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Iván Hidalgo-Cenalmor

@ivanhcenalmor.bsky.social

PhD researcher at Cell Migration Lab, Åbo Akademi, Turku, Finland 🇫🇮 cellmig.org

33 Posts116 Follower97 Folgt
Iván Hidalgo-Cenalmor@ivanhcenalmor.bsky.social · 22h ago

NucleiSky is now published in Journal of Cell Science @jcellsci.bsky.social! 🎉🥳 Using nuclei, it can connect microscopy images across scales and modalities, even helping microscopes automatically find the same FoV. Check out previous posts or our paper for a deeper dive: doi.org/10.1242/jcs....

Iván Hidalgo-Cenalmor@ivanhcenalmor.bsky.social · 2mo ago

Our new preprint 'NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations' is out! 🎉Check out @guijacquemet.bsky.social post first to learn more🤩 In this 🧵 I’ll share how we used NucleiSky in smart microscopy and how you can install and try it yourself 👇

Guillaume Jacquemet@guijacquemet.bsky.social · 2mo ago

No live nuclear label? No problem. Use artificial labelling to infer DAPI-like nuclei, then use #NucleiSky to align your data. For instance, to connect live imaging data to fixed Cell Painting images.

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Guillaume Jacquemet@guijacquemet.bsky.social · 2mo ago

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...

Iván Hidalgo-Cenalmor@ivanhcenalmor.bsky.social · 2mo ago

Our new preprint 'NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations' is out! 🎉Check out @guijacquemet.bsky.social post first to learn more🤩 In this 🧵 I’ll share how we used NucleiSky in smart microscopy and how you can install and try it yourself 👇

Guillaume Jacquemet@guijacquemet.bsky.social · 2mo ago

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...

Ricardo Henriques@henriqueslab.bsky.social · 2mo ago

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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Guillaume Jacquemet@guijacquemet.bsky.social · 2mo ago

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...

Daniel Franco-Barranco@danifranco93.bsky.social · 2mo ago

🎉 Big news: our paper "Representation matters" just got accepted as a Registered Report (Stage 1) in Nature Methods! 🧬 We're building the first rigorous, preregistered benchmark of instance segmentation representations in bioimage analysis. 🧵👇 (1/3)

Examples of intermediate representations used in bottom-up instance segmentation for bioimage analysis. Shown are representative pixel- or voxel-level targets derived from instance annotations, including binary feature maps (for example, foreground, contours, centroids, and skeletons), distance-based representations (for example, horizontal/vertical offsets, radial distances, distance to boundary, and distance to center), and affinity-based representations. Here, neighbor affinities denote local connectivity predictions indicating whether adjacent pixels or voxels belong to the same object. The rows show illustrative examples from different datasets and are not intended to imply a sequential workflow or a one-to-one correspondence between representations. In the benchmarked pipelines, such intermediate representations are subsequently converted into final object instances by downstream grouping or post-processing procedures such as watershed, clustering, or graph partitioning.
Ricardo Henriques@henriqueslab.bsky.social · 2mo ago

🔬🚀 Preprint update for #VLab4Mic - our super-resolution experiments virtual simulation system. Now installs as one-click desktop app: no Python, no setup, thanks to the magic of the @guijacquemet.bsky.social's lab #LabConstrictor packaging engine www.biorxiv.org/content/10.64898/2026.06.02.729521v2

Iván Hidalgo-Cenalmor@ivanhcenalmor.bsky.social · 5mo ago

Excited to share my first PhD project: LabConstrictor 📒🐍 Have you ever created a Jupyter notebook with all your love 🫶, only for others to be unable to install it 🥲? LabConstrictor, comes to solve this! Check out how it works in the preprint 🔗 arxiv.org/abs/2603.107... or follow this thread ⬇️

Estibaliz Gómez de Mariscal, PhD@gomez-mariscal.bsky.social · 3mo ago

🚨Our preprint on DL for single-image super-resolution in microscopy is out!🌟 sl1nk.com/p62yedg Our benchmark recaps an adventure of learning and questioning with @ivanhcenalmor.bsky.social & @iarganda.eurosky.social 🌟 how to objectively assess SISR models & ease the choice for their use in👉 biology🔬

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Iván Hidalgo-Cenalmor@ivanhcenalmor.bsky.social · 3mo ago

Super excited to share a project I’ve worked on since my Master’s thesis, what a journey!🚵 Finally out as a Nature Methods Stage 1 Registered Report preprint doi.org/10.6084/m9.f... We benchmark deep learning-based single-image super-resolution methods for microscopy imaging. Interested? Check out 🧵

Iván Hidalgo-Cenalmor@ivanhcenalmor.bsky.social · 3mo ago

Super excited to share a project I’ve worked on since my Master’s thesis, what a journey!🚵 Finally out as a Nature Methods Stage 1 Registered Report preprint doi.org/10.6084/m9.f... We benchmark deep learning-based single-image super-resolution methods for microscopy imaging. Interested? Check out 🧵

Accuracy versus Perception: a Benchmark of Deep Learning Models for Single-Image Super-Resolution in Microscopy

Virtual super-resolution deep learning methods provide a powerful solution to overcome the physical and temporal constraints of microscopy imaging. Yet, assessing and choosing an ideal methodological strategy complicates their use in life sciences and creates a lack of trust in these methods. Here we propose an objective comparison of nine popular single-image super-resolution (SISR) models in a collection of publicly available microscopy datasets, including cell components like microtubules, endoplasmic reticulum, and actin, using confocal microscopy, SEM, SIM, SMLM and STED microscopy modalities for fixed and live-cell microscopy data. The proposed models will be assessed quantitatively with a collection of metrics in microscopy and computer vision, and qualitatively by experts in the field. The proposed models will be made accessible through open, user-friendly, containerised notebooks. This systematic assessment of SISR approaches will provide a more comprehensive understanding of these methods' performance and contribute to standardising SISR methods in microscopy.

doi.org

Estibaliz Gómez de Mariscal, PhD@gomez-mariscal.bsky.social · 5mo ago

#IMS2026 D1 finishes with great @henriqueslab.bsky.social and @guijacquemet.bsky.social pushing the limits of live-cell super-resolution, democratizing AI and quantitative microscopy, and using all these to study cancer cell transmigration and attachment 🌟

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Estibaliz Gómez de Mariscal, PhD@gomez-mariscal.bsky.social · 5mo ago

Speaking about scalable biology, afternoon at #IMS2026 went from nano to multicellular organoids with Cecile Morlot, Helder Maiato and Catarina Brito🤩

Claire Bedbrook@clairebedbrook.bsky.social · 5mo ago

Aging may feel gradual… but what if it’s not? In our recent paper, we tracked fish continuously from puberty until death. This gave us a unique view of how aging unfolds across the adult lifespan. 🧵

Artur@arturruppel.bsky.social · 5mo ago

First paper as first & corresponding author, out in PLOS Computational Biology! 🎉 napariTFM brings traction force & monolayer stress microscopy into napari, accessible via GUI; open-source, validated and no coding required. 😉 Check it out 👇

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Guillaume Jacquemet@guijacquemet.bsky.social · 5mo ago

Also, the preprint describing LabConstrictor was made with love using the #RxivMaker engine created together with @henriqueslab.bsky.social github.com/HenriquesLab... #RxivMaker now create ready to submit zip files for both @biorxivpreprint.bsky.social and arXiv

GitHub - HenriquesLab/rxiv-maker: Rxiv-Maker is a GitHub-native framework that converts markdown into a publication-ready PDF. It automates scientific preprint generation with a focus on reproducibili...

Rxiv-Maker is a GitHub-native framework that converts markdown into a publication-ready PDF. It automates scientific preprint generation with a focus on reproducibility and version control - Henriq...

github.com

Iván Hidalgo-Cenalmor@ivanhcenalmor.bsky.social · 5mo ago

Excited to share my first PhD project: LabConstrictor 📒🐍 Have you ever created a Jupyter notebook with all your love 🫶, only for others to be unable to install it 🥲? LabConstrictor, comes to solve this! Check out how it works in the preprint 🔗 arxiv.org/abs/2603.107... or follow this thread ⬇️

Iván Hidalgo-Cenalmor@ivanhcenalmor.bsky.social · 5mo ago

Hi Bluesky! This is my first post 🤗 I just wanted to introduce myself. My name is Iván Hidalgo, and I’m a second-year PhD student at CellMigrationLab (cellmig.org). I’ve never really been much of a social media person, but I’ll be sharing my PhD journey and the work that comes along the way 🫶🚵🚀

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Christophe 🔬 Leterrier@christlet.bsky.social · 12mo ago

Sounds like an interesting comparison of resolution assessment methods for super-resolution… Would anyone with access send me the pdf (christophe dot leterrier dot gmail dot com)? Thanks! link.springer.com/article/10.1...

Resolution assessment of super-resolution microscopy imaging: structural and technical dependencies for cell biology - Cytotechnology

Super-resolution fluorescence microscopy (SRM) has enabled visualization of nanoscale cellular structures, but systematic evaluation of resolution assessment methods across diverse biological structur...

link.springer.com