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


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.

TRAINING: 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.

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.


CLARIFY Final Conference Press Release

The press release for the CLARIFY FInal Conference is here! Dice in to discover de highlights of the incredible two days lives in valencia on January 25-26th.

CLARIFY Final Conference!

CLARIFY is proud to organise its Final Conference where we will highlight the main achievements of the project and facilitate discussion on the new era of digital pathology.

Free registration and call for abstracts

The 3rd Clarify Training School is here!

If you don’t belong to the CLARIFY network but you are interested in Data Management and want to physically or remotely attend our training school, register now. Registration is open until April, 10th!

See agenda and venue details

Fifth CLARIFY Newsletter is now here!

CLARIFY is now in the home stretch! if you want to know the latest updates of the project, don’t to read the latest issue of our Newsletter

ESR6 best paper award

Congratulations to our ESR6 for the Best Paper Award at the IDEAL2022 conference for his paper “Challenging Mitosis Detection Algorithms: Global Labels allow Centroid Localization” in Manchester, United Kingdom, last November.

ESR4 and ESR8 have published their work in IEEE Access

On 18May – The title of the journal publication is “The devil is in the details: Whole Slide Image acquisition and processing for artifacts detection, color variation and data augmentation. A review” . This work has been a successful collaboration between the University of Granada and the University of Stavanger.

Fourth CLARIFY Newsletter is already available!

After all this time, many important events have taken place! Lots of congresses attended, published papers, secondments, scientific deliverables, training activities… If you want to keep up to date, don’t forget to read it!

Third CLARIFY Newsletter is now here!

After two years, many interesting things have happened in CLARIFY project! If you want to know the last outcomes of the project, don’t forget to read the latest issue of our Newsletter.

2nd CLARIFY Training School

2nd CLARIFY Training School is here! Online attendance is now open to general public. More information and registration in the button.

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.  





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, University of Alabama at Birmingham


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



ESR4 at FAIEMA 2023

Neel Kanwal (ESR4) discussed on his accepted paper titled, “Balancing Privacy and Progress in Artificial Intelligence: Anonymization in Histopathology for Biomedical Research and Education” at the 1st International Conference on FAIEMA held in Athens, Greece on Sep 25th-26th, 2023

ESR4, ESR5 and ESR9 in EUSIPCO 2023

ESRs 4, 5 and 9 presented their latest work in the 31st European Signal Processing Conference (EUSIPCO) in Helsinki, Finland.

ESR2 and ESR4 in IEEE ICDH 2023

Yuandou Wang (ESR2) and Neel Kanwal (ESR4) published their collaborative work, “Towards a privacy-preserving distributed cloud service for preprocessing very large medical images” in IEEE International Conference on Digital Health. The conference was held in Chicago, U.S. from July 02-08, 2023.


Yuandou Wang (ESR2) attended IEEE COMPSAC 2023 conference which was held in Torino, Italy, June 27-29, 2023.

ESR4 in ACM Europe Summer School 2023

Neel Kanwal (ESR4) attended ACM Europe Summer School 2023 on “HPC Computer Architectures for AI and Dedicated Applications, organized by Barcelona Supercomputing Center and held in Barcelona on July 3-7, 2023.

ESR4 in NORA Summer School 2023

Neel Kanwal (ESR4) participated in NORA Summer School 2023 on Self-Supervised Learning, held at the Arctic University of Norway (UiT), in Tromso on June 12-16, 2023.

ESR1 in The Web Conference 2023

ESR1 (NaLi) presented a poster entitled “CNSVRE: A Query Reformulated Search System with Explainable Summarization for Virtual Research Environment” in The Web Conference 2023 that took place in Texas from 30 Apr – 4 May.

ESR4 in PAKDD 2023

Third training school

The third CLARIFY training school was held in Amsterdam from 24 to 26 April 2023. Three days full of intense learning, interesting seminars, fruitful technical lectures and undoubtedly scientific and personal enrichment. CLARIFY ESRs presented the status of their projects and received advice from the distinguished members of our External Advisory Board.

For more information about the programs and their speakers, visit: Day 1 – Programm, Day 2 – Programm, Day 3 – Programm

ESR10 at IBCN 2022

On September 29 – October 1, 2022, ESR10 attended and presented a poster titled “Dataset preparation to predict response to BCG treatment for high-risk non-muscle-invasive bladder cancer from histopathological images” in the 20th Meeting of the International Bladder Cancer Network . The event was held in Barcelona.

ESR11 at ESP 2022

On September 3-7, 2022, ESR11 attended the 34th European Congress of Pathology  which took place in Basel, Switzerland. At the event, the latest improvements in different fields of pathology, especially in digital pathology, were discussed.


On August 22-26, 2022, ESR2 attended the 36th edition of the annual conference of the ACM Special Interest Group on Data Communication which took place in Amsterdam.

ESR12 at Colombian Congress of Pathology

On August 12-14, 2022, ESR12 participated as a speaker at the 43th Colombian Congress of Pathology, held in Cartagena de las Indias and organised by the Colombian Association of Pathology (ASOCOLPAT).

ESR4 at OxML 2022

On August 7-14, 2022, ESR4 attended the Oxford Machine Learning Summer School which was organised by AI for Global Goals. The event was organised with the aim of providing the best training in a wide range of advanced topics and developments in machine learning (ML) including deep learning.

ESR2 at ACACES 2022 Summer School

On July 10-16, 2022, ESR2 attended the 18th International Summer School on Advanced Computer Architecture and Compilation for High-performance Embedded Systems . This event was organized by the HiPEAC Network.

ESR10 at EAU2022

On July 1-4, 2022, ESR10 attended the European Association of Urology Annual Congress  which is Europe’s biggest urological event. The 37th Annual EAU Congress included a wide range of sessions by urological experts from all around the world and took place in Amsterdam.

3rd CLARIFY Virtual Fieldtrip

On June 21, 2022, ESRs had the pleasure to attend the 3rd CLARIFY Virtual Fieldtrip titled “How to develop a software application. The importance of the usability” led by Tyris Software  one of our consortium members . Javier Oliver, founder, and CEO at Tyris Software explained the importance of the user experience in the development of digital products, specifically in the digital product design.

ESR11 at the 18th European Congress on Digital Pathology

On June 16-18, 2022, ESR11 attended the 18th European Congres son Digital Pathology,  celebrated in Berlin, where the latest topics on digital and computational pathology were discussed.

ESR4 and ESR5 at hAIST conference 2022

On June 13-14, 2022, ESR4 and ESR5 participated and presented their research activities at hAIST conference, held in Stavanger. This conference is arranged by member of Kunstig intelligens i norsk helsetjeneste (Artificial Intelligence in the Norwegian health service).

ESR2 and ESR7 at Flower Summit 2022

On May 31, 2022, ESR2 and ESR7 attend the conference, where presentations with different approaches to the use of the FLOWER framework and the current challenges of federated learning in different fields took place.

ESR11 attended the National Network for Breast Cancer

On March 9-10, 2022, ESR11 presented two posters in the National Network for Breast Cancer, entitled “Relation between prognostic factors and MicroRNAs (miR-18a/miR-18b) in triple negative breast cancer” and “Comparison of proliferation and other prognostic biomarkers in primary invasive lymph node negative breast cancer in Spain and Norway”.

ESR4 and ESR5 at NORA Annual Conference 2022

On June 9-10, the Norwegian Artificial Intelligence Research Consortium organized the NORA Annual conference in Stavanger. In this conference, ESR4 and ESR5 presented abstracts of their ongoing work.

Second training school

The 2nd CLARIFY training school was held in Granada, April 4-7, 2022. These three days have been full of interesting seminars by some distinguished members of our External Advisory Board, fruitful technical lectures by some of CLARIFY supervisors, and productive workshop on different transversal areas.

For more information about the programs and their speakers, visit: Day 1 – Programm, Day 2 – Programm, Day 3 – Programm

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.

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.

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).


ESR4 – Secondment at UvA

Hi, readers! This is Neel, a Ph.D. from the University of Stavanger. This was the last secondment from my Ph.D. project at UvA. Let me tell you what I learned here.

ESR11 – Secondments at Tyris Software and INCLIVA

Umay Kiraz, a Ph.D. student in Stavanger University Hospital, shares her experience in her secondment in Tyris Software and INCLIVA in Spain.

ESR3 – Secondments at the University of Granada

Hi, I am ESR 3, focusing on privacy-preserving techniques and federated learning. 

ESR5 – Secondments at UPV

Hello there! It’s been a while since I posted an update on social media, and I wanted to share something I’ve been working on since the start of my secondment at Universitat Politècnica de València (UPV), Valencia, Spain.

ESR2 – Secondments at the University of Stavanger, bitYoga, and Tyris Software

Secondments among multinational, multisectoral, and interdisciplinary boards enrich my life and enhance knowledge sharing for research.

ESR12 – Secondment at Helse Stavanger HF

Andrés Mosquera, a Ph.D. student in Medicine at Universitat de València, shares his experience in his secondment in Helse Stavanger HF (SUH) in Norway. #digitalpathology #pathologists #artificialintelligence

ESR8 – Secondments at the UPV, Tyris and INCLIVA

Interdisciplinary exchange is the key to the successful application of AI in digital pathology. That’s why I completed different secondments in Valencia in different areas – computer vision, software development, and pathology.

ESR9 – Secondment at Universidad de Granada

Hi, world. This is time to talk about my last secondment at UGR, under supervision of Prof. Rafael Molina and collaborating with Feranado Pérez Bueno.

ESR6, ESR7 & ESR12 – Secondment at Roche Diagnostic

Hello everyone! This is Claudio Fernandez, Laëtitia Launet and Andrés Mosquera, ESR6, ESR7 and ESR12 at CLARIFY, respectively. Today we are going to talk about our experience during our second Secondment at ROCHE Diagnostics.

ESR1 – Secondment at Universitat Politècnica de València

I am Na Li, a PhD student in computer science at University of Amsterdam, currently exploring notebook search for scientific users. In this post I will introduce my observations for researchers’ intents when they search for research resources, which mainly derive from communication with members at the CVBLab in UPV

ESR4 – Secondment at University of Stavanger

Hi readers! This is Neel, a Ph.D. from the University of Stavanger. Let’s look together for the causes of cancer and its routine treatments.

ESR7 – Secondment at University of Amsterdam

That secondment was the starting point of collaborations with Yuandou and the team at UvA that are actually still on-going and that we plan to continue. Hoi! Today, I wanna talk to you about my secondment in Amsterdam ☺

ESR10 – Secondment at Stavanger University Hospital

In this post, I explain how going on secondment could help you gain a broader overview of your project’s topic and make your collaboration more efficiently


ESR5 – Secondment in bitYoga AS

Hello there! For today’s post, I will share my experience during my secondment at bitYoga AS, what I learned by taking blockchain lectures and an ongoing collaboration with ESR3. 


ESR6 – Secondment in Stavanger University Hospital (SUH)

Hello everyone! This is Claudio Fernandez Martín, ESR6 at CLARIFY. Today I am going to tell you all about my experience during my three-month Secondment at the Stavanger University Hospital (SUH) in Norway.

ESR9 – Secondment in Universitetet i Stavanger

Hi, world! Today I am going to share my experiences at UIS, as my second secondment.

ESR4 – Secondment in University of Granada

Hi everyone! I am ESR4, Neel Kanwal, and I am back discussing what I learned from my stay in Granada.

ESR3 – Secondment in University of Amsterdam

Hi, everyone, in this blog I will introduce my secondment experience at the University of Amsterndam.

ESR8 – Virtual Secondment at the University of Stavanger

Today Arne Schmidt (ESR8) talks about his virtual secondment at the University of Stavanger about Whole Slide Image preprocessing, Multiple Instance Learning with attention and the classification of bladder cancer.

ESR1, ESR4, ESR10 – Secondment in Stavanger University Hospital

Hi! Na Li, Neel Kanwal and Farbod Khoraminia will talk about their virtual secondment experience at Stavanger University Hospital.

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


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.

EASE 2021: 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:  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).

FL-AAAI-22: International Workshop on Trustable, Verifiable and Auditable Federated Learning in Conjuction with AAAI 2022 (2 March- 2022; Online)

YJiahui Geng, Ynli Mou, Feifei Li, Qing Li, Oya Beyan, Stefan decker, Chunming Rong, Towards General Deep Leakage in Federated Learning, in the International Workshop on Trustable, Verifiable and Auditable Federated Learning in Conjunction with AAAI 2022 (FL-AAAI-22).

hAIST 2022: Health-related Artificial Intelligence in Stavager (June 2022)

Neel Kanwal, Farbod Khoraminia, Tahlita Zuiverloon, Chunming Rong, and Kjersti Engan, Detection of Histopathological Artifacts in Whole Slide Images, in the Health-related Artificial Intelligence in Stavanger (hAIST-22).

IVMSP 2022: IEEE Image, Video, and Multidimensional Signal Processing Workshop (June 2022)

Neel Kanwal, Saul Fuster, Farbod Khoraminia, Tahlita C.M. Zuiverloon, Chunming Rong, Kjersti Engan, Quantifying the effect of color processing on blood and damaged tissue detection in Whole Slide Images. 14th Image, Video, and Multidimensional Signal Processing Workshop (IVMSP 2022)

IVMSP 2022:  IEEE Image, Video, and Multidimensional Signal Processing Workshop (June 2022)

Saul Fuster, Farbod Khoraminia, Umay Kiraz, Neel Kanwal, Vebjørn Kvikstad, Trygve Eftestøl, Tahlita C.M. Zuiverloon, Emilius A. M. Janssen, Kjersti Engan, Invasive Cancerous Area Detection in Non-Muscle Invasive Bladder Cancer Whole Slide Images. 14th Image, Video, and Multidimensional Signal Processing Workshop (IVMSP 2022)

IVMSP 2022: IEEE Image, Video, and Multidimensional Signal Processing Workshop (June 2022)

Zahra Tabatabaei, Javier Oliver, Valery Naranjo, Kjersti Engan, Residual block Convolutional Auto Encoder in Content- Based Medical Image Retrieval . 14th Image, Video, and Multidimensional Signal Processing Workshop (IVMSP 2022)

eScience 2022: IEEE International Conference on e-Science (October 2022)

Na Li, Siamak Farshidi, Riccardo Bianchi, Spiros Koulouzis, Zhiming Zhao, Context-Aware Notebook Search in a Jupyter-Based Virtual Research Environment. 18th International Conference on e-Science (eScience 2022)

ICIP 2022: International Conference on Image Processing (October 2022)

Launet, L., Colomer, A., Mosquera-Zamudio, A., Moscardó, A., Monteagudo, C., & Naranjo, V., A Self-Training Weakly-Supervised Framework for PathologistLike Histopathological Image Analysis. 29th International Conference on Image Processing (ICIP 2022)

Journal Papers

Rocío del Amor, Adrián Colomer, Carlos Monteagudo, Valery Naranjo, A deep embedded refined clustering approach for breast cancer distinction based on DNA methylation, Neural Computing and Applications, 2021.

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

del Amor, R., Launet, L., Colomer, A., Moscardó, A., MosqueraZamudio, A., Monteagudo, C., & Naranjo, V, An attention-based weakly supervised framework for spitzoid melanocytic lesion diagnosis in whole slide images, Artificial Intelligence in Medicine, 2021.

Rocío del Amor, Laëtitia Launet, Adrián Colomer, Anaïs Moscardó, Andrés Mosquera-Zamudio, Carlos Monteagudo, Valery Naranjo, An attention-based weakly supervised framework for spitzoid melanocytic lesion diagnosis in whole slide images, Artificial intelligence in medicine, 2021.

Arne Schmidt, Julio Silva-Rodríguez, Rafael Molina and Valery Naranjo, Efficient Cancer Classification by Coupling Semi Supervised and Multiple Instance Learning, IEEE Access, 2022.

Yuandou Wang, Spiros Koulouzis, Riccardo Bianchi, Na Li, Yifang Shi, Joris Timmermans, W. Daniel Kissling, Zhiming Zhao, Scaling Notebooks as Re-configurable Cloud Workflows, Data Intelligence, 2022.

Chunming Rong, Jiahui Geng, Thomas J. Hacker, Haakon Bryhni, Martin G. Jaatun, OpenIaC: open infrastructure as code – the network is my computer, Journal of Cloud Computing, 2022.

Zhiming Zhao, Spiros Koulouzis, Riccardo Bianchi, Siamak Farshidi, Zeshun Shi, Ruyue Xin, Yuandou Wang, Na Li, Yifang Shi, Joris Timmermans, W. Daniel Kissling,Notebook-as-a-VRE (NaaVRE): From private notebooks to a collaborative cloud virtual research environmentSoftware – Practice and Experience, 2022.

Neel Kanwal, Fernando Pérez-Bueno, Arne Schmidt, Kjersti Engan and Rafael Molina, The Devil is in the Details: Whole Slide Image Acquisition and Processing for Artifacts Detection, Color Variation, and Data Augmentation: A Review, IEEE Access, 2022.

M. López-Pérez, A. Schmidt, Y. Wu, R. Molina, and A.K. Katsaggelos, Deep Gaussian Processes for Multiple Instance Learning: Application to CT Intracranial Hemorrhage Detection, Computer Methods and Programs in Biomedicine, 2022.

J. Silva-Rodríguez, A. Schmidt, M. A. Sales, R. Molina, and V. Naranjo, Proportion constrained weakly supervised histopathology image classification, Computer in Biology and Medicine, 2022.



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


NEWSLETTER #3 Mar-2022

  • Milestones achieved
  • Things you din’t know about the project
  • CLARIFY ESRs project updates
  • What’s happening? – publications, events and training, secondments
  • 2nd training school in Granada


NEWSLETTER #4 Oct-2022

  • Milestones achieved
  • Scientific Deliverables
  • CLARIFY ESRs project updates
  • What’s happening? – publications, events and training, secondments
  • 3rd training school in Amsterdam


NEWSLETTER #5 Apr-2023

  • Milestones achieved
  • Scientific Deliverables
  • CLARIFY ESRs project updates
  • What’s happening? – publications, events and training, secondments
  • 3rd training school in Amsterdam


NEWSLETTER #6 Dec-2023

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



Deliverable D1.2: ESRs definition and advertisement 
Definition of the different ESRs profiles and advertisements.

Deliverable D5.6: Report on network‐wide training events_v2 
Report including the network training events carried out in the period.

Deliverable D2.1: Metadata standardization strategy and database 
Collection of a substantial reference and anonymized data set of WSIs for a subset of cancer types and subsequent annotation with clinically relevant multidisciplinary information Description of metadata to be included as part of the reference dataset Description of metadata standardization strategy.

Deliverable D5.1: Report on network‐wide training events_v1 
Report including the network training events carried out in the period.

Deliverable 6.4: CLARIFY repositories for open access 
Definition of CLARIFYs open access policies and procedures to store and preserve CLARIFYs data in selected repositories.

Deliverable D1.3: Recruitment completion 
List of the recruited ESRs.

Deliverable D3.1: WSI preprocessing and standardization protocol
Description of WSI preprocessing algorithms and standardization protocol to be used.


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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