PRedictive In-silico Multiscale Analytics to support cancer personalized diaGnosis and prognosis, Empowered by imaging biomarkers

Leistungen

Analysis of the processed data in PRIMAGE Platform

Analysis of the data processed in PRIMAGE Platform.

Visual tools for insilico models

Beta PRIMAGE Diagnostic module combining imaging and biological biomarkers in charge of generation of radiomic data for the clinical prospective studies

Deployment of the final, refined version of the Model Execution Environment

Deployment of the final refined version of the Model Execution Environment

Deployment of the final, refined version of hybrid open cloud and processing middleware

Deployment of the final refined version of the cloud infrastructure

Deployment of intermediate version of hybrid open cloud and processing middleware

Deployment of an intermediate version of Hybrid Open Datacloud and processing middleware layer.

Deployment of an intermediate version of the Model Execution Environment

Deployment of an intermediate version of the Model Execution Environment encompassing all fundamental functionality for PRIMAGE simulation pipeline executions

Record of dissemination and communication activities in year 3 and plan for year 4

Record of dissemination and communication activities in year 3 and plan for year 4 including preliminary exploitation plan

Advancements of in-silico model for simulation of solid tumour growth at whole tumour scale

Advancements of insilico model for solid tumour growth simulation enabling comparison of untreated and treated patient

Readiness to start recruitment for clinical tests

Approval from Ethics Committees at each hospital to start recruitment.

Ethics review plan

Ethical review

Definition of data requirements, e-forms, QC procedures and signed authorisations

Definition of data requirements eforms control procedures for data quality and signed authorisations with different data holders to reuse existing datasets

First year plan for dissemination and communication activities, incl website and dissemination toolkit 1

First year plan for dissemination and communication activities: Website & dissemination toolkit 1.

Record of dissemination and communication activities in year 2 and plan for year 3

Record of dissemination and communication actions in year 2 plan for year 3

Record of dissemination and communication activities in year 1 and plan for year 2, incl. dissemination toolkit 2
Advancements of in-silico models for mechanisms of tumour cells interactions, enabling comparison of untreated and treated patient.

Advancements of insilico models for mechanisms of tumour cells interactions enabling comparison of untreated and treated patient

Conclusions from PRIMAGE Platform clinical assessment

Conclusions on the performance and usability of the platform from the perspective of the paediatric oncologists and radiologists

Contribution to standards for image acquisition, image biomarker extraction and format

Contribution to standardisation of protocols for image acquisition imaging biomarker extraction and format

Advancements of in-silico model for simulation of effect of pharmacology on sub-cellular behaviour of tumour cells

Advancements of insilico model for simulation of effect of pharmacology on subcellular behaviour of tumour cells

Final version of PRIMAGE platform

Final version of PRIMAGE platform.

Data Management Plan

Veröffentlichungen

Bridging gaps between images and data: a systematic update on imaging biobanks

Autoren: Michela Gabelloni, Lorenzo Faggioni, Rita Borgheresi, Giuliana Restante, Jorge Shortrede, Lorenzo Tumminello, Camilla Scapicchio, Francesca Coppola, Dania Cioni, Ignacio Gómez-Rico, Luis Martí-Bonmatí, Emanuele Neri
Veröffentlicht in: European Radiology, 2022, ISSN 0938-7994
Herausgeber: Springer Verlag
DOI: 10.1007/s00330-021-08431-6

Comparative Multicentric Evaluation of Inter-Observer Variability in Manual and Automatic Segmentation of Neuroblastic Tumors in Magnetic Resonance Images

Autoren: Diana Veiga-Canuto; Leonor Cerdà-Alberich; Cinta Sangüesa Nebot; Blanca Martínez de las Heras; Ulrike Pötschger; Michela Gabelloni; José Miguel Carot Sierra; Sabine Taschner-Mandl; Vanessa Düster; Adela Cañete; Ruth Ladenstein; Emanuele Neri; Luis Martí-Bonmatí
Veröffentlicht in: Cancers, 2022, ISSN 2072-6694
Herausgeber: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14153648

explAIner : A Visual Analytics Framework for Interactive and Explainable Machine Learning

Autoren: Thilo Spinner; Udo Schlegel; Hanna Schäfer; Mennatallah El-Assady
Veröffentlicht in: IEEE Transactions on Visualization and Computer Graphics, Ausgabe 2, 2020, ISSN 1077-2626
Herausgeber: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tvcg.2019.2934629

Unravelling cell migration: defining movement from the cell surface

Autoren: Francisco Merino-Casallo; Maria Jose Gomez-Benito; Silvia Hervas-Raluy; Jose Manuel Garcia-Aznar
Veröffentlicht in: Cell Adhesion & Migration, 2022, ISSN 1933-6918
Herausgeber: Landes Bioscience
DOI: 10.1080/19336918.2022.2055520

FLAME GPU 2: A framework for flexible and performant agent based simulation on GPUs

Autoren: Paul Richmond, Robert Chisholm, Peter Heywood, Mozhgan Kabiri Chimeh, Matthew Leach
Veröffentlicht in: Software: Practice and Experience, 2023, ISSN 1097-024X
Herausgeber: Wiley Online Library
DOI: 10.1002/spe.3207

Confined Cell Migration and Asymmetric Hydraulic Environments to Evaluate The Metastatic Potential of Cancer Cells

Autoren: Juste-Lanas Y, Guerrero PE, Camacho-Gómez D, Hervás-Raluy S, García-Aznar JM, Gomez-Benito MJ.
Veröffentlicht in: Journal of Biomechanical Engineering, 2021, ISSN 1528-8951
Herausgeber: The American Society of Mechanical Engineers(ASME)
DOI: 10.1115/1.4053143

Collagen-Laponite Nanoclay Hydrogels for Tumor Spheroid Growth

Autoren: Alamán-Díez, P., Borau, C., Guerrero, P. E., Amaveda, H., Mora, M., Fraile, J. M., ... & Pérez, M. Á
Veröffentlicht in: Biomacromolecules, 2023, ISSN 1526-4602
Herausgeber: American Chemical Society
DOI: 10.1021/acs.biomac.3c00257

DICOM-MIABIS integration model for biobanks: a use case of the EU PRIMAGE project

Autoren: Camilla Scapicchio; Michela Gabelloni; Sara Maria Forte; Leonor Cerdá Alberich; Lorenzo Faggioni; Rita Borgheresi; Paola Erba; Fabiola Paiar; Luis Marti-Bonmati; Emanuele Neri
Veröffentlicht in: European Radiology Experimental, Ausgabe 5, 2021, ISSN 2509-9280
Herausgeber: Springer Open
DOI: 10.1186/s41747-021-00214-4

Hybrid computational models of multicellular tumour growth considering glucose metabolism

Autoren: Gonçalves, Inês G.; García-Aznar, José Manuel
Veröffentlicht in: Computational and Structural Biotechnology Journal, 2023, ISSN 2001-0370
Herausgeber: Elsevier
DOI: 10.1016/j.csbj.2023.01.044

A 3D multi-agent-based model for lumen morphogenesis: the role of the biophysical properties of the extracellular matrix

Autoren: Daniel Camacho-Gómez; José Manuel García-Aznar; María José Gómez-Benito
Veröffentlicht in: Engineering with computers, 2022, ISSN 0177-0667
Herausgeber: Springer Verlag
DOI: 10.1007/s00366-022-01654-1

Position of the AI for Health Imaging (AI4HI) network on metadata models for imaging biobanks

Autoren: Kondylakis, Haridimos; Ciarrocchi, Esther; Cerda-Alberich, Leonor; Chouvarda, Ioanna; Fromont, Lauren A.; Garcia-Aznar, Jose Manuel; Kalokyri, Varvara; Kosvyra, Alexandra; Walker, Dawn; Yang, Guang; Neri, Emanuele; The AI4HealthImaging Working Group on metadata models
Veröffentlicht in: European Radiology Experimental, 2022, ISSN 2509-9280
Herausgeber: Springer
DOI: 10.1186/s41747-022-00281-1

"Supporting data for ""PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects"""

Autoren: Gonçalves IG; Hormuth II DA; Prabhakaran S; Phillips CM; García-Aznar JM
Veröffentlicht in: GigaByte, 2023, ISSN 2709-4715
Herausgeber: BGI and Oxford University Press
DOI: 10.46471/gigabyte.77

A finite element based optimization algorithm to include diffusion into the analysis of DCE-MRI

Autoren: Diego Sainz-DeMena; Wenfeng Ye; María Ángeles Pérez; José Manuel García-Aznar
Veröffentlicht in: Engineering with Computers, 2022, ISSN 0177-0667
Herausgeber: Springer Verlag
DOI: 10.1007/s00366-022-01667-w

Im2mesh: A Python Library to Reconstruct 3D Meshes from Scattered Data and 2D Segmentations, Application to Patient-Specific Neuroblastoma Tumour Image Sequences

Autoren: Diego Sainz-DeMena; José Manuel García-Aznar; María Ángeles Pérez; Carlos Borau
Veröffentlicht in: Applied Sciences, 2022, ISSN 2076-3417
Herausgeber: MDPI
DOI: 10.3390/app122211557

Finite element simulation of the structural integrity of endothelial cell monolayers: A step for tumor cell extravasation

Autoren: A. Nieto; Jorge Escribano; Fabian Spill; José Manuel García-Aznar; M. J. Gómez-Benito
Veröffentlicht in: Engineering Fracture Mechanics, Ausgabe 1, 2020, Seite(n) 106718, ISSN 0013-7944
Herausgeber: Pergamon Press Ltd.
DOI: 10.1016/j.engfracmech.2019.106718

Considerations for artificial intelligence clinical impact in oncologic imaging: an AI4HI position paper

Autoren: Luis Marti-Bonmati; Dow-Mu Koh; Katrine Riklund; Maciej Bobowicz; Yiannis Roussakis; Joan C. Vilanova; Jurgen J. Fütterer; Jordi Rimola; Pedro Mallol; Gloria Ribas; Ana Miguel; Manolis Tsiknakis; Karim Lekadir; Gianna Tsakou
Veröffentlicht in: Insights Into Imaging, 2022, ISSN 1869-4101
Herausgeber: Springer Science and Business Media Deutschland GmbH
DOI: 10.1186/s13244-022-01220-9

MAIC–10 brief quality checklist for publications using artificial intelligence and medical images

Autoren: Leonor Cerdá-Alberich; Jimena Solana; Pedro Mallol; Gloria Ribas; Miguel García-Junco; Angel Alberich-Bayarri; Luis Marti-Bonmati
Veröffentlicht in: Insights into Imaging, 2023, ISSN 1869-4101
Herausgeber: Springer Science and Business Media Deutschland GmbH
DOI: 10.1186/s13244-022-01355-9

MR Denoising Increases Radiomic Biomarker Precision and Reproducibility in Oncologic Imaging

Autoren: Matías Fernández Patón; Leonor Cerdá Alberich; Cinta Sangüesa Nebot; Blanca Martínez de las Heras; Diana Veiga Canuto; Adela Cañete Nieto; Luis Martí-Bonmatí
Veröffentlicht in: Journal of Digital Imaging, Ausgabe 6, 2021, Seite(n) 1134–1145, ISSN 0897-1889
Herausgeber: Springer Verlag
DOI: 10.1007/s10278-021-00512-8

A mechanistic protrusive-based model for 3D cell migration.

Autoren: Francisco Merino-Casallo; Maria Jose Gomez-Benito; Ruben Martinez-Cantin; Jose Manuel Garcia-Aznar
Veröffentlicht in: European Journal of Cell Biology, Ausgabe 1, 2022, ISSN 1618-1298
Herausgeber: Elsevier
DOI: 10.1016/j.ejcb.2022.151255

PRIMAGE project: predictive in silico multiscale analytics to support childhood cancer personalised evaluation empowered by imaging biomarkers

Autoren: Luis Martí-Bonmatí, Ángel Alberich-Bayarri, Ruth Ladenstein, Ignacio Blanquer, J. Damian Segrelles, Leonor Cerdá-Alberich, Polyxeni Gkontra, Barbara Hero, J. M. García-Aznar, Daniel Keim, Wolfgang Jentner, Karine Seymour, Ana Jiménez-Pastor, Ismael González-Valverde, Blanca Martínez de las Heras, Samira Essiaf, Dawn Walker, Michel Rochette, Marian Bubak, Jordi Mestres, Marco Viceconti, Gra
Veröffentlicht in: European Radiology Experimental, Ausgabe 4/1, 2020, ISSN 2509-9280
Herausgeber: European Radiology Experimental
DOI: 10.1186/s41747-020-00150-9

Integration of imaging biomarkers into systems biomedicine: a renaissance for medical imaging

Autoren: Giovanni Lucignani; Emanuele Neri
Veröffentlicht in: Clinical and Translational Imaging, Ausgabe 1, 2019, ISSN 2281-5872
Herausgeber: Springer
DOI: 10.1007/s40336-019-00320-9

A theoretical analysis of the scale separation in a model to predict solid tumour growth

Autoren: Bárbara de Melo Quintela, Silvia Hervas-Raluy, Jose Manuel Garcia-Aznar, Dawn Walker, Kenneth Y. Wertheim, Marco Viceconti,
Veröffentlicht in: Journal of Theoretical Biology, 2022, ISSN 0022-5193
Herausgeber: Academic Press

Independent Validation of a Deep Learning nnU-Net Tool for Neuroblastoma Detection and Segmentation in MR Images

Autoren: Diana Veiga-Canuto; Leonor Cerdà-Alberich; Ana Jiménez-Pastor; José Miguel Carot Sierra; Armando Gomis-Maya; Cinta Sangüesa-Nebot; Matías Fernández-Patón; Blanca Martínez de las Heras; Sabine Taschner-Mandl; Vanessa Düster; Ulrike Pötschger; Thorsten Simon; Emanuele Neri; Ángel Alberich-Bayarri; Adela Cañete; Barbara Hero; Ruth Ladenstein; Luis Martí-Bonmatí
Veröffentlicht in: Cancers, Ausgabe Volume 15; Ausgabe 5, 2023, Seite(n) 1622, ISSN 2072-6694
Herausgeber: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers15051622

Credibility of In Silico Trial Technologies—A Theoretical Framing

Autoren: Viceconti, Marco; Juarez, Miguel A.; Curreli, Cristina; Pennisi, Marzio; Russo, Giulia; Pappalardo, Francesco
Veröffentlicht in: IEEE Journal of Biomedical and Health Informatics, Ausgabe 3, 2019, ISSN 2168-2194
Herausgeber: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/jbhi.2019.2949888

Effect of particularisation size on the accuracy and efficiency of a multiscale tumours’ growth model

Autoren: V. Varella, B de Melo Quintela, M. Kasztelnik, and M. Viceconti
Veröffentlicht in: International Journal for Numerical Methods in Biomedical Engineering, 2022, ISSN 2040-7939
Herausgeber: John Wiley & Sons Ltd.
DOI: 10.1002/cnm.3657

Mathematical Model of Clonal Evolution Proposes a Personalised Multi-Modal Therapy for High-Risk Neuroblastoma

Autoren: Italia, M.; Wertheim, K.Y.; Taschner-Mandl, S.; Walker, D.; Dercole, F.
Veröffentlicht in: Cancers, 2023, ISSN 2072-6694
Herausgeber: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers15071986

Mechanical modeling of lung alveoli: From macroscopic behaviour to cell mechano-sensing at microscopic level

Autoren: Daniel Navajas; José Manuel Garcia-Aznar; Gabriel Beltran
Veröffentlicht in: Journal of the Mechanical Behavior of Biomedical Materials, 2022, ISSN 1751-6161
Herausgeber: Elsevier BV
DOI: 10.1016/j.jmbbm.2021.105043

Extracellular matrix density regulates the formation of tumour spheroids through cell migration

Autoren: Inês G. Gonçalves; José Manuel Garcia-Aznar
Veröffentlicht in: PLoS Computational Biology, Ausgabe 8, 2021, ISSN 1553-734X
Herausgeber: Public Library of Science
DOI: 10.1371/journal.pcbi.1008764

A Confidence Habitats Methodology in MR Quantitative Diffusion for the Classification of Neuroblastic Tumors.

Autoren: Leonor Cerdá Alberich; Cinta Sangüesa Nebot; Angel Alberich-Bayarri; José Miguel Carot Sierra; Blanca Martínez de las Heras; Diana Veiga Canuto; Adela Cañete; Luis Martí-Bonmatí
Veröffentlicht in: Cancers, Ausgabe 3, 2020, Seite(n) 3858, ISSN 2072-6694
Herausgeber: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers12123858

Tumour growth: An approach to calibrate parameters of a multiphase porous media model based on in vitro observations of Neuroblastoma spheroid growth in a hydrogel microenvironment

Autoren: Silvia Hervas-Raluy; Barbara Wirthl; Pedro E. Guerrero; Gil Robalo Rei; Jonas Nitzler; Esther Coronado; Jaime Font de Mora Sainz; Bernhard A. Schrefler; Maria Jose Gomez-Benito; Jose Manuel Garcia-Aznar; Wolfgang A. Wall
Veröffentlicht in: Computers in Biology and Medicine, 2023, ISSN 1879-0534
Herausgeber: Elsevier
DOI: 10.1016/j.compbiomed.2023.106895

The EurValve model execution environment.

Autoren: Marian Bubak; K. Czechowicz; Tomasz Gubała; D. R. Hose; Marek Kasztelnik; Maciej Malawski; Jan Meizner; Piotr Nowakowski; S. Wood
Veröffentlicht in: Interface Focus, Ausgabe 5, 2021, ISSN 2042-8898
Herausgeber: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0006

a report on the experiences of five EU projects

Autoren: Haridimos Kondylakis; Varvara Kalokyri; Stelios Sfakianakis; Kostas Marias; Manolis Tsiknakis; Ana Jimenez-Pastor; Eduardo Camacho-Ramos; Ignacio Blanquer; J. Damian Segrelles; Sergio López-Huguet; Caroline Barelle; Magdalena Kogut-Czarkowska; Gianna Tsakou; Nikolaos Siopis; Zisis Sakellariou; Paschalis Bizopoulos; Vicky Drossou; Antonios Lalas; Konstantinos Votis; Pedro Mallol; Luis Marti-Bonmat
Veröffentlicht in: European radiology experimental, Ausgabe 3, 2023, ISSN 2509-9280
Herausgeber: Springer Open
DOI: 10.1186/s41747-023-00336-x

APRICOT: Advanced Platform for Reproducible Infrastructures in the Cloud via Open Tools.

Autoren: V. Giménez-Alventosa; José Damián Segrelles; Germán Moltó; Mar Roca-Sogorb
Veröffentlicht in: Methods of Information in Medicine, Ausgabe 2, 2020, Seite(n) e33-e45, ISSN 0026-1270
Herausgeber: Schattauer
DOI: 10.1055/s-0040-1712460

SpatialRugs: A compact visualization of space and time for analyzing collective movement data

Autoren: Juri F. Buchmüller; Udo Schlegel; Eren Cakmak; Daniel A. Keim; Evanthia Dimara
Veröffentlicht in: Computers & Graphics, Ausgabe 1, 2021, ISSN 0097-8493
Herausgeber: Pergamon Press Ltd.
DOI: 10.1016/j.cag.2021.08.003

Time Series Model Attribution Visualisations as Explanations

Autoren: Udo Schlegel, Daniel A. Keim
Veröffentlicht in: Workshop on Trust and Expertise in Visual Analytics (TREX) at IEEE Visualization Conference (VIS), 2021
Herausgeber: Cornell University
DOI: 10.1109/trex53765.2021.00010

TS-MULE: Local Interpretable Model-Agnostic Explanations for Time Series Forecast Models

Autoren: Udo Schlegel, Duy Vo Lam, Daniel A. Keim, Daniel Seebacher
Veröffentlicht in: Advances in Interpretable Machine Learning and Artificial Intelligence (AIMLAI) at ECML/PKDD 2021, 2021
Herausgeber: Cornell University

Herramienta de apoyo para cáncer pediátrico

Autoren: Hervas-Raluy, Silvia; Sainz de Mena, Diego; Gómez Benito, Mª José; García-Aznar, José Manuel
Veröffentlicht in: Jornada De Jóvenes Investigadores E Investigadoras Del I3A, 2022
Herausgeber: Jornada De Jóvenes Investigadores E Investigadoras Del I3A
DOI: 10.26754/jjii3a.20226993

Orchestration of multiscale models for computational oncology

Autoren: Varella, Vinicius
Veröffentlicht in: 2023
Herausgeber: University of Bolognia
DOI: 10.5281/zenodo.8025198

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