CSC – IT Center for Science is an integral part of the Finnish national research system. Its mission is to develop, integrate and offer high quality IT services for research, education, culture, public administration and industry.

To take AI development in pathology to the next level, a European consortium combining leading European research centres, hospitals as well as major pharmaceutical industries, is going to develop a repository for the sharing of pathology data.
The 6-year, €70 million project called BIGPICTURE, will herald a new era in pathology. 

Pathology is the cornerstone of the workup of many diseases such as cancer, autoimmune diseases, of the follow up after transplantation and is also critical for the evaluation of the safety of drugs. It’s based on the examination of tissue samples (slides) under the microscope. However, despite its pivotal role, it still relies heavily on the qualitative interpretation by a qualified pathologist.

While the microscope symbolizes the profession, the digitalisation of slides in recent years ignited a revolution: not only images can now be shared and accessed from distant locations, they can also be processed by computers. This opens the door for artificial intelligence (AI) applications to assist the pathologist and help study diseases, find better treatments and contribute to the 3Rs (replace, reduce, and refine animal use in research). However, the development of robust AI applications requires large amounts of data, which in the case of pathology means a huge collection of digital slides and the medical data necessary for their interpretation. Sharing these has so far remained challenging due to the data storage capacity required to host a sufficiently large collection and to concerns regarding the confidential character of the medical information.

To allow the fast development of AI in pathology, the BIGPICTURE project aims to create the first European, ethical and GDPR-compliant (General Data Protection Regulation), quality-controlled platform, in which both large-scale data and AI algorithms will coexist. The BIGPICTURE platform will be developed in a sustainable and inclusive way by connecting communities of pathologists, researchers, AI developers, patients, and industry parties.

The project is divided into four main aspects that concern the large-scale collection of data. First, an infrastructure (hardware and software) must be created to store, share and process millions of images that can be gigabytes each. Second, legal and ethical constraints must be put in place to ensure adequate usage of data while fully respecting patient’s privacy and data confidentiality. Then, an initial set of 3 million digital slides from humans and laboratory animals will be collected and stored into the repository to provide data for the development of pathology AI tools. Finally, functionalities that aid the use of the database as well as the processing of images for diagnostic and research purposes will be developed. 

BIGPICTURE is a public-private partnership funded by IMI, with representation from academic institutions, small- and medium-sized enterprises (SMEs), public organisations and pharmaceutical companies, together with a large network slide contributing partners. The consortium partners involved in the project are: 

Academic institutions: Radboud University Medical Center (NL), Linköping University (SE), Leeds Teaching Hospitals NHS Trust (UK), University Medical Centre Utrecht (NL), Uppsala University (SE, ELIXIR node), Haute Ecole Spécialisé de Suisse Occidentale (CH), Eindhoven University of Technology (NL), University of Warwick (UK), Technical University of Munich (DE), Medical University Graz (AT), Institut Pasteur (FR), University of Liege (BE), University of Semmelweis (HU), National Cancer Institute (NL), Region Östergötland (SE), Medical University Vienna (AT), University of Marburg (DE), Helsingin ja Uudenmaan sairaanhoitopiirin kuntayhtymä (FI),

Pharmaceutical companies: Novartis Pharma AG (CH), Janssen Pharmaceutica NV (BE), Bayer AG (DE), Boehringer Ingelheim International GmbH (DE), Novo Nordisk A/S (DK), Pfizer Ltd (GB), Roche (CH), Sanofi Aventis recherche et Développement (FR), Institut de Recherches Internationales Servier (FR), and UCB Biopharma SRL (BE).

Other public & private organisations: CSC – IT Center for Science Finland (FI, ELIXIR node), Biobanks and biomolecular resources research infrastructure (AT), Azienda Ospedaliera Per L’Emergenza Cannizzaro (IT), Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e.V.(DE), Deutsches Institut für Normung E.V. (DE), European Institute for Innovation through Health Data (BE), European Society of Pathology (BE), Digital pathology association (US), GBG Forschungs Gmbh (DE), ttopstart (NL), Sectra AB (SE), Cytomine SCRLFS (BE), Stichting Lygature (NL), Owkin (FR), Deciphex (IE), MedicalPhit (NL), Timelex (BE), 

In this large-scale project, CSC – IT Center for Science, together with the Universities of Linköping and Uppsala, will build a platform with secure data access mechanism for receiving and storing pathological images and their descriptive data. The implementation utilizes the service components developed in the European life sciences infrastructure ELIXIR and in the Nordic Tryggve project. In particular, CSC has developed tools for research data access mechanism that play a key role in this project. 

– When the CSC’s users can apply for access to comprehensive pathological image datasets,  that data combined with the unique HPC computing resources near by, will be an enticing opportunity to drive digital innovations like diagnostic algorithms,” says Tommi Nyrönen, the Head of Node of ELIXIR Finland from CSC.

BIGPICTURE starts on 1st February 2021 and will run for 6 years. However, the platform is meant to last, and the consortium will elaborate sustainability plans to maintain and continue to develop the platform beyond this term.

More information

Contact in Finland: Tommi Nyrönen, CSC,  +358 50 381 9511, tommi.nyronen at csc.fi

Interview requests and other media questions can be directed towards: [email protected]

Acknowledgement of support and disclaimer

This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 945358. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. www.imi.europe.eu
This communication reflects the consortium’s view. Neither IMI nor the European Union or EFPIA are responsible for any use that may be made of the information contained therein.

This article was first published on 28 January by CSC.

The Irish port of Rosslare has seen a staggering increase in traffic since the Brexit transition period ended, as hauliers seek new routes bypassing Britain to link the Republic with the EU.

“Since the first of January, we’ve seen a 476-percent increase in freight to mainland Europe when compared to last year,” port manager Glenn Carr told AFP.

“We’ve gone from three direct services a week to mainland Europe to now 15.”

Jutting out of the morning fog, a giant ferry makes its landing from the French port of Dunkirk — tracing a new route opened by Danish firm DFDS on January 2.

Soon afterwards, a ship from Cherbourg pulls alongside and lowers its ramp — churning the slate-grey waters of the harbour on Ireland’s southeast coast.

Meat trucks and tankers roll onto the dock. Drivers work together — shouting in French — to delicately reverse a flatbed packed with farm machinery.

Spanish hauliers wait in their cabs for the sailing to Bilbao.

On the sloping approach to the docks, a sign welcomes the steady stream of traffic to “Rosslare Europort: the gateway to Europe”.

Britain left the EU in January 2020 after a seismic referendum in 2016 which voted to sever ties with the bloc. But the full effects were felt only with the end of the so-called “transition period” at the start of 2021.

With Britain now outside the customs union and the single market, new checks and paperwork are snarling traffic at the island nation’s borders.

Delays and hurdles mean Irish hauliers are re-thinking the UK’s “landbridge” route they have traditionally taken to EU markets.

Pre-Brexit, more than 150,000 trucks transported three million tonnes of freight to and from the EU in this way — driving across Britain, crossing the Irish Sea and English Channel by ferry.

But in the early days of January, Dublin Port — a key link in the “landbridge” — experienced a lull in traffic and some sailings were cancelled.

In Rosslare — the second busiest freight hub in Ireland — there are signs logistics firms may be charting a new course to Europe: the one with least resistance.

“When you look at the end-to-end delivery of a trailer to the market, what we’re seeing and what we’re being told now is that it’s not much different from the landbridge,” said Carr.

“However, the big benefits are, you’ve no paperwork, your drivers are well rested, you’re saving on fuel.”

Among the forest of lorry trailers parked on Rosslare’s docks, one colour stands out — the canary blue of Amazon Prime trailers.

Dozens are dotted throughout the port and “tugmasters” — squat, truck-like vehicles used to load unaccompanied freight — shunt them to and fro at pace.

Online shoppers in Ireland — a nation of just five million — often rely on British sites serving larger UK markets to fulfil their orders.

However, since January 1, amazon.co.uk has imposed steep “import fees” on some items — to cover “border taxes, customs duties and fees levied in the country of importation”.

Reports earlier this week suggested people in the British province of Northern Ireland will also see their menu of Amazon products shrink as the site de-lists products due to Brexit customs rules.

But Irish customers can avoid fees and disruption by shifting their allegiances to Amazon proxies in EU markets — amazon.fr, amazon.es and amazon.de.

Already there are signs that the habits of retailers and shoppers alike have changed in the post-Brexit landscape.

“A lot of the major retailers in Ireland are now bringing their products for their shelves directly in from mainland Europe now,” explained Carr.

“We’re seeing big customers, the likes of Amazon, now bringing in a lot of freight on a daily basis.”

Copyright AFP. All rights reserved.

FRA (Fundamental Right Agency) held an online inception meeting of a new project looking into the fundamental rights situation of third-country nationals who are long-term residents in the EU. The meeting on will gather partners from FRA’s research network from nine EU Member States – Belgium, Czechia, France, Germany, Italy, Poland, Portugal, Spain and Sweden – covered by the research.

The project will look into the fundamental rights situation of long-term residents in the EU, including equal treatment and access to rights. FRA will collect the data through online interviews with experts and online focus groups and interviews with migrants who are long-term resident in the EU. The meeting took place on 27 January.