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Dr. Caterina Fuster-Barceló
Postdoctoral researcher in computational bioimage analysis developing robust, efficient, and transferable AI for microscopy.
CV
Academic CV for a postdoctoral researcher in computational bioimage analysis working toward robust, efficient, and transferable AI for microscopy.
Event map
Map of conferences, workshops, hackathons, and other events.
Events
Conferences, workshops, hackathons, and community events.
Writing & Outreach
Writing, outreach, and community resources.
Publications
Peer-reviewed publications, preprints, conference proceedings, and abstracts.
Software & Resources
Software tools, community resources, and reusable outputs.
Talks, Lectures & Posters
Talks, invited lectures, and poster presentations.
Teaching
Courses, thesis supervision, and mentoring activities.
events
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.
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.
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.
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.
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.
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.
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.
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.
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.
GloBIAS Bioimage Analysts Workshop
In November 2024, I took part in the GloBIAS Bioimage Analysts Workshop in Gothenburg, Sweden.
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).
ICLR 2026
In April 2026, I attended ICLR 2026 in Rio de Janeiro, Brazil, where I presented a poster at the Learning Meaningful Representations of Life (LMRL) Workshop.
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:
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.
portfolio
Per què el 5G no us deixarà sense hereus?
Article for the Setmanari Felanitx newspaper about healthcare and 5G (Catalan)
Outcomes of the Hackathon on Web and Cloud Infrastructure for AI-Powered BioImage Analysis
Article in FocalPlane about the outcomes of the hackathon in SciLifeLab, KTH, Stockholm
AI4Life Event Highlights: A Successful Fusion of Workshops, Hackathon, and Uploathon
Article in FocalPlane about the outcomes of the workshop and hackathon in UC3M, Madrid
Read Papers Template for Notion
My own Notion template to keep track of all papers read.
publications
ELEKTRA: ELEKTRokardiomatrix Application to Biometric Identification with Convolutional Neural Networks
Biometric identification using ELEKTRokardiomatrix with Convolutional Neural Networks. Achieved 99.53% accuracy with minimal error rates using simple CNN architectures.
Citation: Fuster-Barceló, C., Peris-Lopez, P., & Camara, C. (2022). ELEKTRA: ELEKTRokardiomatrix application to biometric identification with convolutional neural networks. Neurocomputing, 506, 37–49. https://doi.org/10.1016/j.neucom.2022.07.059
Unveiling Hidden Patterns: Harnessing the Power of Short PPG-Traces for Atrial Fibrillation Detection
Using short PPG traces and musical features to detect atrial fibrillation with high accuracy.
Citation: Peris-Lopez, P., Fuster-Barceló, C., Camara, C., & Martin, H. (2023). Unveiling Hidden Patterns: Harnessing the Power of Short PPG-Traces for Atrial Fibrillation Detection. IEEE BSN 2023. https://ieeexplore.ieee.org/abstract/document/10331002
DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible
Making deep learning in microscopy truly portable and reproducible across environments.
Citation: Hidalgo-Cenalmor, I., Pylvänäinen, J.W., Ferreira, M.G., Russell, C.T., Saguy, A., Arganda-Carreras, I., Shechtman, Y., AI4Life Consortium, Jacquemet, G., Henriques, R., & Gómez-de-Mariscal, E. (2024). DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible. Nature Methods, 21, 925–927. https://doi.org/10.1038/s41592-024-02295-6
Featured in: https://www.biorxiv.org/content/10.1101/2023.11.19.567606v1
Estimación de la proporción de hidrops endolinfático en pacientes con la enfermedad de Ménière
Presentación en póster sobre el uso de técnicas de Deep Learning para estimar la proporción de hidrops endolinfático en pacientes con la enfermedad de Ménière.
Citation: Delicado-Correa, G.R., Fuster-Barceló, C., Suárez-Vega, V.M., Pérez-Fernández, N., Bastarrika, G., & Muñoz-Barrutia, A. (2023). Estimación de la proporción de hidrops endolinfático en pacientes con la enfermedad de Ménière. CASEIB 2023.
Harnessing Deep Learning in Bioimaging: The DeepImageJ Journey
Talk abstract presented at the ECBA Workshop on effectively communicating bioimage analysis.
Citation: Fuster-Barceló, C., Gómez-de-Mariscal, E., Sage, D., Muñoz-Barrutia, A. 'Harnessing Deep Learning in Bioimaging: The DeepImageJ Journey.' ECBA Workshop, 2024.
Exploring the Power of Photoplethysmogram Matrix for Atrial Fibrillation Detection with Integrated Explainability
PPG-based matrix representation and explainable deep learning for accurate and interpretable AF detection.
Citation: Fuster-Barceló, C., Guerrero-López, A., Camara, C., & Peris-Lopez, P. (2024). Exploring the power of photoplethysmogram matrix for atrial fibrillation detection with integrated explainability. Engineering Applications of Artificial Intelligence, 133, 108325.
BioImage.IO Chatbot: A Community-Driven AI Assistant for Integrative Computational Bioimaging
AI-powered assistant transforming the way researchers interact with bioimage analysis tools.
Citation: Lei, W., Fuster-Barceló, C., Reder, G. et al. (2024). BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging. Nature Methods, 21, 1368–1370. https://doi.org/10.1038/s41592-024-02370-y
Featured in: https://www.nature.com/articles/s41592-024-02370-y
The Crucial Role of Bioimage Analysts in Scientific Research and Publication
A perspective on the critical contributions and challenges of bioimage analysts in biological research.
Citation: Cimini, B. A., Bankhead, P., d'Antuono, R., et al. (2024). The Crucial Role of Bioimage Analysts in Scientific Research and Publication. Journal of Cell Science, 137(20). https://doi.org/10.1242/jcs.262322
Bridging the Gap: Integrating Cutting-edge Techniques into Biological Imaging with deepImageJ
Empowering researchers with deepImageJ: bridging deep learning and accessible biological image analysis.
Citation: Fuster-Barceló, C., García López de Haro, C., Gómez-de-Mariscal, E., Ouyang, W., Olivo-Marin, J.C., Sage, D., & Muñoz-Barrutia, A. (2024). Bridging the gap: Integrating cutting-edge techniques into biological imaging with deepImageJ. Biological Imaging, 4, e14. https://doi.org/10.1017/S2633903X24000114
Featured in: https://doi.org/10.1017/S2633903X24000114
Can You Afford to Research? The Financial Strain of Ph.D. Students in Spain
An analysis of the financial challenges facing Ph.D. students in Spain, focusing on scholarships and living costs.
Citation: C. Fuster-Barceló and A. Guerrero-López, 'Can You Afford to Research? The Financial Strain of Ph.D. Students in Spain,' Proceedings of the Precarity and Instability in Academia Symposium (PIAS), 2024.
ECG-Based Patient Identification: A Comprehensive Evaluation Across Health and Activity Conditions
A comprehensive evaluation of ECG-based patient identification under health and activity conditions.
Citation: Fuster-Barceló, C., Cámara, C., & Peris-López, P. (2024). ECG-Based Patient Identification: A Comprehensive Evaluation Across Health and Activity Conditions. IEEE Access. https://doi.org/10.1109/ACCESS.2024.3519462
Scaffolding Collaborative Learning in STEM: A Two-Year Evaluation of a Tool-Integrated Project-Based Methodology
A two-year evaluation of tool-supported project-based learning and peer assessment in a STEM master’s course.
Citation: Caterina Fuster-Barceló, Gonzalo R. Ríos-Muñoz, Arrate Muñoz-Barrutia. "Scaffolding Collaborative Learning in STEM: A Two-Year Evaluation of a Tool-Integrated Project-Based Methodology." arXiv preprint arXiv:2509.02355 (2025).
The impact of gamification on learning outcomes: experiences from a Biomedical Engineering course
An evaluation of digital tool integration and gamification-inspired practices in a Biomedical Engineering course.
Citation: Gonzalo R. Ríos-Muñoz, Caterina Fuster-Barceló, Arrate Muñoz-Barrutia. "The impact of gamification on learning outcomes: experiences from a Biomedical Engineering course." arXiv preprint arXiv:2509.06126 (2025).
OREHAS: A fully automated deep-learning pipeline for volumetric endolymphatic hydrops quantification in MRI
A fully automated pipeline for volumetric quantification of endolymphatic hydrops from routine MRI.
Citation: Caterina Fuster-Barceló, Claudia Castrillón, Laura Rodrigo-Muñoz, Victor Manuel Suárez-Vega, Nicolás Pérez-Fernández, Gorka Bastarrika, Arrate Muñoz-Barrutia. "OREHAS: A fully automated deep-learning pipeline for volumetric endolymphatic hydrops quantification in MRI." arXiv preprint arXiv:2601.18368 (2026).
Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?
Accepted at the Learning Meaningful Representations of Life (LMRL) Workshop at ICLR 2026.
Citation: Caterina Fuster-Barceló, Virginie Uhlmann. "Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?" Learning Meaningful Representations of Life (LMRL) Workshop at ICLR 2026, 2026.
SAMJ: Fast Image Annotation on ImageJ/Fiji via Segment Anything Model
A user-friendly plugin that brings Segment Anything to the Fiji ecosystem for fast, interactive image annotation.
Citation: García-López-de-Haro, C., Fuster-Barceló, C., Rueden, C. T., Heras, J., Ulman, V., Franco-Barranco, D., Inés, A., Eliceiri, K. W., Olivo-Marin, J.-C., Tinevez, J.-Y., Sage, D., & Muñoz-Barrutia, A. (2026). SAMJ: fast image annotation on ImageJ/Fiji via segment anything model. Nature Communications, 17, 5402. https://doi.org/10.1038/s41467-026-71752-x
Assessing the reproducibility of a bioimage analysis workflow characterising tissue flow in Drosophila
A reproducibility study on a bioimage analysis workflow characterising tissue flow in Drosophila, published in Journal of Microscopy.
Citation: Ambroset, M., Valades Cruz, C. A., Tonfack, L. B., D’Antuono, R., & Fuster-Barceló, C. (2026). Assessing the reproducibility of a bioimage analysis workflow characterising tissue flow in Drosophila. Journal of Microscopy, 304(2), 101–115. https://doi.org/10.1111/jmi.70125
AI4Life Open Calls and Public Challenges: why, how, and what we have learned
bioRxiv preprint summarizing lessons from the AI4Life Open Calls and Public Challenges run between 2023 and 2025.
Citation: Galinova, V., Seifi, M., Serrano Solano, B., Lidayova, K., Dalle Nogare, D., Corbat, A. A., Talks, J., Giacomello, E., Gomez-de-Mariscal, E., Ferreira, M. G., Fuster-Barceló, C., Battagliotti, J. M., García-López-de-Haro, C., Salmon, B., Croft, M., Yie, S. Y., Rey-Paniagua, G., Hu, X., Cho, S., Sheth, A., Porwal, C., Li, X., AI4Life Consortium, Henriques, R., Li, X., Krull, A., Klemm, A., Muñoz Barrutia, A., Kreshuk, A., Ouyang, W., Jug, F., & Deschamps, J. (2026). AI4Life Open Calls and Public Challenges: why, how, and what we have learned. bioRxiv. https://doi.org/10.64898/2026.07.21.739486
software
BioImage Model Zoo
Community resource for sharing, discovering, and reusing pre-trained models in bioimage analysis.
BioImage.IO Chatbot
Community-driven assistant for navigating tools, documentation, and workflows in bioimage analysis.
deepImageJ
Fiji/ImageJ plugin for running deep learning models in practical microscopy workflows.
SAMJ
ImageJ/Fiji integration of Segment Anything for fast interactive annotation in microscopy.
talks
Protegiendo el oro con tu corazón
Más información en Women Techmakers Madrid.
Protegiendo el oro con tu corazón y un poco de Python
La charla entera la podéis ver aquí:
Skype A Scientist
Thanks to the Skype A Scientist Program I was connected to Gerda Resinger from the Linzer Technikum high school to give a talk to final-year students.
IDOVEN - Protegiendo el oro con tu corazón
I had the pleasure to visit IDOVEN and give a small talk about my PhD Thesis in the Telefónica Building in Gran Vía, where their office is placed.
GitHub Copilot, what is it and how can I get it?
I had the pleasure to show to my colleagues from the Department a short presentation about GitHub Copilot and its features. I hope you enjoy it!
¿Quién me lo habría dicho?
He tenido el placer de dar una pequeña charla en la semifinal de Unidreams sobre mi trayectoria profesional. La he titulado ¿Quién me lo habría dicho? porque si alguien me llega a preguntar cuando tenía 18 años qué quería ser de mayor, no hubiera dicho ni de lejos que iba a ser ingeniera y menos aún que iba a tener un doctorado en Ciencia y Tecnología Informática.
Leveraging Cloud-Based Virtual Desktops for Bioimage Analysis with BAND and deepImageJ
I had the pleasure to present our work on leveraging cloud-based virtual desktops for bioimage analysis with BAND and deepImageJ at the I2K 2023 conference.
Estimación de la proporción de hidrops endolinfático en pacientes con la enfermedad de Ménière
In November 2023, I presented the poster “Estimación de la proporción de hidrops endolinfático en pacientes con la enfermedad de Ménière” at CASEIB 2023 in Cartagena, Spain.
Harnessing deep learning in bioimaging: the deepImageJ journey
I had the pleasure to attend and give a talk at the Workshop for Effectively Communicating Bioimage Analysis (12–15 February 2024, Buxted Park, East Sussex, UK), organised by The Company of Biologists and Focal Plane. In this workshop not only did I have a wonderful time at Buxted Park, but I also had the opportunity to present the deepImageJ project and learn from the best in the field.
The BioImage.IO Chatbot
I had the pleasure to present our precious BioImage.IO Chatbot at the Virtual Pub of Euro-Bioimaging as part of the AI4Life Project.
Meet the BioImage.IO Chatbot
Since January 2024, Elixir has been hosting virtual talks on generative AI. I was fortunate to secure a presentation slot to showcase the BioImage.IO Chatbot and its latest features. This includes the integration of bio.tools from Elixir into our chatbot’s knowledge base.
Transformers, Vision Transformers and SAMJ
During the AI4Life Workshop of Zero-Code Tools and BioImage Model Zoo Community Partners I had the pleasure to give a presentation about Transformers, Vision Transformers and our new development for a Fiji plugin: SAMJ. Many thanks to Daniel Sage and Carlos J. García López de Haro whom I had the pleasure to present with.
BioImage.IO Chatbot
During the AI4Life Workshop of Zero-Code Tools and BioImage Model Zoo Community Partners I had the pleasure to give a presentation about the BioImage.IO Chatbot together with Wanlu Lei, Benedict Diederich, Songtao Cheng, and Wei Ouyang.
BioImage.IO Chatbot Talk
In June 2024 I had the pleasure to present the BioImage.IO Chatbot at the ZIDAS Summer School at ETH Zurich, Switzerland. The ZIDAS Summer School is a unique event that brings together leading experts in the field of bioimage analysis, providing a platform for knowledge exchange and collaboration.
Prompt Engineering: How to Generate Good and Functional Code with the BioImage.IO Chatbot
In October 2024, I gave a talk titled “Prompt Engineering: How to Generate Good and Functional Code with the BioImage.IO Chatbot” at the YMIA Python Event, an initiative to support early-career imaging scientists.
Introduction to AI4Life and BioImage Model Zoo
Presented at: SPAOM 2024
Speakers: Arrate Muñoz-Barrutia and myself
Can You Afford to Research? The Financial Strain of Ph.D. Students in Spain
Presented at: Precarity and Instability in Academia Symposium (PIAS)
Authors: Caterina Fuster-Barceló, Alejandro Guerrero-López
ECG and PPG Applications in Healthcare
In February 2025, I was invited to speak at the Biosignals course at Universidad Pontificia Comillas, where I presented a talk titled “ECG and PPG Applications in Healthcare”.
Deep Learning for Bioimage Analysis
In March 2025, I participated in the EPFL Workshop on Open Microscopy & AI, where I gave a presentation and led a hands-on workshop on Deep Learning for Bioimage Analysis, aligned with the AI4Life initiative.
Lecture & Practical Session on Advanced CNNs
In April 2025, together with my master’s students Claudia Castrillón-Álvarez and Laura Rodrigo-Muñoz, I delivered a session titled “Lecture & Practical Session on Advanced CNNs” at the Ágora Journal Club organized by the Signal Theory and Communications Department at Universidad Carlos III de Madrid.
AI-Based Pipelines for Bioimage Analysis
In May 2025, I delivered a session titled “AI-Based Pipelines for Bioimage Analysis” at the NEUBIAS Bioimage Analysis Course hosted at Institut Pasteur, Paris. This course is part of the prestigious NEUBIAS training series, focused on advancing bioimage analysis across Europe.
Transforming BioImage Analysis: The AI4Life Approach
In October 2025, I gave the talk “Transforming BioImage Analysis: The AI4Life Approach” at Cell Physics 2025, hosted at Universität des Saarlandes in Saarbrücken, Germany.
BioImage Model Zoo
🎓 Institution: EMBL-EBI Training
📘 Course: Microscopy data analysis: machine learning and the BioImage Archive
👩🏫 Role: Lecturer
🗓️ Session: 18 March 2026, 13:00-14:00 GMT
Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?
On 27 April 2026, I presented a poster on “Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?” at the Learning Meaningful Representations of Life (LMRL) Workshop during ICLR 2026, held in Rio de Janeiro, Brazil.
BioImage Model Zoo
On 22 May 2026, I gave an online talk on BioImage Model Zoo as part of the ZMB-BVC Lunch Seminar Series, hosted by the BioVisionCenter at the University of Zurich.
When open data and code are not enough: a reproducibility case study of a published Drosophila tissue-flow analysis workflow
In November 2026, I will present the poster “When open data and code are not enough: a reproducibility case study of a published Drosophila tissue-flow analysis workflow” at the Crick BioImage Analysis Symposium (CBIAS) 2026, held at the Francis Crick Institute in London.
When do vision foundation models transfer to microscopy and when do they fail?
In November 2026, I will give a 15-minute oral presentation titled “When do vision foundation models transfer to microscopy and when do they fail?” at the Crick BioImage Analysis Symposium (CBIAS) 2026, held at the Francis Crick Institute in London.
teaching
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
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
AI for Radiology and Microscopy
Artificial Intelligence in Radiology and Microscopy
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
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
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
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
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
ZIDAS 2026
🎓 Institution: ZIDAS
📘 Course: Zurich Image and Data Analysis School (ZIDAS) 2026
👩🏫 Role: Teaching Assistant, Python day
🗓️ Dates: 5-10 July 2026