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---
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title: "TOSBI – Towards Scalable and Generalized Solutions in Biomedical Images (2025-2028)"
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summary: TOSBI develops scalable and generalizable deep learning methods for biomedical image analysis, focusing on limited annotation, computational efficiency and robust transferability.
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title: "TOSBI – Towards Scalable and Generalized Solutions in Biomedical Images (2025–2028)"
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summary: TOSBI develops scalable and generalizable deep learning methods for biomedical image analysis, with a focus on limited annotation, computational efficiency and robust transferability.
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date: 2025-09-01
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authors: ["Ignacio Arganda-Carreras", "Fadi Dornaika", "Nagore Barrena", "Unai Elordi", "Aitor González-Marfil", "Daniel Franco-Barranco"]
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tags:
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- Biomimage Analysis
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- Bioimage Analysis
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- Deep Learning
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- Scalability
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- Domain Generalization
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- Foundation Models
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---
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The **TOSBI** project — *"Towards Scalable and Generalized Solutions in Biomedical Images"* — aims to develop deep learning methodologies that scale to large bioimage datasets and generalize across imaging modalities and laboratories, with a particular emphasis on annotation-efficient approaches and adapting foundation models to bioimage tasks.
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The **TOSBI** project — *Towards Scalable and Generalized Solutions in Biomedical Images* — aims to create deep learning methodologies that scale to large bioimage datasets and generalize across imaging modalities, laboratories and experimental settings. The project emphasizes annotation-efficient learning and the adaptation of foundation models to biomedical imaging tasks.
2020

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Led by the **Computer Vision and Pattern Discovery (CVPD)** group at the **University of the Basque Country (UPV/EHU)**, TOSBI addresses key bottlenecks in modern biomedical image analysis: scarcity of high-quality annotations, computational cost of state-of-the-art models, and limited cross-domain generalization.
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Led by the **Computer Vision and Pattern Discovery (CVPD)** group at the **University of the Basque Country (UPV/EHU)**, TOSBI addresses central challenges in modern biomedical image analysis: limited high-quality annotations, the computational cost of state-of-the-art models, and the difficulty of achieving robust cross-domain generalization.
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### 🔬 Scientific Goals
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---
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- Design and evaluate **annotation-efficient learning strategies** (self-supervised, semi-supervised, few-/zero-shot) tailored to biomedical images.
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- Improve **scalability** of model training and inference for large microscopy and histopathology datasets.
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- Develop **domain adaptation and domain generalization** techniques to transfer models between imaging modalities, labs, or experimental conditions.
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- Adapt and validate **foundation models** for downstream bioimage tasks (segmentation, detection, classification), including practical tooling for the community.
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- Deliver open and reproducible software components and evaluation pipelines compatible with community platforms (e.g., BiaPy).
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### 🔬 Scientific Goals
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### 👥 Project Team
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- Develop and benchmark **annotation-efficient learning strategies** (self-supervised, semi-supervised, few-shot and zero-shot) tailored to biomedical imaging.
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- Improve **scalability** of training and inference workflows for large microscopy and histopathology datasets.
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- Create **domain adaptation and domain generalization** methods enabling models to transfer across imaging modalities, laboratories or acquisition conditions.
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- Adapt and validate **foundation models** for downstream bioimage tasks (segmentation, detection, classification), providing practical tools for the research community.
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- Release open and reproducible software components and evaluation pipelines fully compatible with community platforms such as **BiaPy**.
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- **Principal Investigators**:
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- Dr. **Fadi Dornaika** (Ikerbasque Research Professor, UPV/EHU)
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- Dr. **Ignacio Arganda-Carreras** (Ikerbasque Research Associate Professor, UPV/EHU, DIPC, Biofisika Institute)
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---
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- **Research Team**:
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- Dr. **Urtzi Ayesta** (Ikerbasque Research Professor, UPV/EHU)
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- Dr. **Nagore Barrena** (Assistant Professor, UPV/EHU)
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- Dr. **Unai Elordi** (Assistant Professor, UPV/EHU)
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### 👥 Project Team
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- **Work Team / Collaborators**:
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- **Aitor González-Marfil** (PhD student, CVPD)
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- **Estibaliz Gómez de Mariscal** (Postdoctoral researcher, Portugal)
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- **Daniel Franco-Barranco** (Postdoctoral researcher / collaborator, UK)
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- **Dr. Jinan Charafeddine** (De Vinci Higher Education, France)
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- **Dr. Fares Bougourzi** (University of Salento, Italy)
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- **Dr. Donglai Wei** (Boston College, USA)
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- **Software engineer (SE)** (to be hired — WP8)
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- **PhD candidate (FPI)** (to be recruited — linked FPI contract)
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#### Principal Investigators
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- Dr. **Fadi Dornaika** (Ikerbasque Research Professor, UPV/EHU)
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- Dr. **Ignacio Arganda-Carreras** (Ikerbasque Research Associate Professor, UPV/EHU; DIPC; Biofisika Institute)
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#### Research Team
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- Dr. **Urtzi Ayesta** (Ikerbasque Research Professor, UPV/EHU)
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- Dr. **Nagore Barrena** (Assistant Professor, UPV/EHU)
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- Dr. **Unai Elordi** (Assistant Professor, UPV/EHU)
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#### Work Team / Collaborators
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- **Aitor González-Marfil** (PhD student, CVPD)
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- **Estibaliz Gómez de Mariscal** (Postdoctoral researcher, Portugal)
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- **Daniel Franco-Barranco** (Postdoctoral researcher / collaborator, UK)
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- **Dr. Jinan Charafeddine** (De Vinci Higher Education, France)
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- **Dr. Fares Bougourzi** (University of Salento, Italy)
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- **Dr. Donglai Wei** (Boston College, USA)
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- **Software Engineer (SE)** — to be hired (WP8)
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- **PhD Candidate (FPI)** — to be recruited (linked FPI contract)
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For the complete list of roles and the contribution of each member, see the project application PDF linked below.
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---
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### 🕒 Timeline
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- **Start**: September, 1 2025
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- **Duration**: August, 31 2028
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- **Start date**: 1 September 2025
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- **End date**: 31 August 2028
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### 💰 Funding
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---
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- Funded by the **Spanish Ministry of Science, Innovation and Universities (MCIU)** under the **Generación de Conocimiento 2024 (Proyectos de Investigación No Orientada)** program, MICIU/AEI /10.13039/501100011033/, and by FEDER, EU.
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- **Total funding**: 143,250.00€ (including indirect costs)
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- Reference code: **PID2024-157485NB-I00**
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### 💰 Funding
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- Funded by the **Spanish Ministry of Science, Innovation and Universities (MCIU)** through the **Generación de Conocimiento 2024 (Proyectos de Investigación No Orientada)** program (**MICIU/AEI / 10.13039/501100011033** and **FEDER, EU**).
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- **Total project funding**: 143,250 € (including indirect costs)
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- **Reference code**: **PID2024-157485NB-I00**
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<img src="/assets/media/MICIU_Cofinanciado_AEI_logo.jpg" alt="Spanish State Agency for Research (AEI) Logo" width="500">
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---
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### 📄 Project documentation
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### 📄 Project Documentation
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- Related [PhD announcement](/post/2025-09-30-phd-offer-tosbi/).
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- Related post: [PhD announcement](/post/2025-09-30-phd-offer-tosbi/)
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### 📬 Contacts
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- For project-specific enquiries: [Dr. Fadi Dornaika](mailto:fadi.dornaika@ehu.eus) and [Dr. Ignacio Arganda-Carreras](mailto:ignacio.arganda@ehu.eus)
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For project enquiries, please contact:
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- [Dr. Fadi Dornaika](mailto:fadi.dornaika@ehu.eus)
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- [Dr. Ignacio Arganda-Carreras](mailto:ignacio.arganda@ehu.eus)

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