CLoud ARtificial Intelligence For pathologY

About project


CLARIFY is an innovative, multinational, multi-sectorial, and multidisciplinary research and training programme that links two highly differentiated specialities: engineering and medicine, to produce 12 Early Stage Researchers (ESRs) in artificial intelligence (AI), cloud computing and clinical pathology with the focus on digital pathology.

CLARIFY’s main goal is to develop a robust automated digital diagnostic environment based on artificial intelligence and cloud-oriented data algorithms that facilitates whole-slide-image (WSI) interpretation and diagnosis everywhere with the aim of maximising the benefits of digital pathology and aiding pathologists in their daily work.

CLARIFY gathers relevant scientific staff from academia, industry and leading hospitals ensuring that CLARIFY’s ESRs, as well as, future PhD students following the same tracks, will have outstanding Career Opportunities within the digital pathology sector and beyond.

Specific and challenging cancer types have been selected to test the tools and methods developed through the project reflecting the existing variability in cancer diagnosis: Triple negative breast cancer (TNBC), High-risk non-muscle invasive bladder cancer (HR-NMIBC) and Spitzoid melanocytic lesions (SML).

Project ID


H2020 -MSCA - ITN - 2019

Total Cost

€ 3 220 753,32

EU Contribution



12 Early Stage Researchers


Resultado de imagen de icono objetivo SCIENTIFIC: The main scientific goal of CLARIFY is to create a research infrastructure based on digital image processing, artificial intelligence and cloud computing to enhance knowledge sharing and reach better-informed decisions in pathology. This ambitious goal breaks down as follows:


Advanced image processing techniques and artificial intelligence methods for automatic WSI interpretation with two purposes: diagnosis and image retrieval.


Novel cloud-oriented data infrastructure and algorithms: to securely store, retrieve and share a publicly available WSI database assuring data interoperability and portability


Innovative and user-friendly software: computer-aided diagnosis and content-based image retrieval tools based on artificial intelligence and cloud-computing algorithms to improve workflow efficiency, stimulate collaboration and increase diagnostic confidence at pathology labs no matter their location.

Resultado de imagen de icono objetivo TRAINNING: CLARIFY will provide a high-level personalised multidisciplinary training program. This will include enrolment in a PhD program (in two tracks: engineering and medicine) as well as further education in transferable skills (such as entrepreneurship, project management, ethical issues, IPR, open access). The long-term ambition is evolving scientific leadership – a foundation for ERC starting grants and/or industry leadership – Industry Fellow.

Resultado de imagen de icono objetivo DISSEMINATION AND OUTREACH: Disseminate the digital pathology methods and tools developed by the ITN to a wide spectrum of stakeholders ranging from the scientific community to clinicians and industry; create awareness in the pathology field about the need of using new technologies to reduce their workload; to encourage pathology and computer engineer vocational careers among young students, with special emphasis on women.


Second CLARIFY Newsletter available!

CLARIFY is almost two-year-old, read our newsletter to know the last outcomes of the CLARIFY project, including scientific results, ESR project updates, dissemination actions, events, training activities, secondments, etc.

ESR7 starts her secondment in INCLIVA

Laëtitia (ESR7 at UPV) started last month her 2-month on-site secondment at the INCLIVA foundation, where Andrés (ESR12) is doing his Ph.D., under the supervision of Carlos Monteagudo.

Laëtitia is the first ESR to have the opportunity to do an on-site secondment because of the pandemic restrictions, as all other on-going secondments are currently held online.

Welcome to the first CLARIFY newsletter!

Keep updated about the CLARIFY project and be one of our first readers!

Secondments start!

First CLARIFY secondments secondments started from March 2021. Due to COVID mobility restrictions, most of them were virtual.

All ESRs in place!

All CLARIFY’s ESRs are already enrolled and starting their careers. Welcome to Na Li, Yuandou Wang, Jiahui Geng, Neel Kanwal, Saul Fuster Navarro, Claudio Fernandez, Laëtitia Launet, Arne Schmidt, Zahra TabaTabaei, Farbod Khoraminia, Umay Kiraz, Andrés Mosquera-Zamudio. A great team!

Visit Researchers section to get to know them!

More about CLARIFY

CLARIFY: a European project about digital pathology to aid in diagnosis of three types of cancer

CLARIFY returns

The COVID-19 outbreak had also consequences on CLARIFY project. The incorporation of the ESRs had to be postponed. First ESRs joined CLARIFY network in sep-2020.

Visit Researchers section to get to know them.

CLARIFY's positions available!

Visit EURAXESS and Researchers section for more information.
Application deadline: 15-Feb-2020

CLARIFY starts

CLARIFYCLoud ARtificial Intelligence For pathologYstarts on 1-nov-2019 and ends 31-oct-2023. The project, coordinated by the Universitat Politècnica de València (Spain), is funded under the programme: H2020-EU.1.3.1. – Fostering new skills by means of excellent initial training of researchers.  



ESR9 – Secondment in INCLIVA

Hi everyone! Today I am going to share my perfect experience in INCLIVA, where I was for one month of my project.

ESR12 – Virtual secondment in Erasmus Medisch Centrum in Rotterdam.

The virtual secondment in EMC in Rotterdam consisted in attending to the weekly lab meeting with the bladder cancer group and a course with the uropathologist explaining bladder cancer.

ESR5 - Virtual secondment at Erasmus MC Rotterdam

Hello there! For today’s post, I will share my experience during my virtual secondment at Erasmus MC Rotterdam, what I learned and my thoughts.

ESR7 - Secondment at INCLIVA

Hi! Today, I will talk a bit about my experience at the INCLIVA foundation where I did a 2-month on-site secondment.

ESR6, ESR7 & ESR12 - Online secondment at ROCHE

Hi everyone! Today we (Claudio, Laëtitia and Andrés) will talk about the online secondment we did at Roche Diagnostics S.L.U.

Topic: Tools, good practices and use cases for digital pathology




Supervisory Board (SB) and ESR Supervisors (ES)

Valery Naranjo (SB/ES)

Valery Naranjo (SB/ES)

Universitat Politècnica de València


Kjersti Engan (SB/ES)

Kjersti Engan (SB/ES)

University of Stavanger


Chunming Rong (ES)

Chunming Rong (ES)

University of Stavanger


Zhiming Zhao (SB/ES)

Zhiming Zhao (SB/ES)

Universiteit Van Amsterdam


Rafael Molina (SB/ES)

Rafael Molina (SB/ES)

Universidad de Granada


Carlos Monteagudo (SB/ES)

Carlos Monteagudo (SB/ES)

Instituto de Investigación Sanitaria INCLIVA


Emiel Janssen (SB/ES)

Emiel Janssen (SB/ES)

Helse Stavanger HF


Tahlita Zuiverloon (SB/ES)

Tahlita Zuiverloon (SB/ES)

Erasmus Medisch Centrum Rotterdam


Russel Wolff (SB/ES)

Russel Wolff (SB/ES)



Javier Oliver (SB/ES)

Javier Oliver (SB/ES)

Tyris Software


Antonio Ferrández (SB)

Antonio Ferrández (SB)

Universitat de València


Davide Zaccagnini (SB)

Davide Zaccagnini (SB)



Carlos Manchado (SB)

Carlos Manchado (SB)

Roche Diagnostics


External Advisory Board

Ritu Aneja

Ritu Aneja

Professor of Cancer Biology Georgia State University


Malkom Atkinson

Malkom Atkinson

Professor - The University of Edinburgh


Delia DeBuc

Delia DeBuc

Research Associate Professor of Ophthalmology - Bascom Palmer Eye Institute


Keith Jeffery

Keith Jeffery

Independent Consultant on Information Systems, Metadata and Cloud Computing


Aggelos K. Katsaggelos

Aggelos K. Katsaggelos

Professor of Electrical and Computer Engineering – Northwestern University


Juan Merlo

Juan Merlo

Professor in Public Health and Community Medicine – Lund University


Victor G Prieto

Victor G Prieto

Professor and Chair – University of Texas – MD Anderson Cancer Center


Eugen Petcu

Eugen Petcu

Associate Professor at Department of Biomedical Sciences - New York Institute of Technology



Na Li

Na Li

ESR1 - Universiteit Van Amsterdam


Yuandou Wang

Yuandou Wang

ESR2 - Universiteit Van Amsterdam


Jiahui Geng

Jiahui Geng

ESR3 - bitYoga AS


Neel Kanwal

Neel Kanwal

ESR4 - University of Stavanger


Saul Fuster Navarro

Saul Fuster Navarro

ESR5 - University of Stavanger


Claudio Fernandez

Claudio Fernandez

ESR6 - Universitat Politècnica de València


Laëtitia Launet

Laëtitia Launet

ESR7 - Universitat Politècnica de València


Arne Schmidt

Arne Schmidt

ESR8 - Universidad de Granada


Zahra Tabatabaei

Zahra Tabatabaei

ESR9 - Tyris Software


Farbod Khoraminia

Farbod Khoraminia

ESR10 - Erasmus Medisch Centrum Rotterdam


Umay Kiraz

Umay Kiraz

ESR11 - Helse Stavanger HF


Andrés Mosquera-Zamudio

Andrés Mosquera-Zamudio

ESR12 - Instituto de Investigación Sanitaria INCLIVA



ESR5, ESR7 and ESR12 at AI in pathology event

On November 4-5, 2021, ESR5, ESR7 and ESR12 participated as speakers in an online Colombian event organized by Keralty about AI and its opportunities to transform the healthcare field. ESR7 and ESR12 presented the medical vs. engineering perspectives of histological image analysis, while ESR5 talked about the challenges of the implementation of intelligent systems in the clinical practice. ESR12 also spoke about the recent advances of AI in the digital pathology field.

ESR4, ESR6 and ESR11 at Diaceutics Webinar

On October 12, 2021, ESR4, ESR6 and ESR11 attended a Diaceutics Webinar: “Digital pathology and implementation of AI scoring algorithms in clinical practice”. Dr. Bert van der Vegt discussed digital pathology and the implementation of artificial intelligence scoring algorithms in clinical practice from a laboratory perspective. He shared some insights on the current state of digital pathology and the use of artificial intelligence scoring algorithms in various European countries.

ESR6 and ESR11 at Stavanger Day in Pathology

On September 30, 2021, the Stavanger University Hospital (SUH) organized the seminar “Stavanger Day in Pathology” with more of 50 attendants among members of the SUH Pathology department (included CLARIFY ESR6 and ESR11) and students of Pathology.

ESR8 in MICCAI 2021

On 27Sep – 1Oct 2021, ESR8 presented a paper on the topic of Multiple Instance Learning in the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). This work is a successful collaboration between the University of Granada and the Northwestern University.

ESR10 and ESR11 in EMPAIA Academy

On Sep 17-22, 2021, ESR10 and ESR11 attended EMPAIA Academy training program where renowned speakers from the fields of IT, artificial intelligence (AI) and pathology talked about their experiences, use cases and the latest developments in digital pathology. Courses: (i) Introduction to Pathology and AI in Pathology, (ii) Introduction to Computational Pathology, (iii) Requirements for Application of AI.

ESR12 presentation in ASOCOLPAT

On 26th of August 2021, Andrés Mosquera ESR12 explained in the Colombian Association of Pathologists (ASOCOLPAT) the utility and concepts of deep learning in digital pathology in his lecture “Deep learning for pathologists” (presentation in Spanish).

ESR9 in Beyond AI Summer School

From 13 to 15 September 2021, Zahra (ESR9) attended a summer school on artificial intelligence (AI), organized by Virtual Vehicle Research GmbH, Graz University of Technology and University of Graz.

ESR4 and ESR5 at NOBIM conference

On 13-14 September 2021, ESR4 Neel Kanwal and ESR5 Saul Fuster Navarro presented their ongoing research about CLARIFY at NOBIM (Norwegian Association of Image Processing and Machine Learning) held at Oslo Gardermoen.

ESR12 in 2021 Online Dermpedia CME Course

On May 26, Andres ESR12 attended to the Online Course “Spitzoid Melanocytic Tumors: Histological-Genetic Correlations: Expert Analysis of 70 Spitzoid Melanocytic Proliferations With Known Genetic Changes” directed by Dr.Artur Zembowicz and Pedram Gerami. By

2nd CLARIFY Virtual Fieldtrip

On June 22, 2021, ESRs had the pleasure to attend the 2nd CLARIFY Virtual Fieldtrip titled “Anatomic pathology instruments and reagents” led by ROCHE, one of our partner organizations. ROCHE showed a virtual demo of some of their solutions for the Anatomic Pathology Lab.

ESR4 at DPA Webinar

On April 22, 2021, Neel, ESR4 at UiS, attended a webinar on “Enabling Interoperability for Digital and Computational Pathology in the Age of Artificial Intelligence: Current Status and Future Directions”  by the Digital Pathology Association (DPA).

First annual meeting

On 14-16 Apr 2021, after closing the CLARIFY training school, the first CLARIFY annual meeting started, in which all CLARIFY ESRs presented themselves, their background, their individual research projects and the work performed until then. A meeting with the distinguished members of the CLARIFY External Advisory Board was held and the different CLARIFY committees were joined. Finally, the first CLARIFY annual meeting concluded with the Mid-term check by the REA – European Research Executive Agency – to assess the project at that point.

First online training school

On 13-14 Apr 2021, the first CLARIFY training school was held. The event was composed of 3 technical courses lectured by some of the CLARIFY supervisors and 3 master classes by some distinguished members of our External Advisory Board. Besides, we had also a workshop and two seminars to cover relevant transferable skills issues.

For more information about the sessions and their speachers, visit: Day 1 – morning session, Day 1 – afternoon session, Day 2 – morning session.

ESR2 at the HPCS 2020

On 23-27 March 2021, ESR2 has attended the 2020 international conference on high performance Computing & Simulation (HPCS 2020) online event, Under the theme of “HPC and Modeling & Simulation for 21st Century”, HPCS 2020 focused on a wide range of the state-of-the-art as well as emerging topics pertaining to high performance and large-scale computing systems at both the client and backend levels.

ESR11 at Molecular diagnostics and genomics in breast cancer event

On 1-5 March 2021, ESR11 attended the Molecular diagnostics and genomics in breast cancer event organized by Onco Corner, the e-learning platform from Sharing Progress in Cancer Care (SPCC).

ESR7 in a MATLAB-Python webinar

On the 23rd of February 2021, ESR7 participated in a MATLAB seminar to learn more about using MATLAB libraries within Python.

ESR6 and ESR7 at the IEEE EMBS Forum

Claudio Fernandez and Laëtitia Launet, respectively ESR6 and ESR7 at the UPV, attended the IEEE EMBS Grand Challenge Forum on Data Science and Engineering in Healthcare, held virtually on Feb 10-13, 2021.

ESR10 at Bridge Digital and Molecular Pathology

On 11-Feb-2021, ESR10 attended the Bridge meeting on Molecular and Digital Pathology with the aim of diving deeper into disease pathology.

ESR12 at SEAP-IAP Annual Meeting

From the 4th to the 5th of February 2021, ESR12 attended the XLIV Annual Meeting of the Sociedad Española de Anatomía Patológica, the Spanish Division of the International Academy of Pathology.

1st Virtual Fieldtrip

On Jan 26, 2021, took place the first on-line networking training session of CLARIFY. Supervisors, co-supervisors and ESRs introduced themselves as an introduction to partner’s expertise and disciplines. This training was hosted by UPV.

ESR1 at ISWC 2020

Na Li, ESR1 from UvA, participated at the 19th International Semantic Web Conference (ISWC 2020), the premier international forum for the Semantic Web and Linked Data Community.

ITN 2019 Coordinators’ Info Day

Universitat Politècnica de València attended  to the H2020 MSCA ITN 2019 – Coordinators’ Info Day organised by the European Commission on 22nd November in Brussels.

Kick-off meeting

On 7th and 8th November, CLARIFY’s kick-off meeting took place in Valencia (Spain).


Conference Papers

2020 IEEE ServicesIEEE World Congress on Services (19-24 Oct-2020; Online)

Wang, Y., Zhao, Z., Decentralized workflow management on software defined infrastructure, 1st Workshop On Data-Centric Workflows On Heterogeneous Infrastructures: Challenges And Directions (DAWHI) in the context of IEEE Services Congress, 2020.

HPCS 2020: International Conference on High Performance Computing & Simulation (22-27 March-2021; Online)

Kruijer W., Wang Y., Koulouzis S., Li N., Bianchi R., Zhao, Z.: FAIR-Cells: an interactive tool for enabling the FAIRness of code fragments in Jupyter notebooks, in the proceedings of international conference of High Performance Computing and Simulation (HPCS) (2020), Spain [to appear]

EASE: International Conference on Evaluation and Assessment in Software Engineering (21-24 June 2021; Online)

Jiahui Geng, Neel Kanwal, Martin Gilje Jaatun, Chunming Rong, DID-eFed: Facilitating Federated Learning as a Service with Decentralized Identities. 25th International Conference on Evaluation and Assessment in Software Engineering

ECML-PKDD 2021: European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (13-17
September 2021; Online)

Yongli Mou, Jiahui Geng, Sascha Welten, Chunming Rong, Stefan Decker, and Oya Beyan, Optimized Federated Learning on Class-biased Distributed Data Sources. 4th Workshop on Parallel, Distributed and Federated Learning at ECML-PKDD 2021.

MICCAI 2021: MICCAI 2021: International Conference on Medical Image Computingand Computer Assisted Intervention (27 Sep – 1 Oct 2021; Online)

Yunan Wu, Arne Schmidt, Enrique Hernández Sánchez, Rafael Molina, and Aggelos K. Katsaggelos, Combining Attention-based Multiple Instance Learning and Gaussian Processes for CT Hemorrhage Detection. 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021).

Journal Papers

Sandra Morales, Kjersti Engan, Valery Naranjo, Artificial intelligence in computational pathology – challenges and future directions, Digital Signal Processing, 2021, 103196, ISSN 1051-2004,



NEWSLETTER #1 Mar-2021

  • What is Digital Pathology?
  • What will CLARIFY network do?
  • Key elements of CLARIFY
  • What’s happening? – publications, events and training, secondments



NEWSLETTER #2 Sep-2021

  • Milestones achieved
  • Scientific Deliverables
  • CLARIFY ESR project updates
  • What’s happening? – publications, events and training, secondments


Discover our blog: From Clarify to the world

This is the CLARIFY project blog where our researchers will share their motivations, aspirations and achievements

Contact us


Project Coordinator

 Universitat Politècnica de València

Camino de Vera s/n,

46022 Valencia (España)

Ciudad Politécnica de la Innovación

Edificio 8B – Cubo Azul – Acceso N



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