iiinova — where your digital self keeps evolving

Reposted by Daniel Franco-Barranco

Ignacio Arganda-Carreras @iarganda.eurosky.social · 13/08/2026

Do you need to think about something else after the amazing #eclipse experience 😎? Check our latest work with @bokelab.bsky.social, together with @danifranco93.bsky.social and using @biapyx.bsky.social, of course 🤗 @informatikaehu.eurosky.social @dipcehu.bsky.social

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Daniel Franco-Barranco @danifranco93.bsky.social · 30/06/2026

🎉 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.

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Daniel Franco-Barranco @danifranco93.bsky.social · 25/06/2026

🚀 Excited to share our new work in Scientific Reports! 🧠🔬 “Automated segmentation of neurons and spinal cord structures in immunofluorescence images using SpineDL” Happy to have contributed as co-first author together with Pablo Ruiz-Amezcua. 🔗https://doi.org/10.1038/s41598-026-57519-w 🧵👇

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Daniel Franco-Barranco @danifranco93.bsky.social · 21/10/2025

BiaPy is now In Galaxy!! Don't miss the chance of using it to build your workflows in the cloud ;D

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Daniel Franco-Barranco @danifranco93.bsky.social · 30/09/2025

Looking for a PhD in AI & bioimage analysis? 🤠This is basically the ‘boss level’ of opportunities: cutting-edge research + a mentor you’d actually want to have coffee with. Don’t miss it 👇

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BiaPy @biapyx.bsky.social · 15/07/2025

In the meantime, we have more than 46 pretrained models from ⛴️ BiaPy available now in the 🦒 Bioimage Model Zoo 🫶 @ai4life.bsky.social 🔗 Have a look at: bioimage.io#/models As usual, they are accesible from BiaPy's GUI 🖥️, Colab notebooks 📔 and our API 🤓

bioimage.io

BioImage.IO - Model Zoo

BioImage Model Zoo - A community-driven, open resource for sharing standardized AI models for bioimage analysis

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Reposted by Daniel Franco-Barranco

BiaPy @biapyx.bsky.social · 15/07/2025

⛴️ BiaPy just reached version 3.6.1 💫 (latest release)! github.com/BiaPyX/BiaPy... ➡️ v3.6.1 came right after (the more dense) v3.6.0 to fix some small bugs 🐞 Let me tell you a bit about what's new 👇

github.com

Release Version 3.6.1 · BiaPyX/BiaPy

Minor: Disable painting matching instances by default as it takes a lot of time, i.e. TEST.MATCHING_STATS_THS_COLORED_IMG to [] (#135) Refine DA notebook Update notebooks to install BiaPy v3.6.0 ...

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Arrate Munoz-Barrutia @arratemunoz.bsky.social · 29/05/2025

Prou (ex-)supervisor & (always) mentor of @ai4life.bsky.social @egomezm.bsky.social Teresa Zulueta Coarasa; @danifranco93.bsky.social @cfusterbarcelo.bsky.social Carlos Garcia Lopez de Haro @uc3m @cienciauc3m

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Reposted by Daniel Franco-Barranco

AI4Life @ai4life.bsky.social · 28/05/2025

💬 After lunch, we’re back with the AI4Life Community: tool builders, research infrastructures, and industry voices. Community tools like @biapyx.bsky.social and SpotMAX show how AI4Life partners are building bridges between developers and end users.

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Daniel Franco-Barranco @danifranco93.bsky.social · 15/05/2025

Don’t miss the opportunity to work with a scientist like @iarganda.bsky.social !! Kind, honest and brilliant! Plus, the position is located in the beautiful Donostia / San Sebastian. What more do you need? 👇👇

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 29/04/2025

So happy to see this finally out! 🤗 Amazing job from an awesome team: @ivanhcenalmor.bsky.social, @aaitorg.bsky.social, @caporalclement.bsky.social, @lmescu.bsky.social, @arratemunoz.bsky.social munoz.bsky.social, & more! Specially proud of @danifranco93.bsky.social that dedicated his PhD to this 🥰

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Daniel Franco-Barranco @danifranco93.bsky.social · 29/04/2025

Finally BiaPy is out in Nature Methods! 🥳🥳🥳 A major milestone in my research! I'm incredibly proud of the progress made. Huge thanks to my PhD supervisors, @iarganda.bsky.social and @arratemunoz.bsky.social , for their invaluable guidance and support throughout this journey. Check out the thread🧵👇

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BiaPy @biapyx.bsky.social · 28/03/2025

🆕 Did you experience troubles ⚠️ while installing BiaPy in our Google Colab notebooks? We did too! This is due to some updates in the default libraries of Colab. As a temporary solution, we have now included a new cell in the notebooks to reinstall the conflicting libraries 👇

Screenshot of BiaPy notebook showing the installation section. The first part of section reads "Play to reinstall Colab libraries so they are compatible wiht BiaPy. ⚠️ Wait until this cell is fully executed to run the next one ⚠️ This will make the notebook restart. Do not worry and continue executing the next cell once this one is finished."

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Reposted by Daniel Franco-Barranco

BiaPy @biapyx.bsky.social · 25/01/2025

🆕 Now that the bugs have been fixed 🙃, we have a new video 📹 tutorial on how to import pretrained models from the BioImage Model Zoo 🦒 into your #BiaPy workflow using our friendly GUI 🖥️, by @iarganda.bsky.social: youtu.be/Zq50Ew1s8ag

youtu.be

BiaPy GUI: Import models from the BioImage Model Zoo

YouTube video by BiaPy

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Reposted by Daniel Franco-Barranco

Christoph Fischer Photography @beautysurroundsyou.com · 23/01/2025

It took me more than 4 years to capture a scene I could only dream of. A magnificent Condor soars above the peaks of Argentina's Mount Fitz Roy, as they are spot lit in beautiful morning light. 🪶 #bluesky #photography #landscape #birds #nature #landscapephotography #naturephotography #travel #scape

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Daniel Franco-Barranco @danifranco93.bsky.social · 24/01/2025

Don't miss the chance to check what's new in BiaPy's GUI! 😍

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Leah Caplan @lrcap.bsky.social · 06/12/2024

When you’re imaging and your sample takes a Pikachu! Having fun playing around with our new #Nikon NSPARC for #FluorescenceFriday #microscopy #myosin #epithelial #cellbiology #meme @tyskalabactual.bsky.social

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Dani cRabaiotti 🦀 @danirabaiotti.bsky.social · 10/02/2024

Welcome to the Science feed! Please read our FAQs for instructions for how to be added as a contributor: bossett.io/science-feed/ Mod introductory posts linked below⬇️ Use the test tube emoji on posts you want to appear in the feed🧪 Please like the feed and make sure you follow our feed rules:

Science Feed Rules:
🧪 No misinformation
🧪 Keep posts relevant to science
🧪 Use alt text
🧪 Credit images
🧪 Give context to links to external sites
🧪 Have fun!

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Zebrafish Rock! @zebrafishrock.bsky.social · 01/12/2024

Check out #ZebrafishZunday every Sunday for fintastic fish #sciart! 🧪

Girl in red dress meme. Science feed holding hand of #FluorescenceFriday checking out #ZebrafishZunday

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Daniel Franco-Barranco @danifranco93.bsky.social · 24/11/2024

Is there any list I can join to see posts related to connectomics? 🧪🧪

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BiaPy @biapyx.bsky.social · 22/11/2024

Did you like what you heard about BiaPy at #SPAOM2024? 🔬 Are you interested in giving its GUI a try? 🖥️🧙 Search no more! Here you have our walkthrough video tutorial on BiaPy's GUI by @danifranco93.bsky.social 🤗 Let us know your thoughts, all feedback is welcome! 🤩 youtu.be/vY7aBh5FUNk?...

youtu.be

BiaPy graphical user interface walkthrough

YouTube video by BiaPy

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Daniel Franco-Barranco @danifranco93.bsky.social · 21/11/2024

With how easily I get cold, I’ve had the luck to come to Cambridge during the coldest weeks of the year, according to the locals! Lucky me! 🧊🧊❄️❄️

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Daniel Franco-Barranco @danifranco93.bsky.social · 21/11/2024

Don't miss the chance of knowing the last updates of BiaPy in #SPAOM2024!!! 🔬🤓

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Andrew Hires @andrewhires.bsky.social · 14/11/2024

This paper is incredible. EM level connectomics on a light microscope. www.biorxiv.org/content/10.1...

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Jesper Dr.amsch @jesper.drams.ch · 19/11/2024

Discover the key to unlocking impactful scientific contributions in the world of machine learning! 🤖📈 This tutorial aims to increase the quality of scientific contributions using reproducible methods, appropriate validation techniques, and better code quality. 🧪

amplt.de

Discover the key to unlocking impactful scientific contributions in the world of machine learning! 🤖📈

Making models and data available increases the visibility of work and enables easier collaboration on future work.

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Guille Martín @farmaenfurecida.bsky.social · 19/11/2024

Los tuits con bulos sobre salud tienen mucho más alcance que los científicos porque sus seguidores son mucho más activos y fanáticos. Así que si veis información interesante y de calidad: compartid y dad like. Es otra forma de luchar contra ellos.

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Daniel Franco-Barranco @danifranco93.bsky.social · 19/11/2024

Today was my first day in Cardona's lab at MRC LMB. It was a pleasure to meet my new lab colleagues and I'm excited for the upcoming projects to develop. Stay tunned!

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/11/2024

🆕 We have updated our preprint in @biorxivpreprint.bsky.social 📰 It explains better the current state of #BiaPy ⛴️ while describing as well its limitations 🤗 Hope you like it! "BiaPy: Accessible deep learning on bioimages" www.biorxiv.org/content/10.1...

biorxiv.org

BiaPy: Accessible deep learning on bioimages

BiaPy is an open-source library and application that streamlines the use of common deep learning approaches for bioimage analysis. Designed to simplify technical complexities, it offers an intuitive i...

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