Cancer

Cancer

I have significant experience in analysing data from cancer-related experiments as observed with a variety of techniques; from light microscopy to fluorescence to multiphoton microscopy to electron microscopy.

Many of the experiments were conducted in animal models in dorsal skin chambers, which allow in vivo repeated observations. Others were from tissue extracted and immunostained for CD31, H&E and other stains.

I have also done volumetric analysis of cells as observed with electron microscopy. These images allow an exquisite detail to be observed in the cells and the three dimensional approach provides very interesting details of cells that are lost when only one slice is observed.

Besides images, I have also done data mining of PubMed and other databases to analyse the changes in research. Interestingly, cancer-related publications have grown from 6% to more than 16% in 70 years.

Research in this area is closely related to Microcirculation and Cell Migration; please explore the other research pages and the publications below.

Team members:

Cefa Karabağ

Lecturer in Computer Science

Kokeb Dese Gebremeskel

PhD Student
Alumni, City, University of London

Mauricio Alberto Ortega-Ruiz

PhD Student
City, University of London

Youssef Arafat

PhD Student
City, University of London

Tengfei Yin

PhD Student
Alumni, University of Sussex

Collaborators:

Chryso Kanthou

School of Medicine, University of Sheffield

Francesco Bianconi

Department of Engineering at the Università degli Studi di Perugia, Italy

Greg Slabaugh

Director of the Digital Environment Research Institute, Queen Mary, University of London

Gillian Tozer

School of Medicine, University of Sheffield

Helfrid Hochegger

Genome Damage and Stability Centre, University of Sussex

Jakob Nikolas Kather

University Hospital RWTH Aachen and German Cancer Research

Lucy Collinson

Electron Microscopy Science Technology Platform, Francis Crick Institute, UK

Martin Jones

Electron Microscopy Science Technology Platform, Francis Crick Institute, UK

Publications:

DRD-UNet, a UNet-like architecture for multi-class breast cancer semantic segmentation Mauricio Alberto Ortega-Ruiz, Cefa Karabağ, Edgar Roman-Rangel, Constantino Carlos Reyes-Aldasoro Published in IEEE Access, March 2024 (see publication) Research themes: Cancer, Machine Learning, AI, Deep Learning, Microscopy Type: Paper

Modelling the Tumour Microenvironment, but What Exactly Do We Mean by “Model”? Constantino Carlos Reyes-Aldasoro Published in Cancers, July 2023 (see publication) Research themes: Cancer Type: Paper

Modelling the Tumour Microenvironment, but What Exactly Do We Mean by “Model”? Constantino Carlos Reyes-Aldasoro Published in PrePrints, June 2023 (see publication) Research themes: Cancer Type: Pre-print

Impact of Training Data, Ground Truth and Shape Variability in the Deep Learning-Based Semantic Segmentation of HeLa Cells Observed with Electron Microscopy Cefa Karabağ, Mauricio Alberto Ortega-Ruíz, Constantino Carlos Reyes-Aldasoro" Published in Journal of Imaging, March 2023 (see publication) Research themes: Cancer, Machine Learning, AI, Deep Learning, Microscopy Type: Paper

Computational Image Analysis Techniques, Programming Languages and Software Platforms Used in Cancer Research: A Scoping Review Youssef Arafat, Constantino Carlos Reyes-Aldasoro" Published in Lecture Notes in Computer Science, July 2022 (see publication) Research themes: Cancer, Machine Learning, AI, Deep Learning, Medical Imaging, Microscopy Type: Paper

Special Issue on Computational Pathology: An Overview Anant Madabhushi, Constantino Carlos Reyes-Aldasoro Published in Medical Image Analysis, June 2021 (see publication) Research themes: Cancer, Machine Learning, AI, Deep Learning, Microscopy Type: Paper

Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells Cefa Karabağ, Martin L. Jones, Constantino Carlos Reyes-Aldasoro" Published in Journal of Imaging, June 2021 (see publication) Research themes: Cancer, Machine Learning, AI, Deep Learning, Microscopy Type: Paper

Experimental Assessment of Color Deconvolution and Color Normalization for Automated Classification of Histology Images Stained with Hematoxylin and Eosin Francesco Bianconi, Jakob N. Kather, Constantino Carlos Reyes-Aldasoro Published in Cancers, November 2020 (see publication) Research themes: Cancer Type: Paper

Morphological Estimation of Cellularity on Neo-Adjuvant Treated Breast Cancer Histological Images Mauricio Alberto Ortega-Ruiz, Cefa Karabağ, Victor García Garduño, Constantino Carlos Reyes-Aldasoro Published in Journal of Imaging, October 2020 (see publication) Research themes: Cancer, Machine Learning, AI, Deep Learning, Microscopy Type: Paper

Semantic segmentation of HeLa cells An objective comparison between one traditional algorithm and four deep-learning architectures Cefa Karabağ, Martin Jones, Christopher J. Peddie, Anne E Weston, Lucy M Collinson, Constantino Carlos Reyes-Aldasoro" Published in PLoS ONE, October 2020 (see publication) Research themes: Cancer, Machine Learning, AI, Deep Learning, Microscopy Type: Paper

Prophase-Specific Perinuclear Actin Coordinates Centrosome Separation and Positioning to Ensure Accurate Chromosome Segregation Tom Stiff, Fabio R. Echegaray-Iturra, Harry J. Pink, Alex Herbert, Constantino Carlos Reyes-Aldasoro, Helfrid Hochegger Published in Cell Reports, May 2020 (see publication) Research themes: Cancer Type: Paper

Geometric differences between nuclear envelopes of Wild-type and Chlamydia trachomatis-infected HeLa cells Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-Aldasoro, Published in bioRxiv, April 2020 (see publication) Research themes: Cancer, Machine Learning, AI, Deep Learning, Microscopy Type: Pre-print

Segmentation and Modelling of the Nuclear Envelope of HeLa Cells Imaged with Serial Block Face Scanning Electron Microscopy Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Reyes-Aldasoro, Constantino Carlos Published in Journal of Imaging, September 2019 (see publication) Research themes: Cancer Type: Paper

Segmentation And Modelling of HeLa Nuclear Envelope C. Karabağ, M.L. Jones, C.J. Peddie, A.E. Weston, L.M. Collinson, C.C. Reyes-Aldasoro Published in ISBI, April 2019 (see publication) Research themes: Cancer, Medical Imaging Type: Conference

Predicting survival from colorectal cancer histology slides using deep learning A retrospective multicenter study Jakob Nikolas Kather, Johannes Krisam, Pornpimol Charoentong, Tom Luedde, Esther Herpel, Cleo-Aron Weis, Timo Gaiser, Alexander Marx, Nektarios A. Valous, Dyke Ferber, Lina Jansen, Constantino Carlos Reyes-Aldasoro, Inka Zörnig, Dirk Jäger, Hermann Brenner, Jenny Chang-Claude, Michael Hoffmeister, Niels Halama Published in PLoS Medicine, January 2019 (see publication) Research themes: Cancer, Machine Learning, AI, Deep Learning, Microscopy Type: Paper

Guest Editorial: Computer Vision in Cancer Data Analysis Greg Slabaugh, Constantino Carlos Reyes-Aldasoro Published in IET Computer Vision, November 2018 (see publication) Research themes: Cancer, Medical Imaging Type: Editorial

Large-scale database mining reveals hidden trends and future directions for cancer immunotherapy Jakob Nikolas Kather, Anna Sophie Berghoff, Dyke Ferber, Meggy Suarez-Carmona, Constantino Carlos Reyes-Aldasoro, Nektarios A. Valous, Rodrigo Rojas-Moraleda, Dirk Jäger, Niels Halama Published in Oncoimmunology, January 2018 (see publication) Research themes: Cancer Type: Paper

The proportion of cancer-related entries in PubMed has increased considerably; is cancer truly ‘The Emperor of All Maladies’? Constantino Carlos Reyes-Aldasoro Published in PLoS ONE, January 2017 (see publication) Research themes: Cancer Type: Paper

Mapping tumour tissue: quantitative maps of histological whole slide images Kather, N. J., Weis, C. A., Zöllner, F. G. & Reyes-Aldasoro, C. C Published in Oncology News, January 2016 (see publication) Research themes: Cancer Type: Paper

Continuous representation of tumor microvessel density and detection of angiogenic hotspots in histological whole-slide images Jakob Nikolas Kather, Alexander Marx, Constantino Carlos Reyes-Aldasoro, Schad, Lothar R. and Zöllner, Frank Gerrit and Weis, Cleo-Aron Published in Oncotarget, August 2015 (see publication) Research themes: Cancer Type: Paper

A Robust and Artifact Resistant Algorithm of Ultrawideband Imaging System for Breast Cancer Detection Tengfei Yin, Falah H. Ali, Constantino Carlos Reyes-Aldasoro Published in IEEE transactions on bio-medical engineering, June 2015 (see publication) Research themes: Cancer, Image Processing, Medical Imaging Type: Paper

An in vivo role for Rho kinase activation in the tumour vascular disrupting activity of combretastatin A-4 3-O-phosphate L.J. Williams, D. Mukherjee, M Fisher, C. C. Reyes-Aldasoro, S. Akerman, C. Kanthou, G.M. Tozer Published in British Journal of Pharmacology, November 2014 (see publication) Research themes: Cancer Type: Paper

Haemodynamics and Oxygenation of the Tumour Microcirculation Gillian M. Tozer, Rachel Daniel, Sarah Jane Lunt, Constantino C. Reyes-Aldasoro, Vincent J. Cunningham Published in Advances in Intravital Microscopy, September 2014 (see publication) Research themes: Cancer, Circulation Type: Book Chapter

Tumour cells expressing single VEGF isoforms display distinct growth, survival and migration characteristics Chryso Kanthou, Gabi U. Dachs, Diane V. Lefley, Andrew J. Steele, Claudia Coralli-Foxon, Sheila Harris, Olga Greco, Sofia A. Dos Santos, Constantino C. Reyes-Aldasoro, William R. English, Gillian M. Tozer Published in PLoS ONE, January 2014 (see publication) Research themes: Cancer, Cell Migration Type: Paper

Influence of soluble or matrix-bound isoforms of vascular endothelial growth factor-A on tumor response to vascular-targeted strategies Simon Akerman, Matthew Fisher, Rachel A. Daniel, Diane Lefley, Constantino C. Reyes-Aldasoro, Sarah Jane Lunt, Sheila Harris, Meit Bjorndahl, Leigh J. Williams, Helen Evans, Paul R. Barber, Vivien E. Prise, Borivoj Vojnovic, Chryso Kanthou, Gillian M. Tozer Published in International Journal of Cancer, December 2013 (see publication) Research themes: Cancer Type: Paper

Cancer Image Analysis Reyes-Aldasoro, C. C Published in Oncology News, November 2013 (see publication) Research themes: Cancer Type: Paper

Online chromatic and scale-space microvessel-tracing analysis for transmitted light optical images Constantino Carlos Reyes-Aldasoro, Meit A. Björndahl, Simon Akerman, Jamila Ibrahim, Michael K. Griffiths, Gillian M. Tozer Published in Microvascular Research, November 2012 (see publication) Research themes: Cancer, Circulation Type: Paper

Vascular effects dominate solid tumor response to treatment with combretastatin A-4-phosphate Sarah Jane Lunt, Simon Akerman, Sally A. Hill, Matthew Fisher, Victoria J. Wright, Constantino C. Reyes-Aldasoro, Gillian M. Tozer, Chryso Kanthou Published in International Journal of Cancer, October 2011 (see publication) Research themes: Cancer Type: Paper

Microflow of fluorescently labelled red blood cells in tumours expressing single isoforms of VEGF and their response to vascular targeting agents Simon Akerman, Constantino Carlos Reyes-Aldasoro, Matthew Fisher, Katie L. Pettyjohn, Meit A. Björndahl, Helen Evans, Gillian M. Tozer Published in Medical Engineering & Physics, September 2011 (see publication) Research themes: Cancer, Cell Migration, Circulation Type: Paper

CAIMAN an online algorithm repository for Cancer Image Analysis Constantino Carlos Reyes-Aldasoro, Michael K. Griffiths, Deniz Savas, Gillian M. Tozer Published in Computer Methods and Programs in Biomedicine, August 2011 (see publication) Research themes: Cancer, Circulation, Medical Imaging Type: Paper

An automatic algorithm for the segmentation and morphological analysis of microvessels in immunostained histological tumour sections C. C. Reyes-Aldasoro, L. J. Williams, S. Akerman, C. Kanthou, G. M. Tozer Published in Journal of Microscopy, June 2011 (see publication) Research themes: Cancer, Circulation Type: Paper

Application of intravital microscopy in studies of tumor microcirculation Sarah Jane Lunt, Colin Gray, Constantino Carlos Reyes-Aldasoro, Stephen J. Matcher, Gillian M. Tozer Published in Journal of Biomedical Optics, February 2010 (see publication) Research themes: Cancer, Cell Migration, Circulation Type: Paper

Measuring cellular migration with image processing C. C. Reyes-Aldasoro, D. Biram, G. M. Tozer, C. Kanthou Published in Electronics Letters, June 2008 (see publication) Research themes: Cancer, Cell Migration Type: Paper

Blood vessel maturation and response to vascular-disrupting therapy in single vascular endothelial growth factor-A isoform-producing tumors Gillian M. Tozer, Akerman, Simon and Cross, Neil A. and Barber, Paul R. and Björndahl, Meit A. and Greco, Olga and Harris, Sheila and Hill, Sally A. and Honess, Davina J. and Ireson, Christopher R. and Pettyjohn, Katie L. and Prise, Vivien E. and Reyes-Aldasoro, Constantino C. and Ruhrberg, Christiana and Shima, David T, Chryso Kanthou Published in Cancer Research, April 2008 (see publication) Research themes: Cancer, Circulation Type: Paper

Measuring the velocity of fluorescently labelled red blood cells with a keyhole tracking algorithm C. C. Reyes-Aldasoro, G. M. Tozer Published in Journal of Microscopy, January 2008 (see publication) Research themes: Cancer, Circulation Type: Paper

Estimation of apparent tumor vascular permeability from multiphoton fluorescence microscopic images of P22 rat sarcomas in vivo Constantino Carlos Reyes-Aldasoro, Ian Wilson, Vivien E. Prise, Paul R. Barber, M. Ameer-Beg, Borivoj Vojnovic, Vincent J. Cunningham, Gillian M. Tozer Published in Microcirculation, January 2008 (see publication) Research themes: Cancer, Cell Migration, Circulation Type: Paper