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1 | 1 | --- |
2 | | -title: "TOSBI – Towards Scalable and Generalized Solutions in Biomedical Images (2025-2028)" |
3 | | -summary: TOSBI develops scalable and generalizable deep learning methods for biomedical image analysis, focusing on limited annotation, computational efficiency and robust transferability. |
| 2 | +title: "TOSBI – Towards Scalable and Generalized Solutions in Biomedical Images (2025–2028)" |
| 3 | +summary: TOSBI develops scalable and generalizable deep learning methods for biomedical image analysis, with a focus on limited annotation, computational efficiency and robust transferability. |
4 | 4 | date: 2025-09-01 |
5 | 5 | authors: ["Ignacio Arganda-Carreras", "Fadi Dornaika", "Nagore Barrena", "Unai Elordi", "Aitor González-Marfil", "Daniel Franco-Barranco"] |
6 | 6 | draft: false |
|
9 | 9 | focal_point: "center" |
10 | 10 | preview_only: false |
11 | 11 | tags: |
12 | | - - Biomimage Analysis |
| 12 | + - Bioimage Analysis |
13 | 13 | - Deep Learning |
14 | 14 | - Scalability |
15 | 15 | - Domain Generalization |
16 | 16 | - Foundation Models |
17 | 17 | --- |
18 | 18 |
|
19 | | -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. |
| 19 | +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. |
20 | 20 |
|
21 | | -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. |
| 21 | +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. |
22 | 22 |
|
23 | | -### 🔬 Scientific Goals |
| 23 | +--- |
24 | 24 |
|
25 | | -- Design and evaluate **annotation-efficient learning strategies** (self-supervised, semi-supervised, few-/zero-shot) tailored to biomedical images. |
26 | | -- Improve **scalability** of model training and inference for large microscopy and histopathology datasets. |
27 | | -- Develop **domain adaptation and domain generalization** techniques to transfer models between imaging modalities, labs, or experimental conditions. |
28 | | -- Adapt and validate **foundation models** for downstream bioimage tasks (segmentation, detection, classification), including practical tooling for the community. |
29 | | -- Deliver open and reproducible software components and evaluation pipelines compatible with community platforms (e.g., BiaPy). |
| 25 | +### 🔬 Scientific Goals |
30 | 26 |
|
31 | | -### 👥 Project Team |
| 27 | +- Develop and benchmark **annotation-efficient learning strategies** (self-supervised, semi-supervised, few-shot and zero-shot) tailored to biomedical imaging. |
| 28 | +- Improve **scalability** of training and inference workflows for large microscopy and histopathology datasets. |
| 29 | +- Create **domain adaptation and domain generalization** methods enabling models to transfer across imaging modalities, laboratories or acquisition conditions. |
| 30 | +- Adapt and validate **foundation models** for downstream bioimage tasks (segmentation, detection, classification), providing practical tools for the research community. |
| 31 | +- Release open and reproducible software components and evaluation pipelines fully compatible with community platforms such as **BiaPy**. |
32 | 32 |
|
33 | | -- **Principal Investigators**: |
34 | | - - Dr. **Fadi Dornaika** (Ikerbasque Research Professor, UPV/EHU) |
35 | | - - Dr. **Ignacio Arganda-Carreras** (Ikerbasque Research Associate Professor, UPV/EHU, DIPC, Biofisika Institute) |
| 33 | +--- |
36 | 34 |
|
37 | | -- **Research Team**: |
38 | | - - Dr. **Urtzi Ayesta** (Ikerbasque Research Professor, UPV/EHU) |
39 | | - - Dr. **Nagore Barrena** (Assistant Professor, UPV/EHU) |
40 | | - - Dr. **Unai Elordi** (Assistant Professor, UPV/EHU) |
| 35 | +### 👥 Project Team |
41 | 36 |
|
42 | | -- **Work Team / Collaborators**: |
43 | | - - **Aitor González-Marfil** (PhD student, CVPD) |
44 | | - - **Estibaliz Gómez de Mariscal** (Postdoctoral researcher, Portugal) |
45 | | - - **Daniel Franco-Barranco** (Postdoctoral researcher / collaborator, UK) |
46 | | - - **Dr. Jinan Charafeddine** (De Vinci Higher Education, France) |
47 | | - - **Dr. Fares Bougourzi** (University of Salento, Italy) |
48 | | - - **Dr. Donglai Wei** (Boston College, USA) |
49 | | - - **Software engineer (SE)** (to be hired — WP8) |
50 | | - - **PhD candidate (FPI)** (to be recruited — linked FPI contract) |
| 37 | +#### Principal Investigators |
| 38 | +- Dr. **Fadi Dornaika** (Ikerbasque Research Professor, UPV/EHU) |
| 39 | +- Dr. **Ignacio Arganda-Carreras** (Ikerbasque Research Associate Professor, UPV/EHU; DIPC; Biofisika Institute) |
| 40 | + |
| 41 | +#### Research Team |
| 42 | +- Dr. **Urtzi Ayesta** (Ikerbasque Research Professor, UPV/EHU) |
| 43 | +- Dr. **Nagore Barrena** (Assistant Professor, UPV/EHU) |
| 44 | +- Dr. **Unai Elordi** (Assistant Professor, UPV/EHU) |
| 45 | + |
| 46 | +#### Work Team / Collaborators |
| 47 | +- **Aitor González-Marfil** (PhD student, CVPD) |
| 48 | +- **Estibaliz Gómez de Mariscal** (Postdoctoral researcher, Portugal) |
| 49 | +- **Daniel Franco-Barranco** (Postdoctoral researcher / collaborator, UK) |
| 50 | +- **Dr. Jinan Charafeddine** (De Vinci Higher Education, France) |
| 51 | +- **Dr. Fares Bougourzi** (University of Salento, Italy) |
| 52 | +- **Dr. Donglai Wei** (Boston College, USA) |
| 53 | +- **Software Engineer (SE)** — to be hired (WP8) |
| 54 | +- **PhD Candidate (FPI)** — to be recruited (linked FPI contract) |
51 | 55 |
|
52 | | -For the complete list of roles and the contribution of each member, see the project application PDF linked below. |
| 56 | +--- |
53 | 57 |
|
54 | 58 | ### 🕒 Timeline |
55 | 59 |
|
56 | | -- **Start**: September, 1 2025 |
57 | | -- **Duration**: August, 31 2028 |
| 60 | +- **Start date**: 1 September 2025 |
| 61 | +- **End date**: 31 August 2028 |
58 | 62 |
|
59 | | -### 💰 Funding |
| 63 | +--- |
60 | 64 |
|
61 | | -- 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. |
62 | | -- **Total funding**: 143,250.00€ (including indirect costs) |
63 | | -- Reference code: **PID2024-157485NB-I00** |
| 65 | +### 💰 Funding |
64 | 66 |
|
| 67 | +- 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**). |
| 68 | +- **Total project funding**: 143,250 € (including indirect costs) |
| 69 | +- **Reference code**: **PID2024-157485NB-I00** |
65 | 70 |
|
66 | 71 | <img src="/assets/media/MICIU_Cofinanciado_AEI_logo.jpg" alt="Spanish State Agency for Research (AEI) Logo" width="500"> |
67 | 72 |
|
68 | 73 | --- |
69 | 74 |
|
70 | | -### 📄 Project documentation |
| 75 | +### 📄 Project Documentation |
71 | 76 |
|
72 | | -- Related [PhD announcement](/post/2025-09-30-phd-offer-tosbi/). |
| 77 | +- Related post: [PhD announcement](/post/2025-09-30-phd-offer-tosbi/) |
73 | 78 |
|
74 | 79 | --- |
75 | 80 |
|
76 | 81 | ### 📬 Contacts |
77 | 82 |
|
78 | | -- For project-specific enquiries: [Dr. Fadi Dornaika](mailto:fadi.dornaika@ehu.eus) and [Dr. Ignacio Arganda-Carreras](mailto:ignacio.arganda@ehu.eus) |
79 | | - |
| 83 | +For project enquiries, please contact: |
| 84 | +- [Dr. Fadi Dornaika](mailto:fadi.dornaika@ehu.eus) |
| 85 | +- [Dr. Ignacio Arganda-Carreras](mailto:ignacio.arganda@ehu.eus) |
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