future state, then use tracking to map it back to the previous state. We called it weMERFISHfate) www.science.org/doi/10.1126/...

science.org

Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis

Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...

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Ricardo Henriques @henriqueslab.bsky.social · 21/07/2026

Oh, love this, thank you! Will patch it in =)

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Ricardo Henriques @henriqueslab.bsky.social · 21/07/2026

🚀🔬 Can cell shape, signal and movement tell us about a cell's future? #DeepLearning studies now predict cell fate from #microscopy. Together w Rita, @mariodelr.bsky.social, @inesmcunha.bsky.social, @juliettegriffie.bsky.social + @guijacquemet.bsky.social👇 www.preprints.org/manuscript/202607.1414/v1

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Juliette Griffié @juliettegriffie.bsky.social · 17/07/2026

We're thrilled to unveil our fantastic line-up of selected speakers for SMLMS 2026 at smlms.org Huge congratulations to them! 🎉 Missed the deadline? Good news! Registration and poster abstract submission have been extended until 31st July! 🔬✨

smlms.org

SMLMS 2026 – Stockholm

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Reposted by Ricardo Henriques

Constantin Pape @cppape.bsky.social · 16/07/2026

Segmenting individual cells in microscopy is much easier these days thanks to foundation models. Can we use these models for other tasks, such as cell classification? We investigate in our latest work, finding big improvements for object and pixel classification compared to classical approaches.

Evaluation of different methods for pixel classification (top) and object classification (bottom) on the LIVECell dataset. Dark green bars show the F1-Score, which measures the classification / segmentation quality (higher is better), light green bars show the runtimes. Five different settings are compared for each task: Ilastik features + random forest (RF), microSAM embeddings + RF, SAM2 embeddings + RF, and uSAM, SAM2 + attentive probing (DeAP and ObAP). microSAM feature perform best for RF based methods, attentive probing outperforms RF based approaches, but at a much higher runtime.

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Kevin Dean @kevin-dean.bsky.social · 16/07/2026

New preprint! Using multiscale ExM/OPM/ASLM, we show that oncogenic drivers leave distinct 3D architectural fingerprints in intact liver tissue: NRAS primarily remodels cell shape, whereas CTNNB1 shifts mitochondrial architecture toward a pericentral-like state. tinyurl.com/kepy33m6

biorxiv.org

Deciphering the Multiscale Morphology of Somatic Oncogenic Alterations in Hepatocellular Carcinoma

Somatic oncogenic mutations are typically defined by their molecular alterations, yet how they reorganize cellular architecture within intact tissues remain largely unknown. Here, we demonstrate that ...

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Reposted by Ricardo Henriques

Estibaliz Gómez de Mariscal, PhD @gomez-mariscal.bsky.social · 15/06/2026

Come and join us at #SPAOM26!! Hands-on workshops and abstract accepted, amazing list of speakers, beautiful location and a great community!!

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Reposted by Ricardo Henriques

taylashakespeare.bsky.social @taylashakespeare.bsky.social · 13/07/2026

Our paper is now featured in focal plane! Check it out if you're looking for a platform to predict and plan imaging experiments before entering the microscope room! Very proud to be a part of this project - biggest congratulations to the team @henriqueslab.bsky.social who made this happen 🔬🛠️

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Ricardo Henriques @henriqueslab.bsky.social · 10/07/2026

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. We built it for easy writing with amazing formatting, avoiding this leak is a welcome side effect

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FocalPlane @focalplane.bsky.social · 09/07/2026

🔬🔦In our latest Imaging spotlight, Damián Martinez, Bruno Saraiva, @taylashakespeare.bsky.social @mariodelr.bsky.social & @henriqueslab.bsky.social introduce VLab4Mic, an open-source platform that allows researchers to optimise microscopy experiments before performing them.

focalplane.biologists.com

Imaging spotlight: VLab4Mic - FocalPlane

Imaging spotlight: VLab4Mic - Tools

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Ricardo Henriques @henriqueslab.bsky.social · 30/06/2026

Nuclei as constellations 🔭 #NucleiSky aligns microscopy images across modalities and scales by reading nuclei like stars to map between them. Joy to contribute, led by @ivanhcenalmor.bsky.social and @guijacquemet.bsky.social's team. #RxivMaker powered preprint. Check it out!

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Reposted by Ricardo Henriques

Guillaume Jacquemet @guijacquemet.bsky.social · 30/06/2026

Delighted to share our latest preprint "NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations" www.biorxiv.org/content/10.6... Code and App: github.com/CellMigratio...

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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 16/06/2026

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

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Reposted by Ricardo Henriques

Johannes Soltwedel @jo-soltwedel.bsky.social · 16/06/2026

Great interactive talk about surveys/interactive survey about talks and cognitive biases from my colleague @lisa-schaefer.bsky.social from @gerbi-gmb.de at #ELMI2026

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Johannes Soltwedel @jo-soltwedel.bsky.social · 16/06/2026

Just gave a talk at #ELMI2026 and a panel discussion about how #FAIR data impacts #AI and its use in #bio-image-analysis 🔬🧪- and what we at @gerbi-gmb.de do about it 👷👷‍♀️ Slides available here: zenodo.org/records/2070...

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Heilemann Lab @heilemannlab.bsky.social · 17/06/2026

👇🏻 don't miss this one if you're into single-molecule microscopy, computational/AI analysis tools and new discoveries in biology 🔬 www.smlms.org

smlms.org

SMLMS 2026 – Stockholm

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Chris Schmidt @schmchris.bsky.social · 16/06/2026

@jo-soltwedel.bsky.social presenting about how important FAIR data management is for efficiently leveraging AI in a trustworthy manner. Small differences in underlying data annotation and metadata can effect AI-based analysis output a lot. #ELMI2026 @gerbi-gmb.de #OME-Zarr

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Ricardo Henriques @henriqueslab.bsky.social · 17/06/2026

SMLM people, ASSEMBLE!! 🔬 The single-molecule localization crowd descends on Stockholm this August (26-28). MINFLUX, DNA-PAINT, blinking dyes, the lot. Properly good line-up and registration's still open. Don't sit this one out 👇 smlms.org

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SMLMS 2026 @smlms2026.bsky.social · 31/03/2026

Hej! We are excited to announce SMLMS 2026! 🔬✨ Join us in Stockholm 📍🇸🇪 from the 26th to the 28th of August for a great opportunity to connect with the super-resolution microscopy community. Find out more and register 👉 smlms.org #SMLM #Microscopy #SuperRes #Stockholm #conference #SMLMS26

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SMLMS 2026 @smlms2026.bsky.social · 24/04/2026

We’re counting down to SMLMS 2026 🔬 ✨️ — kicking off our keynote speaker spotlight with Izzy Jayasinghe from UNSW, Sidney, Australia! Secure your spot and register now at smlms.org/registration...

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SMLMS 2026 @smlms2026.bsky.social · 27/04/2026

Continuing our keynote speaker spotlight with Bernd Rieger from TU Delft, the Netherlands! Register now at smlms.org/registration...

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SMLMS 2026 @smlms2026.bsky.social · 28/04/2026

Thinking about joining us in Stockholm for SMLMS 2026? Our logo designed by Emma Latron, a PhD student in Juliette Griffie lab already shows hints of beautiful Stockholm in summer! 🌞 smlms.org

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SMLMS 2026 @smlms2026.bsky.social · 30/04/2026

Continuing our series with the invited speaker spotlight! First up, Ke Xu from UC Berkley, USA. Want to join us in Stockholm this summer? Check out the speaker lineup and register at smlms.org/speakers/

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SMLMS 2026 @smlms2026.bsky.social · 04/05/2026

Our next invited speaker we are highlighting is Sabrina Simoncelli from UCL, the UK! To find out more and register for the conference, visit smlms.org/speakers/

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