AI-Based Pipelines for Bioimage Analysis
Talk at NEUBIAS Bioimage Analysis Course, Institut Pasteur, Paris, France
CV
I’m Caterina Fuster-Barceló, currently in the post-doc world with my focus on AI4Life project, Bioimage Model Zoo, the BioImage.IO Chatbot, and deepImageJ. My Ph.D. in Computer Science and Technology kickstarted this journey, leading me into the fascinating realm of bioimage analysis. Through projects like deepImageJ and the Bioimage Model Zoo, I’m on the front lines of integrating artificial intelligence into biomedical imaging, making strides in how we analyze and interpret biological images. Whether it’s developing a chatbot to streamline bioimage analysis or pushing the boundaries with AI4Life, my work is all about leveraging technology to unveil the microscopic mysteries of biology. It’s not just about the tech; it’s about opening new doors in healthcare and research, one pixel at a time.
Academic Background
- Ph.D. in Computer Science and Technology, Universidad Carlos III de Madrid, 13 Dec. 2022
- M.Sc. in Cibersecurity, Universidad Carlos III de Madrid, 2020
- B.Sc. in Telematics Engineering, Universitat de les Illes Balears, 2019
Professional History
Post-doctoral Researcher: Jan 2023 - Aug 2025
Where: UC3M, Bioengineering Department
Field: Bioimage analysis
PI: Dra. Arrate Muñoz Barrutia
Projects: AI4Life, Bioimage Model Zoo, deepImageJPost-doctoral 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
Publications
Peer-review Journals
- ELEKTRA: ELEKTRokardiomatrix Application to Biometric Identification with Convolutional Neural Networks
Neurocomputing, 2022
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 📄 - Exploring the Power of PPG Matrix for Atrial Fibrillation Detection with Integrated Explainability
Engineering Applications of Artificial Intelligence, 2023
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. 📄 - DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible
Nature Methods, 2023
Hidalgo-Cenalmor, I., Pylvänäinen, J.W., Ferreira, M.G., Russell, C.T., Arganda-Carreras, I., 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 📄 - Bridging the Gap: Integrating Cutting-edge Techniques into Biological Imaging with deepImageJ
bioRxiv, 2023
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. *bioRxiv*. https://doi.org/10.1101/2024.01.12.575015 📄 - BioImage.IO Chatbot: A Personalized Assistant for BioImage Analysis Augmented by Community Knowledge Base
Nature Methods, 2023
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 📄 - The Crucial Role of Bioimage Analysts in Scientific Research and Publication
Journal of Cell Science, 2024
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 📄 - ECG-Based Patient Identification: A Comprehensive Evaluation Across Health and Activity Conditions
IEEE Access, 2024
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 📄
Preprints
- SAMJ: Fast Image Annotation on ImageJ/Fiji via Segment Anything Model
, 2025
Carlos García-López-de-Haro, Caterina Fuster-Barceló, Curtis T. Rueden, Jónathan Heras, Vladimír Ulman, Daniel Franco-Barranco, Adrián Inés, Kevin W. Eliceiri, Jean-Christophe Olivo-Marin, Jean-Yves Tinevez, Daniel Sage, Arrate Muñoz-Barrutia. "SAMJ: Fast Image Annotation on ImageJ/Fiji via Segment Anything Model." arXiv preprint arXiv:2506.02783 (2025). 📄
Conference Proceedings
- Unveiling Hidden Patterns: Harnessing the Power of Short PPG-Traces for Atrial Fibrillation Detection
IEEE 19th International Conference on Body Sensor Networks (BSN), 2023
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 📄 - Estimación de la proporción de hidrops endolinfático en pacientes con la enfermedad de Mènière
CASEIB 2023, 2023
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 Mènière. *CASEIB 2023*. 📄 - Can You Afford to Research? The Financial Strain of Ph.D. Students in Spain
Precarity and Instability in Academia Symposium (PIAS), 2024
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. 📄
Conference Abstracts
- Harnessing Deep Learning in Bioimaging: The DeepImageJ Journey
Effectively Communicating Bioimage Analysis Workshop, 2024
Fuster-Barceló, C., Gómez-de-Mariscal, E., Sage, D., Muñoz-Barrutia, A. 'Harnessing Deep Learning in Bioimaging: The DeepImageJ Journey.' ECBA Workshop, 2024. 📄
Talks
2025
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
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
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)
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
CASEIB 2023
CASEIB 2023 — Conference Presentation
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
Certifications
- Academic Teaching Excellence
- Microscopy Data Analysis
- Microscopy and Application Course
- Autopsy Software for Forensic Analysis
- Ethical Hacking
- English Level C1 (MECR)
- French Level A2
- Machine Learning with Python (edX)
- Deep Learning (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