Ignacio Arganda-Carreras

@iarganda.eurosky.social

Bioimage analysis and computer vision enthusiast. Whenever I can, I do software too. Ikerbasque | University of the Basque Country (UPV/EHU) | DIPC | Biofisika Institute ORCID: 0000-0003-0229-5722

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🎉 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.

🚀 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 🧵👇

📢📢 We are hiring a Bioimage Analyst at the BioVisionCenter! 📢📢 Join our collaboration with the Flow Cytometry Facility and contribute back to the international efforts on open standards for bioimaging data! More information here, reach out if you have any question: jobs.uzh.ch/job-vacancie...

UZH: Bioimage Analyst

The University of Zurich is the largest university in Switzerland and one of the most prominent in Europe. For research purposes the Biovision Center and Flow Cytometry Facility offer services to supp...

jobs.uzh.ch

This award is such a beautiful surprise! 🤩 Tons of thanks to the @royalmicrosoc.bsky.social, the amazing #BioimageAnalysis, #Fiji, #ImageJ & #OpenSource communities, my mentors and mentees, my employers, and whoever nominated me (I still don't know how that person was 😅)!

Royal Microscopical Society@royalmicrosoc.bsky.social · 4mo ago

We are very pleased to announce Dr Ignacio Arganda-Carreras @iarganda.eurosky.social as winner of the RMS Award for Data Analysis in Imaging (DAIM) 🙂 🔬 Read more about Ignacio's achievements: www.rms.org.uk/resource/dr-...

Ignacio Arganda-Carreras pictured smiling in a pink t-shirt. Image credit: Paula Arbide

The Cimini lab is hiring for both postdocs and interns! The postdoc role will cover bioimage analysis projects and educational material creation; the intern will be working on our Bilayers project for helping distribute and access deep learning tools for bioimage analysis. Click below to learn more!

Postdoctoral Associate and Data Science Intern roles - Broad Institute, Cambridge MA USA

The Broad Institute Imaging Platform (the team behind CellProfiler, Piximi, and Bilayers) is currently hiring for postdoctoral and intern roles! Postdoc role: we are looking for 1-2 candidates who ha...

forum.image.sc

🚨 Registration closing soon! Join the AIM-Net Deep Learning Summer School (2–6 June 2026, La Ràpita 🇪🇸) 🔬 Hands-on training in AI for microscopy & bioimage analysis 👩‍🔬 For PhDs & early-career researchers 💻 Lectures + practicals + project work ⏳ Apply before April 10 aim-net.net/eventos/aim-...

AIM-Net · Deep Learning Summer School

Introduction to AI methods for microscopy and quantitative bioimaging The AIM-Net Summer School is a core training activity of the AIM-Net thematic network (AEI–REDES) in collaboration […]

aim-net.net

You still have time to apply if you are interested in joining my lab!!

Guillaume Jacquemet@guijacquemet.bsky.social · 8mo ago

🚨 We are hiring TWO postdocs to join the Cell Migration Lab (cellmig.org) 🇫🇮 as part of the new Centre of Excellence in Immune–Endothelial Interfaces (IMMENs). Join us to decode immune regulation & develop next-gen imaging tools! 🧪🔬 Details in thread 🧵👇 #ScienceSky #Postdoc #AcademicJobs Please RT🫶

❗The official application call for our PhD position has already started: www.ehu.eus/es/web/ikerk... Since most of the application is in either Spanish or Basque, I have prepared a document in English 👇 drive.google.com/file/d/1q0mH... Looking forward to receiving applications! 🤩

Summary of the FPI 2025 PhD Call at UPV_EHU.pdf

drive.google.com

Ignacio Arganda-Carreras@iarganda.eurosky.social · 12mo 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...

👇 The official call opening has been delayed ⌛ by the university to the end of this week. Sorry about that, I'll keep you posted! 🙏

Ignacio Arganda-Carreras@iarganda.eurosky.social · 12mo 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...