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Daniel Franco-Barranco

@danifranco93.bsky.social

Postdoc in Albert Cardona's lab at MRC LMB

21 Posts49 Follower60 Folgt
Daniel Franco-Barranco@danifranco93.bsky.social · last mo.

🎉 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.
Daniel Franco-Barranco@danifranco93.bsky.social · last mo.

🚀 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 🧵👇

Daniel Franco-Barranco@danifranco93.bsky.social · 10mo ago

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 👇

Ignacio Arganda-Carreras@iarganda.eurosky.social · 10mo ago

📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social! Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬 📅 Applications open Oct 6 (deadline: ~Oct 27) 📍 San Sebastian, Spain. 👉 cvpd.github.io/post/2025-09...

BiaPy@biapyx.bsky.social · last yr.

⛴️ 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 👇

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 ...

github.com

AI4Life@ai4life.bsky.social · last yr.

💬 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.

BildBild
Daniel Franco-Barranco@danifranco93.bsky.social · last yr.

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? 👇👇

Ignacio Arganda-Carreras@iarganda.eurosky.social · last yr.

🆕 We're hiring! We're looking for postdoc 🎓 candidates to work at the intersaction of bioimage analysis 🖥️🔬, tissue biomechanics 🧫, and neuroscience 🧠. 👉 Application deadline: 2025/06/02 👉 Duration: July 2025 - December 2026 (for now) Come work with us! 🤗 dipc.ehu.eus/en/dipc/join...

Ignacio Arganda-Carreras@iarganda.eurosky.social · last yr.

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 🥰

BiaPy@biapyx.bsky.social · last yr.

🚀 Excited to share that our work on BiaPy has been published today in Nature Methods! BiaPy makes deep learning accessible for bioimage analysis, from small datasets to terabyte-scale 3D images. 👇 (1/7) 🔗 www.nature.com/articles/s41... #DeepLearning #BioimageAnalysis #OpenSource #BiaPy

Daniel Franco-Barranco@danifranco93.bsky.social · last yr.

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🧵👇

BiaPy@biapyx.bsky.social · last yr.

🚀 Excited to share that our work on BiaPy has been published today in Nature Methods! BiaPy makes deep learning accessible for bioimage analysis, from small datasets to terabyte-scale 3D images. 👇 (1/7) 🔗 www.nature.com/articles/s41... #DeepLearning #BioimageAnalysis #OpenSource #BiaPy

BiaPy@biapyx.bsky.social · last yr.

🆕 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."
Jesper Dr.amsch @jesper.drams.ch · 2y ago

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. 🧪

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 · 2y ago

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.