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Engineering and Computational Science for Oncology Network (ECSON)

The general objective of the ECSON network is to create an effective research focus around medical data analysis, with the network functioning as a hub to co-ordinate an effective, regulated flow of knowledge, people and data between, academic and clinical institutions, and liaise with interested equipment suppliers.

For more information about the network please contact Professor Bogdan Matuszewski.

ECSON Cell Segmentation

Facts

Engineering and Computational Science for Oncology Network (ECSON) stem from a research project funded by the UK Engineering and Physical Sciences Research Council (grant No. EP/F013698/1) under “Collaboration for Success through People” call. The project was hosted by the University of Central Lancashire and run within the School of Computing, Engineering and Physical Sciences in ADSIP research centre in partnership with the Christie Hospital NHS Foundation Trust and General Engineering Research Institute at the Liverpool John Moorse University.

Project start date: 1 October 2007

Project end date: 31 March 2009

Principle Investigator

Co-investigators

Project Collaborators

  • Dr Gregoire Malandain, INRIA, Sophia-Antipolis, France.
  • Dr Mariusz Duplaga, Department of Scientific Information, Institute of Public Health, Jagiellonian University Collegium Medicum, Kraków, Poland.
  • Prof. Ayoub Al-Hamadi, Dr Gerald Krell, Prof. Bernd Michaelis; Institute for Electronics Signal Processing and Communications (IESK) in Otto von Guericke Universität Magdeburg, Germany
  • Dr Aymeric Histace, Prof. Sylvie Philipp-Foliguet, Prof. Frédéric Precioso; IMAGE section of the Signal and Image Processing research laboratory ETIS-CNRS, Université de Cergy-Pontoise, Paris, France
  • Prof. Ovidio Salvetti, Signals and Images Laboratory at the Institute of Information Science and Technologies - Italian National Research Council (ISTI-CNR), Italy
  • Prof. Behzad Shariat, Research Centre for Images and Intelligent Information Systems (LIRIS-CRNS), Université Claude Bernard Lyon 1, Lyon, France.
  • Prof. Tomasz Zieliński, AGH University of Science and Technology, Kraków, Poland.
  • 3dMD, 3D medical dynamic surface measurements.

Following the completion of the EPSRC funded project, the ECSON network has continued to be active. Over the years the network has engaged with numerous academic, clinical and industrial institutions. The network has been instrumental in facilitating academic exchanges, research activities, knowledge transfer and provided platform for research funding applications.

Objectives

  • Objective of supporting: There exist a number of different scientific approaches to similar medical data analysis problems. Advantages should be taken through the network activities to gain knowledge of other methodologies, to exchange test data and results, and to undertake comparative performance evaluation.
  • Objective of complementing: In recognition of the complementary and high calibre research work carried out by the collaborating organizations and their different clinical focuses, the network should concentrate on transfer of their respective scientific knowledge and distinctive expertise through different activities for adoption and adaptation to improve outcomes and broaden outputs of the research carried by different collaborating organizations.
  • Objective of extending: Building on previously developed tools by the network partners (e.g. high precision optical sensors, low-dose cone beam imaging and anatomy based deformation models) the network should work towards extending the underling science and technologies for new clinical applications, investigating its effectiveness on different modalities of data and considering different anatomical sites.
  • Objective of utilizing: The collaborating organizations form a solid base which should enable the formation of a strong partnership to make use of the developed methodologies and technologies in other medical treatments and to attract further partners. The network activities should provide an excellent breeding ground for cross-fertilisation of ideas, and to enable the development of an engineering and computational science road-map for medical data analysis e.g. through support of joint projects.
  • Objective of research training: Opportunities are provided through the proposed activities to allow a number of bright researchers to work at different organizations for a short period of time thereby enabling them to gain additional, multidisciplinary research experience in a different culture and environment, and training them to become future leaders of research in this field. Opportunities are also provided for other research students of the consortium to benefit from the visiting experts via the invited seminar/lecture series.

News

2016

  • 14-15 December - UCLan team to participate in the SEMEOTICONS project showcase in Pisa.
  • July/August – 3 MSc students form Nice – Sophia Antipolis University work on the “Circuit Reconstruction from Electron Microscopy Images” project as part of a summer internship at UCLan.
  • 21-23 February – ECSON partners co-organise special session on Smart Embedded Biomedical Devices for In Situ Physiological Signal Processing – Smart – BIODEV 2016 at the 9th International Conference on Bio-Inspired Systems and Signal Processing BIOSIGNALS, Rome, Italy,

2015

  • 26-28 October – International Workshop on Big Data and Smart Sustainable Society at the 14th IEEE International Conference on Ubiquitous Computing and Communications (IUCC-2015), Liverpool, UK.
  • 9 October - Joint UCLan/Nice team participates in the MICCAI’s “EndoVis: Endoscopic Vision” Challenge.
  • 5 October – UCLan team participates in the MICCAI’s “GlaS: Gland Segmentation in Colon Histology Images” Challenge.

2014

  • 27-28 October - International Symposium on Biomaterials and Smart Systems: Towards Repair of Human Body, Cergy-Pontoise, France
  • 18 September - UCLan team participates in the MICCAI 2014 MACHINE LEARNING CHALLENGE (MLC): Predicting Binary and Continuous Phenotypes from Structural Brain MRI Data.
  • 27 March 2014- ECSON participated in the EPSRC Network of Networks meeting

  • 5 March 2014- Dr Bartłomiej Papież from the Institute of Biomedical Engineering at the University of Oxford visits UCLan

2013

  • 5 - 6 December 2013- "SEMEiotic Oriented Technology for Individual’s CardiOmetabolic risk self-assessment and Self-monitoring SEMEOTICONS" project Kick-off meeting in Pisa, Italy

  • 28 November – Dr Leila Meziou defended her PhD entitled “Active contour segmentation based on alpha-divergences: application to medical and biomedical image segmentation”

  • 1 November- FP7 funded “SEMEiotic Oriented Technology for Individual’s CardiOmetabolic risk self-assessment and Self-monitoring SEMEOTICONS” project has started.

  • June – 3 MSc students form Nice – Sophia Antipolis University (France) start work on “Mitosis Detection” project as part of their summer internship at UCLan.

  • 13-16 May - Professor Arvid Lundervold from University of Bergen (Norway) visits UCLan under Distinguished Visitor Programme

  • 13-15 May – Dr Aymeric Histace from Cergy-Pontoise University visits UCLan

  • 11 January – Ms H. Gao defended her MPhil Thesis entitled “Segmentation of Cell Structures in Fluorescence Confocal Microscopy Images”

2012

  • 15 September – Ms E. Bonnefoye defended her final year MSc project on "3D segmentation of RV in Cine Cardiac MRI"

  • 25 June – Dr Bartłomiej Papież defended his PhD Thesis entitled “Diffeomorphic Image Registration with Applications to Deformation Modelling between Multiple Data Sets”

  • July – Ms Leila Meziou received the "Best Student Paper Award" at the MIUA12 conference for the paper entitled "Fractional entropy based active contour for nuclei cell segmentation in 3D confocal microscopy images"

  • June – 2 MSc students form Nice – Sophia Antipolis University started work on “Coronary Artery Stenosis Detection” project as part of their summer internship at UCLan.

  • April - Mr E. Bonnefoye from ETIS (University of Cergy-Pontoise) started her five-months MSc student placement at UCLan.

  • 10-13 April - Dr Aymeric Histace from Cergy-Pontoise University visited UCLan

  • 17 January- F.Precioso and B.Matuszewski participated in the MedViz Conference, Bergen , Norway.

2011

  • 22-23 June- International Workshop on Image Processing Techniques and Applications, Centre for Mathematical Imaging Techniques, Liverpool University.
  • 11-14 September- Special Session at the ICIP2011
    ECSON partners co-organised special session on "Analysis of microscopy and reconstructive images for applications in medicine and biology" at the ICIP2011 Conference

  • 14-28 March - Ms Leila Meziou from Cergy-Pontoise University visit in UCLan

  • 16-19 March - Dr Aymeric Histace from Cergy-Pontoise University visit UCLan

2010

  • December – Dr Bogdan Matuszewski visits IESK at the Otto Von Guericke University

  • September – Dr Bogdan Matuszewski visits ETIS lab CNRS at the ENSEA- University of Cery-Pontoise

  • 16 September – Mr Piotr Urban defended his PhD Thesis entitled “Deformable Object Modelling and Estimation for Metrology Guided Radiation Therapy”

  • May – Dr Bogdan Matuszewski visits ETIS lab CNRS at the ENSEA- University of Cery-Pontoise

  • 17-21 May- Special session for Engineering and Computational Sciences for Medical Image in Oncology (ECSMIO) at International Conference on Computer Vision Theory and Applications 2010, Angers, France.

2009

  • 20 August- Ms Marine Breuilly defended her final year engineering project on "Investigation of medical active contour image segmentation techniques"
  • 10 June- Prof. Emanuele Trucco seminar at UCLan
  • 27 April- ECSON partners from ENSEA visiting UCLan

  • April- Ms Marine Breuilly from ENSEA (ETIS) and Mr Bartek Papiez from AGH University started their five and three months placements at UCLan

  • 16-18 March- ECSON Meeting in Magdeburg, Germany
  • 15-17 January- ECSON project workshop in Mottram Hall, Near Manchester
  • 14 January- Dr. Davide Moroni Seminar at the University of Central Lancashire

  • 14 January- Dr. Gerald Krell Seminar at the University of Central Lancashire

2008

  • 31 October- ECSON partners and collaborators meeting in Pisa (ISTI CNR), Italy
  • 10 September- ECSON partners meeting at the Cergy-Pontoise University (ETIS), France
  • 8 May- ECSON partners meeting at the University of Central Lancashire

  • 12-14 March- ECSON meeting at University Claude Bernard, Lyon, France

  • 18-22 February- ECSON meeting at Holy Cross Hospital, Kielce, Poland and at the AGH University of Science and Technology, and the Jagiellonian University, Krakow, Poland

  • 23 January- Prof. C. Moore Seminar
  • 23 January- ECSON partners meeting at the University of Central Lancashire

2007

  • 26 October- ECSON partners meeting at Christie Hospital
  • 25-26 October- Prof. T. Zieliński and Dr M. Duplaga visit ECSON partners
  • 3 October- ECSON partners meeting at Liverpool John Moores University

  • 3 September- Tutorial at 2007 Eusipco Conference

  • 30-31 August- Visit at AGH University of Science and Technology

Seminars

Dr Peter Dunne
“Deep auto-encoder networks using Restricted Boltzmann Machines”, 3 August 2016, Computer Vision and Machine Learning Research Group, University of Central Lancashire

Dr Liangxiu Han
School of Computing, Mathematics & Digital Technology, Future Networks and Distributed Systems (FUNDS) Research Group, Manchester Metropolitan University, “Large-scale data processing and analytics in images and its applications in BioScience”, 22 April 2015, Computer Vision and Machine Learning Research Group, University of Central Lancashire

Dr Bartłomiej Papież
Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, “Recent work on complex lung motion via deformable image registration with an adaptive filtering of the deformation field” 5 March 2014, Robotics and Computer Vision Research Laboratory, University of Central Lancashire, Preston.

Prof Arvid Lundervold
Department of Biomedicine, Neuroinformatics and Image Analysis Laboratory & Molecular Imaging Center, Bergen fMRI Group; University of Bergen & Department of Radiology Haukeland University Hospital, “Quantitative medical imaging in health research - impact on the study of cognitive aging”, “Health Research with Real Impact’ Conference, 15 May 2013, University of Central Lancashire

Prof Arvid Lundervold
Department of Biomedicine, Neuroinformatics and Image Analysis Laboratory & Molecular Imaging Center, Bergen fMRI Group; University of Bergen & Department of Radiology Haukeland University Hospital, “Imaging of connections in brains and cells - the role of graph theory and network analysis”, 13 May 2013, Distinguished Visitor Programme Seminar, University of Central Lancashire

Dr Aymeric Histace
ETIS lab, University of Cergy-Pontoise, "Histogram-based segmentation with extremization of alpha-divergences: application to medical and biomedical image segmentation", 11 April 2012, UCLan, Preston,

Dr Bogdan Matuszewski
Digital Signal and Image Processing (ADSIP) Research Centre, University of Central Lancashire, “Cellular Structures Segmentation in Fluorescence Confocal Microscopy Images”, September 2011, Liverpool John Moores University.

Dr Bogdan Matuszewski
Digital Signal and Image Processing (ADSIP) Research Centre, University of Central Lancashire, “Medical Image Segmentation with Prior-Shape Knowledge”, 22-13 June 2011, International Workshop on Image Processing Techniques and Applications, Liverpool University.

Leila Meziou and Dr Aymeric Histace
ETIS lab, University of Cergy-Pontoise, “Active contour segmentation with application to medical and biomedical image segmentation”, March 2011, Digital Signal and Image Processing (ADSIP) Research Centre, University of Central Lancashire, Preston

Dr Frederic Precioso
ETIS lab, University of Cergy-Pontoise, “Machine learning techniques for image and video content analysis”, 15th of October 2010, UCLan, Preston

Dr Aymeric Histace
ETIS lab, University of Cergy-Pontoise, "Boosting from the medical image analysis perspective", , 14th October 2010, UCLan, Preston

Dr Bogdan Matuszewski
Digital Signal and Image Processing (ADSIP) Research Centre, University of Central Lancashire, “Facial Articulation and Body Posture Analysis”, 13 December 2010, Otto von-Guericke University, Magdeburg, Germany.

Dr Bogdan Matuszewski
Digital Signal and Image Processing (ADSIP) Research Centre, University of Central Lancashire, “Facial Articulation and Body Posture Analysis”, 13 December 2010, Otto von-Guericke University, Magdeburg, Germany.

Dr Bogdan Matuszewski
Digital Signal and Image Processing (ADSIP) Research Centre, University of Central Lancashire, “Deformable Models in Medical Computer Vision”, 7 September 2010, ETIS ENSEA-University of Cergy Pontoise, France.

Prof. Emanuele Trucco
School of Computing, University of Dundee, "Computer Vision Research at the University of Dundee: Human Motion Capture and Retinal Image Analysis", 10 June 2009, UCLan.

Dr. Frédéric Precioso and Dr. Aymeric Histace
Signal and Image Processing Research Laboratory (ETIS), ENSEA, University of Cergy-Pontoise, France, "Active Contours: From Basic to Recent Advances in Medical Imaging", 27 April 2009, UCLan.

Dr. Davide Moroni
Signal and System Laboratory, Institute of Information Science and Technologies (ISTI), CNR Pisa, Italy, "Image Segmentation, 3D Geometry and Shape Matching", 14 January 2009, UCLan.

Dr. Gerald Krell
Institute for Electronics Signal Processing and Communications (IESK), Otto-von-Guericke University, Magdeburg, Germany, "From Low Level Image Processing to Motion and Emotion Analysis – Selected Applications in Medicine, Biology and Industry", 14 January 2009, UCLan.

Dr. Bogdan Matuszewski
Applied Digital Signal and Image Processing (ADSIP) Research Centre, University of Central Lancashire, "Notes on Deformable Segmentation, Registration and Tracking", 11 December 2008, Otto-von-Guericke University, Germany.

Dr. Bogdan Matuszewski
Applied Digital Signal and Image Processing (ADSIP) Research Centre, University of Central Lancashire, "Medical Computer Vision and the ECSON Project", 21 July 2008, Signal and Image Processing Research Laboratory (ETIS), ENSEA, University of Cergy-Pontoise, France.

Prof. Lik-Kwan Shark and Dr. Bogdan Matuszewski
Applied Digital Signal and Image Processing (ADSIP) Research Centre, University of Central Lancashire, "Introduction to ECSON Project", 7 July 2008, Signal and System Laboratory, Institute of Information Science and Technologies (ISTI), CNR Pisa, Italy.

Prof. Christopher Moore
North Western Medical Physics, The Christie NHS Foundation Trust, "Combining X-rays and Light for a Dynamic View in Image Guided Radiation Therapy", 23 January 2008, UCLan.

Prof. Tomasz Zieliński (1) and Dr. Mariusz Duplaga (2)
(1)Telemedicine Group, Department of Telecommunication AGH University of Science and Technology, Krakow, Poland, (2) Department of Scientific Information, Institute of Public Health Jagiellonian University Collegium Medicum, Krakow, Poland, "Image and Video Processing Tasks in Computer Aided Medical Intervention on the Example of Transbronchial Biopsy", 25 October 2007, UCLan.

Dr. Bogdan Matuszewski
Applied Digital Signal and Image Processing (ADSIP) Research Centre, University of Central Lancashire, "Deformable Models in Medical Image Processing", 1 September 2007, AHG University of Science and Technology, Krakow, Poland.

RESOURCES

The ECSON network has been instrumental in developing number of medial image analysis software and hardware systems:

The software tools originated from the ECSON network include:

  • Hybrid level set based segmentation
  • Interactive level set segmentation
  • Level set segmentation with topological constraints 
  • Level set segmentation with shape priors
  • Approximate entropy level set segmentation
  • Deformable 2D/3D image registration toolkit
  • Phase unwrappers for 3D surface reconstruction
  • Fiducial markers tracking in CT projection images
  • Surface registration for radiotherapy patient positioning 
  • Patient position monitoring
  • Deformable surface characterisation

The hardware systems originated from the ECSON network include:

  • Multi-projector fringe projection wraparound surface reconstruction
  • Real-time in treatment patient position monitoring
  • Real-time head position tracking

Funding

The ECSON network has been instrumental in securing following research funding:

  • SEMEiotic Oriented Technology for Individual’s CardiOmetabolic risk self-assessmeNt and Self-monitoring (SEMEOTICONS); funded by EC 7th Framework, FP7-ICT-2013-10, Project No. 611516; 2013-2016; project partners: UCLan, CNR (Italy), Foundation for Research and Technology – FORTH (Greece), Linköping University (Sweden), Norwegian University of Science and Technology Trondheim NTNU (Norway), CRNH (France), INTECS SPA (Italy), Hellenic Telecommunications & Telematics Applications Company - FORTHNET (Greece), DRACO Systems SL (Spain), COSMED SRL (Italy); Total project value €5,383,126.
  • 3DCell; funded by ENSEA Scientific Council; 2012; project partners: ETIS CRNS Laboratory at ENSEA Cergy-Pontoise University (France), UCLan; total project value 5k€.
  • Dynamic Real-Time Three Dimensional Surface Sensor for Biomedical and Biometrics Applications; funded by UCLan’s Research Equipment Development (RED) Fund; 2009-2010; total project value £65,000.
  • Technology in Radiotherapy Feasibility Studies (TeRaFS); funded by EPSRC grant under the Cross-Disciplinary Feasibility Account, Grant No. EP/H024913/1; 2009-2011; project partners: UCLan, Christie Hospital; Liverpool John Moores University, Rosemere Cancer Centre at the Royal Preston Hospital; ETIS CRNS Laboratory at ENSEA Cergy-Pontoise University (France); Otto von Guericke Universität Magdeburg (Germany); total project value: £201,041.
  • BIOMICMAC; funded by ENSEA Scientific Council; 2010; project partners: ETIS CNRS Laboratory at ENSEA Cergy-Pontoise University (France), UCLan; total project value 10k€.
  • ENSEA and ADSIP research exchange programme; funded by ENSEA Scientific Council; 2009; project partners: ETIS CNRS Laboratory at ENSEA Cergy-Pontoise University (France), UCLan; total project value 5k€-.