When do vision foundation models transfer to microscopy and when do they fail?
Talk at Crick BioImage Analysis Symposium (CBIAS) 2026, The Francis Crick Institute, London, UK
CV
I am a postdoctoral researcher in the Bioimaging and Data Analysis Group (Uhlmann Lab), led by Dr. Virginie Uhlmann, at the Department of Molecular Life Sciences, 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: Bioimaging and Data Analysis Group (Uhlmann Lab), Department of Molecular Life Sciences, University of Zurich (UZH)
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; and IISGM
Field: Bioimage analysis and Artificial Intelligence in biomedical imaging
PI: Dr. Arrate Muñoz Barrutia, Dr. Javier Pascau González
Projects: AI4Life, BioImage Model Zoo, deepImageJ, SAMJVisiting 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, Dr. Carmen Cámara
Project: CYNAMON-CMResearch Assistant: Oct 2019 - Dec 2022
Where: UC3M, COSEC Laboratory
Field: Cybersecurity
Supervisors: Dr. Pedro Peris-López, Dr. 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
- Global Young Scientists Summit (GYSS) 2027 — 2026, National Research Foundation Singapore
- Selected to represent the University of Zurich at the GYSS 2027 in Singapore (4–8 January 2027). Event page
- 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:
- Bioinformatics
- Biomedical Engineering Letters
- Engineering Applications of Artificial Intelligence
- Pattern Recognition
Publications
For full citations and publication details, see the Publications page.
Peer-review Journals
- Assessing the reproducibility of a bioimage analysis workflow characterising tissue flow in Drosophila
Journal of Microscopy, 2026 📄 - SAMJ: Fast Image Annotation on ImageJ/Fiji via Segment Anything Model
Nature Communications, 2026 📄 - ECG-Based Patient Identification: A Comprehensive Evaluation Across Health and Activity Conditions
IEEE Access, 2024 📄 - Bridging the Gap: Integrating Cutting-edge Techniques into Biological Imaging with deepImageJ
Biological Imaging, 2024 📄 - The Crucial Role of Bioimage Analysts in Scientific Research and Publication
Journal of Cell Science, 2024 📄 - BioImage.IO Chatbot: A Community-Driven AI Assistant for Integrative Computational Bioimaging
Nature Methods, 2024 📄 - Exploring the Power of Photoplethysmogram Matrix for Atrial Fibrillation Detection with Integrated Explainability
Engineering Applications of Artificial Intelligence, 2024 📄 - DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible
Nature Methods, 2023 📄 - ELEKTRA: ELEKTRokardiomatrix Application to Biometric Identification with Convolutional Neural Networks
Neurocomputing, 2022 📄
Preprints
- AI4Life Open Calls and Public Challenges: why, how, and what we have learned
bioRxiv, 2026 📄 - 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 📄
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 Ménière
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, Lectures & Posters
2026
When open data and code are not enough: a reproducibility case study of a published Drosophila tissue-flow analysis workflow
Poster at Crick BioImage Analysis Symposium (CBIAS) 2026, The Francis Crick Institute, London, UK
BioImage Model Zoo
Talk at ZMB-BVC Lunch Seminar Series, Virtual
Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?
Poster at LMRL Workshop at ICLR 2026, Rio de Janeiro, Brazil
BioImage Model Zoo
Lecture at EMBL-EBI Training: Microscopy data analysis: machine learning and the BioImage Archive, Virtual
2025
Transforming BioImage Analysis: The AI4Life Approach
Talk at Cell Physics 2025, Saarbrücken, Germany
AI-Based Pipelines for Bioimage Analysis
Lecture at NEUBIAS Bioimage Analysis Course, Institut Pasteur, Paris, France
Lecture & Practical Session on Advanced CNNs
Lecture at Ágora – Journal Club, Universidad Carlos III de Madrid, Universidad Carlos III de Madrid, Spain
Deep Learning for Bioimage Analysis
Talk at EPFL Open Microscopy & AI Workshop, EPFL, Lausanne, Switzerland
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
Lecture 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, Comunidad de Madrid, 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, Virtual
BioImage.IO Chatbot Talk
Lecture at ZIDAS Summer School, ETH Zurich, Switzerland
BioImage.IO Chatbot
Talk at AI4Life Workshop of Zero-Code Tools and BioImage Model Zoo Community Partners, UC3M Campus Puerta de Toledo, Madrid, Spain
Transformers, Vision Transformers and SAMJ
Talk at AI4Life Workshop of Zero-Code Tools and BioImage Model Zoo Community Partners, UC3M Campus Puerta de Toledo, Madrid, Spain
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, Buxted Park, East Sussex, UK
2023
Estimación de la proporción de hidrops endolinfático en pacientes con la enfermedad de Ménière
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?
Talk 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 Skype a Scientist, Virtual
Protegiendo el oro con tu corazón y un poco de Python
Talk at PyConES 2022, Granada, Andalucía
Protegiendo el oro con tu corazón
Talk at Women Techmakers Madrid 2022, Puerta de Toledo, Madrid
Teaching
2026
ZIDAS 2026
🎓 Institution: ZIDAS
📘 Course: Zurich Image and Data Analysis School (ZIDAS) 2026
👩🏫 Role: Teaching Assistant, Python day
🗓️ Dates: 5-10 July 2026
Deep Learning for Microscopy Image Analysis
🎓 Institution: Janelia Research Campus (HHMI)
📘 Course: DL@Janelia 2026
👩🏫 Role: Teaching Assistant
🗓️ Dates: 4-18 June 2026
💻 Exercises repository: DL-Janelia-2026
2025
Deep Learning-Based Segmentation and Quantification of Endolymphatic Hydrops in Inner Ear MRI
🎓 Program: Master in Machine Learning for Health
🏫 Institution: Universidad Carlos III de Madrid
🤝 In collaboration with: Clínica Universidad de Navarra
👩🎓 Student: Laura Rodrigo Muñoz
📆 Academic Year: 2024/2025
📝 Grade: 10 / 10
🔗 Related thesis: Claudia Castrillón Álvarez – Classification and Localization of Inner Ear Structures
Automated Classification and Localization of Inner Ear Structures in MRI Using Deep Learning
🎓 Program: Master in Machine Learning for Health
🏫 Institution: Universidad Carlos III de Madrid
🤝 In collaboration with: Clínica Universidad de Navarra
👩🎓 Student: Claudia Castrillón Álvarez
📆 Academic Year: 2024/2025
📝 Grade: 9.5 / 10
🔗 Related thesis: Laura Rodrigo Muñoz – Segmentation of Inner Ear Structures
2024
C3IS International Research Mentorship Program
🌍 Program: C3IS Research Labs – International Summer Research Experience
🏫 Institution: Universidad Carlos III de Madrid
👩🔬 Students Mentored: 2 undergraduate students from U.S. universities
📆 Duration: 8 weeks (Summer 2024)
🧪 Topic: Bioimage Analysis and Biomedical AI
Among Coursemates Tutorship Program
🧑🏫 Program: Among Coursemates
🏫 Institution: Universidad Carlos III de Madrid
👥 Tutored Students: 4 second-year students mentoring first-year peers
📅 Academic Year: 2024/2025
AI for Radiology and Microscopy
Artificial Intelligence in Radiology and Microscopy
2023
Biomedical Image Processing
🎓 Institution: Universidad Carlos III de Madrid
📘 Program: Master in Machine Learning for Health
👩🏫 Role: Teaching Assistant
📆 Years Taught: 2023/2024, 2024/2025
🔗 Course page
Estimation of Endolymphatic Hydrops Ratios in Ménière’s Disease
🎓 Institution: Universidad Carlos III de Madrid
📚 Program: Degree in Biomedical Engineering
👥 Co-Tutors: Arrate Muñoz-Barrutia and myself
🏅 Grade: 10 / 10
Events
2027
Global Young Scientists Summit (GYSS) 2027
I have been selected to represent the University of Zurich at the Global Young Scientists Summit (GYSS) 2027, which will take place in Singapore from 4 to 8 January 2027.
2026
Crick BioImage Analysis Symposium 2026
On 23–24 November 2026, I will attend the Crick BioImage Analysis Symposium (CBIAS) 2026 at the Francis Crick Institute in London, UK, where two of my abstracts have been accepted:
2024
Precarity and Instability in Academia Symposium (PIAS)
On December 13, 2024, I co-organized the Precarity and Instability in Academia Symposium (PIAS) alongside José Miguel Moreno (UC3M).
GloBIAS Bioimage Analysts Workshop
In November 2024, I took part in the GloBIAS Bioimage Analysts Workshop in Gothenburg, Sweden.
AI4Life Workshop-Hackathon-Uploathon
From 10 to 14 June 2024, I co-organized the AI4Life Workshop-Hackathon-Uploathon at the UC3M Campus Puerta de Toledo in Madrid alongside Prof. Arrate Muñoz-Barrutia.
ImgLib2 and BigDataViewer Hackathon Prague
In April 2024, I took part in the ImgLib2 and BigDataViewer Hackathon held in Prague, Czech Republic. The hackathon brought together developers and researchers to work on Java-based image analysis tooling, especially focused on ImgLib2 and BDV.
BioImage Model Zoo Enhancements Hackathon
In March 2024, I participated in the BioImage Model Zoo Enhancements Hackathon at EMBL Heidelberg, focused on improving the BioImage Model Zoo ecosystem.
Effectively Communicating Bioimage Analysis Workshop
From 12 to 15 February 2024, I participated in the Effectively Communicating Bioimage Analysis Workshop held at Buxted Park, East Sussex, UK.
deepImageJ and friends Hackathon
In January 2024, I co-organized and participated in the deepImageJ and friends Hackathon hosted at Universidad Carlos III de Madrid, where developers and researchers collaborated to improve the deepImageJ ecosystem and its integration with other Fiji plugins.
2023
AI4Life Hackathon and Solvathon
In October 2023, I joined the AI4Life Hackathon and Solvathon, held at EMBL Heidelberg in Germany. This joint event focused on identifying challenges in deploying AI models in life sciences and collaboratively solving them through hands-on development and cross-disciplinary discussions.
Cloud Based and AI Hackathon
In June 2023, I participated in the Hackathon on Web and Cloud Infrastructure for AI-Powered BioImage Analysis, hosted at SciLifeLab in Stockholm, Sweden. The event was part of the AI4Life project and focused on building and optimizing cloud-based platforms to deploy and run deep learning models for microscopy and biomedical image analysis.
Accessibility of DL Models from Java Hackathon
In February 2023, I participated in the Accessibility of Deep Learning Models from Java Hackathon hosted at the Human Technopole in Milan, Italy. This event brought together developers and researchers to explore how deep learning models can be made accessible and interoperable from Java environments.
2022
PyConES 2022
At PyConES 2022, held in Granada, I presented a talk on my PhD thesis research on ECG-based biometric identification with Python. I also actively participated in the full conference program, engaging with the Spanish Python community.
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 (CEFR)
- German Level A2.1 (CEFR), certified by the Language Center of UZH and ETH Zurich
- French Level A2
- Machine Learning with Python (edX)
- Deep Learning, Universidad Carlos III de Madrid (UC3M)
Other Recognition
- Finalist in Thesis Talks 2021, video
- Honours in Linear Algebra & Discrete Mathematics, 2016
- Short-story contest winner, 2016
Other Experience
- 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
- Waitress at Sa Cova Dets Ases, 2015–2016