Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?
Poster at LMRL Workshop at ICLR 2026, Rio de Janeiro, Brazil
CV
I am a postdoctoral researcher at the Uhlmann Group and the BioVision Center, University of Zurich, working in computational bioimage analysis. My current research focuses on foundation models, efficient adaptation, and reproducible AI for microscopy, with an emphasis on robust and transferable methods for real scientific workflows. My academic profile combines methodological research with software, training, and community-facing contributions.
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Academic Background
- Ph.D. in Computer Science and Technology, Universidad Carlos III de Madrid, 13 Dec. 2022
- M.Sc. in Cybersecurity, Universidad Carlos III de Madrid, 2020
- B.Sc. in Telematics Engineering, Universitat de les Illes Balears, 2019
Professional History
Postdoctoral Researcher: Sep 2025 – Present
Where: University of Zurich (UZH), BioVision Center
Field: Computational bioimage analysis Focus: Foundation models, efficient adaptation, and transferable AI for microscopy PI: Dr. Virginie UhlmannPostdoctoral Researcher: Jan 2023 - Aug 2025
Where: UC3M, Bioengineering Department
Field: Bioimage analysis
PI: Dra. Arrate Muñoz Barrutia
Projects: AI4Life, BioImage Model Zoo, deepImageJ, SAMJPostdoctoral Researcher: Jan 2024 - Aug 2025
Where: IISGM
Field: Artificial Intelligence in biomedical imaging
PI: Dra. Arrate Muñoz Barrutia, Dr. Javier Pascau GonzálezVisiting Researcher: Sept 2023 - Oct 2023
Where: KTH, SciLifeLab, AICell Lab, Stockholm, Sweden
Field: Bioimage analysis
PI: Dr. Wei Ouyang
Projects: AI4Life, BioImage Model ZooPhD Candidate: Sept 2020 - Dec 2022
Where: UC3M
Field: Deep Learning applied to Biometrics
Supervisors: Dr. Pedro Peris-López, Dra. Carmen Cámara
Project: CYNAMON-CMResearch Assistant: Oct 2019 - Dec 2022
Where: UC3M, COSEC Laboratory
Field: Cybersecurity
Supervisors: Dr. Pedro Peris-López, Dra. Carmen CámaraSecurity and DevOps Systems Technician: Jun 2019 - Sep 2019
Where: Air Europa, S.L.
Field: Server/infrastructure maintenance and cybersecurity
Supervisor: Bernat Mut González
Awards, Fellowships & Grants
- MSCA Postdoctoral Fellowship - Seal of Excellence - 2025, European Commission
- Recognized for high-quality research proposal in the Marie Skłodowska-Curie Actions (MSCA) Postdoctoral Fellowship programme.
- UC3M Mobility Grant for Research Stays — 2023, Universidad Carlos III de Madrid
- Awarded to support a one-month research stay at KTH, SciLifeLab with Wei Ouyang.
Academic Service
Peer Review
Reviewer for journals including:
- Biomedical Engineering Letters
- Engineering Applications of Artificial Intelligence
- Pattern Recognition
Publications
For full citations and publication details, see the Publications page.
Peer-review Journals
- ECG-Based Patient Identification: A Comprehensive Evaluation Across Health and Activity Conditions
IEEE Access, 2024 📄 - The Crucial Role of Bioimage Analysts in Scientific Research and Publication
Journal of Cell Science, 2024 📄 - BioImage.IO Chatbot: A Personalized Assistant for BioImage Analysis Augmented by Community Knowledge Base
Nature Methods, 2023 📄 - Bridging the Gap: Integrating Cutting-edge Techniques into Biological Imaging with deepImageJ
bioRxiv, 2023 📄 - DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible
Nature Methods, 2023 📄 - Exploring the Power of PPG Matrix for Atrial Fibrillation Detection with Integrated Explainability
Engineering Applications of Artificial Intelligence, 2023 📄 - ELEKTRA: ELEKTRokardiomatrix Application to Biometric Identification with Convolutional Neural Networks
Neurocomputing, 2022 📄
Preprints
- OREHAS: A fully automated deep-learning pipeline for volumetric endolymphatic hydrops quantification in MRI
Preprints, 2026 📄 - The impact of gamification on learning outcomes: experiences from a Biomedical Engineering course
Preprints, 2025 📄 - Scaffolding Collaborative Learning in STEM: A Two-Year Evaluation of a Tool-Integrated Project-Based Methodology
Preprints, 2025 📄 - SAMJ: Fast Image Annotation on ImageJ/Fiji via Segment Anything Model
Preprints, 2025 📄
Conference Proceedings
- Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?
Learning Meaningful Representations of Life (LMRL) Workshop at ICLR 2026, 2026 📄 - Can You Afford to Research? The Financial Strain of Ph.D. Students in Spain
Precarity and Instability in Academia Symposium (PIAS), 2024 📄 - Estimación de la proporción de hidrops endolinfático en pacientes con la enfermedad de Mènière
CASEIB 2023, 2023 📄 - Unveiling Hidden Patterns: Harnessing the Power of Short PPG-Traces for Atrial Fibrillation Detection
IEEE 19th International Conference on Body Sensor Networks (BSN), 2023 📄
Conference Abstracts
- Harnessing Deep Learning in Bioimaging: The DeepImageJ Journey
Effectively Communicating Bioimage Analysis Workshop, 2024 📄
Talks
2026
2025
Transforming BioImage Analysis: The AI4Life Approach
Talk at Cell Physics 2025, Saarbrücken, Germany
AI-Based Pipelines for Bioimage Analysis
Talk at NEUBIAS Bioimage Analysis Course, Institut Pasteur, Paris, France
Deep Learning for Bioimage Analysis
Talk at EPFL Open Microscopy & AI Workshop, EPFL, Lausanne, Switzerland
Lecture & Practical Session on Advanced CNNs
Talk at Ágora – Journal Club, Universidad Carlos III de Madrid, Universidad Carlos III de Madrid, Spain
Desinformación y Antenas de Telecomunicación: Cómo Combatir el Miedo con Ciencia
Talk at T3chFest Community Talks, Universidad Carlos III de Madrid, Spain
ECG and PPG Applications in Healthcare
Talk at Biosignals Course, Universidad Pontificia Comillas, Madrid, Spain
2024
Can You Afford to Research? The Financial Strain of Ph.D. Students in Spain
Talk at Precarity and Instability in Academia Symposium (PIAS), Leganés, Spain
Introduction to AI4Life and BioImage Model Zoo
Talk at SPAOM 2024, Toledo, Spain
Prompt Engineering: How to Generate Good and Functional Code with the BioImage.IO Chatbot
Talk at YMIA Python Event, Online
BioImage.IO Chatbot Talk
Talk at ZIDAS Summer School, ETH Zurich, Switzerland
BioImage.IO Chatbot
Talk at AI4Life Workshop of Zero-Code Tools and BioImage Model Zoo Community Partners, Universidad Carlos III de Madrid
Transformers, Vision Transformers and SAMJ
Talk at AI4Life Workshop of Zero-Code Tools and BioImage Model Zoo Community Partners, Universidad Carlos III de Madrid
Meet the BioImage.IO Chatbot
Talk at ELIXIR, Virtual
The BioImage.IO Chatbot
Talk at Euro-Bioimaging Virtual Pub, Virtual
Harnessing deep learning in bioimaging: the deepImageJ journey
Talk at Effectively Communicating Bioimage Analysis Workshop, East Sussex, UK
2023
Estimación de la proporción de hidrops endolinfático en pacientes con la enfermedad de Mènière
Poster at XLI Congreso Anual de la Sociedad Española de Ingeniería Biomédica (CASEIB), Cartagena, Spain
Leveraging Cloud-Based Virtual Desktops for Bioimage Analysis with BAND and deepImageJ
Talk at I2K 2023, Virtual
¿Quién me lo habría dicho?
talk at Unidreams, Virtual
GitHub Copilot, what is it and how can I get it?
Seminar at UC3M, Universidad Carlos III de Madrid, Departamento de Bioingeniería
2022
IDOVEN - Protegiendo el oro con tu corazón
Talk at Idoven, Gran Vía, Madrid
Skype A Scientist
Talk at SkypeAScientist, Virtual
Protegiendo el oro con tu corazón y un poco de Python
Talk at PyconES, Granada, Andalucía
Protegiendo el oro con tu corazón
Talk at Women Techmakers Madrid 2022, Puerta de Toledo, Madrid
Teaching
2026
BioImage Model Zoo
BioImage Model Zoo
2025
Deep Learning-Based Segmentation and Quantification of Endolymphatic Hydrops in Inner Ear MRI
Deep Learning-Based Segmentation and Quantification of Endolymphatic Hydrops in Inner Ear MRI
Automated Classification and Localization of Inner Ear Structures in MRI Using Deep Learning
Automated Classification and Localization of Inner Ear Structures in MRI Using Deep Learning
2024
C3IS International Research Mentorship Program
C3IS International Research Mentorship Program
Among Coursemates Tutorship Program
Among Coursemates Tutorship Program
AI for Radiology and Microscopy
Artificial Intelligence in Radiology and Microscopy
2023
Biomedical Image Processing
Biomedical Image Processing
Estimation of Endolymphatic Hydrops Ratios in Ménière’s Disease
Estimation of Endolymphatic Hydrops Ratios in Ménière’s Disease
Events
2024
Precarity and Instability in Academia Symposium (PIAS)
Precarity and Instability in Academia Symposium (PIAS)
GloBIAS Bioimage Analysts Workshop
GloBIAS Bioimage Analysts Workshop
AI4Life Workshop-Hackathon-Uploathon
AI4Life Workshop-Hackathon-Uploathon (Madrid)
ImgLib2 and BigDataViewer Hackathon Prague
ImgLib2 and BigDataViewer Hackathon Prague
BioImage Model Zoo Enhancements Hackathon
BioImage Model Zoo Enhancements Hackathon
Effectively Communicating Bioimage Analysis Workshop
Effectively Communicating Bioimage Analysis Workshop
deepImageJ and friends Hackathon
deepImageJ and friends Hackathon
2023
AI4Life Hackathon and Solvathon
AI4Life Hackathon and Solvathon
Cloud Based and AI Hackathon
Cloud Based and AI Hackathon
Accessibility of DL Models from Java Hackathon
Accessibility of DL Models from Java Hackathon
2022
PyConES 2022
PyConES 2022 — Conference Talk and Participation
Dissertations
Biopotential Signals and their Applicability to Cybersecurity, cum laude
Ph.D. Thesis, UC3M, Dec. 2022
Supervised by Pedro Peris-López, Carmen CámaraA Novel Biometrics Technique based on Electrocardiomatrix
M.Sc. Thesis, UC3M, 2020
Supervised by Pedro Peris-López and Carmen CámaraEvent Management and Safety Information
B.Sc. Thesis, UIB, 2019
Supervised by M. Francisca Hinarejos Campos
Training & Certifications
- Grant Writing Workshop for Postdocs, Graduate Campus, University of Zurich (UZH)
- Academic Teaching Excellence, Universidad Carlos III de Madrid (UC3M)
- Microscopy Data Analysis, EMBL-EBI
- Microscopy and Application Course, CSIC
- Autopsy Software for Forensic Analysis
- Ethical Hacking
- English Level C1 (MECR)
- French Level A2
- Machine Learning with Python (edX)
- Deep Learning, Universidad Carlos III de Madrid (UC3M)
Others
- Finalist in Thesis Talks 2021, video
- Maintainer of university webpage for online courses, 2018
- Trainee at Fundació Bit, May–Sep 2018
- Waitress at Es Port (Portocolom), 2017
- Volunteer at UIB Science Fair, 2016–2017
- Honours in Linear Algebra & Discrete Mathematics, 2016
- Short-story contest winner, 2016
- Waitress at Sa Cova Dets Ases, 2015–2016