CLoud ARtificial Intelligence For pathologY

About project

OVERVIEW

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

860627

H2020 -MSCA - ITN - 2019

Total Cost

€ 3 220 753,32

EU Contribution

%

Researchers

12 Early Stage Researchers

OBJECTIVES

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:

1

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

2

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

3

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.

News

Welcome to the first CLARIFY newsletter!

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

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.  

 

Secondments

ESR6, 7 & 12 - 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

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.

Consortium

BENEFICIARIES

PARTNER ORGANIZATIONS

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)

bitYoga

  

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)

Lynkeus

    

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

  

Researchers

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

    

Events

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 Dermpedia.org.

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).

Dissemination

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. http://doi.org/10.1109/SERVICES48979.2020.00059

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]

Journal Papers

Newsletters

 

NEWSLETTER #1 Mar-2021

  • What is Digital Pathology?
  • What will CLARIFY network do?
  • Key elements of CLARIFY
  • CLARIFY ESRs

Deliverables

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

VALERY NARANJO

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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