Shan E Ahmed Raza

Vita

03/2017 - Present
Post-Doctoral Training Fellow, Division of Molecular Pathology, the Institute of Cancer Research, London, UK
03/2014 - 03/2017
Research Fellow, Department of Computer Science, University of Warwick, UK
03/2011 - 03/2014
PhD, Computer Science, University of Warwick, UK
12/2008 - 11/2010
MS Systems Engineering, Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
10/2004 - 09/2008
BSc, Electrical Engineering, University of Engineering and Technology, Taxila, Pakistan

Teaching and Student Supervision Experience

Teaching Assistant

  • CS403 Multimedia Processing, Communications and Storage, University of Warwick, 2011/2012.
  • CS131 Mathematics for Computer Scientists II, University of Warwick, 2012/2013.

Co-Supervision

  • Guannan Li, PhD Student, Computer Science, University of Warwick, UK. (Graduated 2015-2016)
  • Najah Alsubaie, PhD Student, Computer Science, University of Warwick, UK. (2015-2017)
  • Nasim Kashif, MSc Student, Pakistan Institute of Engineering and Applied Sciences, Pakistan.(2016)

Publications

Journal papers

  1. G. Li, S.E.A. Raza , N.M. Rajpoot, "Multi-resolution cell orientation congruence descriptors for epithelium segmentation in endometrial histology images", Medical Image Analysis, 37, p. 91-100, Apr. 2017.
  2. N. Alsubaie, N. Trahearn, S.E.A. Raza , D. Snead, N.M. Rajpoot, "Stain Deconvolution using statistical analysis of multi-resolution stain colour representation", PLoS ONE, 12(1) p. e0169875, Jan. 2017.
  3. S.E.A. Raza , D. Langenkämper, K. Sirinukunwattana, D. Epstein, T. W. Nattkemper, and N. M. Rajpoot, "Robust normalization protocols for multiplexed fluorescence bioimage analysis," BMC BioData Mining, 9(1) p. 11, Dec 2016.
  4. K. Sirinukunwattana, S.E.A. Raza , Y.-W. Tsang, D. Snead, I. Cree, and N. Rajpoot, "Locality sensitive deep learning for detection and classification of nuclei in routine Colon cancer histology images," IEEE Transactions on Medical Imaging special issue on Deep Learning in Medical Imaging, 35(5) p. 1196-1206, May 2016.
  5. S.E.A. Raza , V. Sanchez, G. Prince, J. Clarkson, and N. M. Rajpoot, "Registration of thermal and visible light images of diseased plants using silhouette extraction in the wavelet domain," Pattern Recognition, 48 p. 2119-2128, 2015.
  6. S.E.A. Raza , G. Prince, J. Clarkson, and N. M. Rajpoot, "Automatic detection of diseased Tomato plants using thermal and stereo visible light images", PLoS ONE 10(4) p. e0123262, 2015.
  7. S.E.A. Raza , H. K. Smith, G. J. J. Clarkson, G. Taylor, J. Clarkson, and N. M. Rajpoot, "Automatic detection of regions in spinach canopies responding to soil moisture deficit using combined visible and thermal imagery.," PLoS ONE 9(6) p. e97612, 2014.
  8. S.E.A. Raza , A. Humayun, S. Abouna, T. W. Nattkemper, D. B. Epstein, M. Khan, and N. M. Rajpoot, "RAMTaB: Robust alignment of multi-tag bioimages," PLoS ONE, 7(2) p. e30894, 2012.
  9. A. M. Khan, S.E.A. Raza , M. Khan, and N. M. Rajpoot, "Cell phenotyping in multi-tag fluorescent bioimages," Neurocomputing 134 p. 254-261, Jun 2014.

Conference papers

  1. N. Alsubaie, K. Sirinukunwattana, S.E.A. Raza, D. Snead, N. M. Rajpoot, "A bottom-up approach for tumour differentiation in whole slide images of lung adenocarcinoma", in Medical Imaging: Digital Pathology, pp. 105810E, 2018.
  2. S.E.A. Raza, L. Cheung, D. Epstein, S. Pelengaris, M. Khan, N.M. Rajpoot, "MIMONet: Gland Segmentation Using Multi-Input-Multi-Output Convolutional Neural Network", in Medical Image Understanding and Analysis, MIUA, pp. 698-706, 2017.
  3. S.E.A. Raza , L. Cheung, D. Epstein, S. Pelengaris, M. Khan, N.M. Rajpoot, "Mimo-Net: A Multi-Input Multi-Output Convolutional Neural Network for Cell Segmentation in Fluorescence Microscopy Images", in 2016 IEEE International Symposium on Biomedical Imaging (ISBI), pp., 2017.
  4. M. N. Kashif, S.E.A. Raza , K. Sirinukunwattana, M. Arif, and N. Rajpoot, "Handcrafted features with convolutional neural networks for detection of tumor cells in histology images," in 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), pp. 1029-1032, 2016.
  5. N. Alsubaie, S.E.A. Raza , and N. Rajpoot, "Stain deconvolution of histology images via independent component analysis in the wavelet domain," in 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), pp. 803-806, 2016.
  6. K. Sirinukunwattana, S.E.A. Raza , Y.-W. Tsang, D. Snead, I. Cree, and N. Rajpoot, "A Spatially Constrained Deep Learning Framework for Detection of Epithelial Tumor Nuclei in Cancer Histology Images," in 1st International Workshop on Patch-based Techniques in Medical Imaging, MICCAI, pp. 154-162, 2015.
  7. G. Li, S.E.A. Raza , and N. Rajpoot, "A Novel Cell Orientation Congruence Descriptor for Superpixel Based Epithelium Segmentation in Endometrial Histology Images," in 1st International Workshop on Patch-based Techniques in Medical Imaging, MICCAI, pp. 172-179, 2015.
  8. S.E.A. Raza , N. M. Rajpoot, "Cell Nuclei Segmentation in Variable Intensity Fluorescence Microscopy Images", Medical Image Understanding and Analysis, MIUA, pp. 28-33, 2015.
  9. S.E.A. Raza , M. Q. Marjan, M. Arif, F. Butt, F. Sultan, and N. M. Rajpoot, "Anisotropic tubular filtering for automatic detection of acid-fast bacilli in Ziehl-Neelsen stained sputum smear samples," in SPIE Medical Imaging, 9420, p. 942005, 2015.
  10. N. Alsubaie, N. Trahearn, S.E.A. Raza , and N. M. Rajpoot, "A Discriminative Framework for Stain Deconvolution of Histopathology Images in the Maxwellian Space," in Medical Image Understanding and Analysis, MIUA, pp. 132-137, 2015.
  11. A. M. Khan, A. Humayun, S.E.A. Raza , M. Khan, and N. M. Rajpoot, "A novel paradigm for mining cell phenotypes in multi-tag Bioimages using a locality preserving nonlinear embedding," in The International Conference on Neural Information Processing (ICONIP), 2012.
  12. A. Humayun, S.E.A. Raza , C. Waddington, S. Abouna, M. Khan, and N. M. Rajpoot, "A Framework for molecular co-expression pattern analysis in multi-channel Toponome fluorescence images," in Microscopic Image Analysis with Applications in Biology, 2011.

Awards and Scholarships

  • Bestway Foundation Scholarship for Bachelors in Electrical Engineering at University of Engineering and Technology, Taxila, Pakistan, 2004 - 2008.
  • IT Endowment Scholarship for MS Systems Engineering at Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan, 2008 - 2010.
  • Horticultural Development Company (HDC) Studentship for PhD Computer Science at University of Warwick, UK, 2011-2014.
  • Travel and Accommodation grant by Institute for Pure & Applied Mathematics, University of California, Los Angeles, to attend Graduate Summer School, IPAM, UCLA, 2013.
  • Lesion Quantification in Parsnip Root, by Elsoms and Innovate UK, 2015.
  • Computerised Profiling for Improved Diagnosis and Stratification of Oral Cancers in the Indian Subcontinent, Warwick Impact Fund Award, 2016.

Technical Training

  • International Summer School on Pattern Recognition (ISSPR), Plymouth (UK), 2011.
  • Medical Image Understanding and Analysis, Swansea (UK), July 2012.
  • Secondment at the CIA Laboratory, Ohio State University (USA), Oct - Dec 2012.
  • PAVIS School on Computer Vision, Pattern Recognition, and Image Processing, Sestri Levante (Italy), 2013.
  • Digital Pathology Congress. London, 2014.
  • Invited Presentation at Cyto 2015, Glasgow, June 2015.
  • Medical Image Understanding and Analysis, Lincoln (UK), July 2015.
  • Medical Image Computing and Computer Assisted Intervention, MICCAI, Munich, 2015.
  • Digital Pathology Congress. London, 2015.
  • Short courses by Learning and Development Centre at University of Warwick on Data Management, Leadership roles in Academia.
  • Institute of Applied Sciences (IAS) workshops on writing successful grant applications and research articles.

Extra Curricular Activities

  • Member Table Tennis team UET Taxila at All Pakistan Inter-University Games 2005 Islamabad, Pakistan.
  • Member Field Hockey team UET Taxila from 2006 - 2008.
  • Member Sports Committee PIEAS for year 2010.

Post-Doctoral Training Fellow

Dr Shan E Ahmed Raza
Division of Molecular Pathology &
Centre for Evolution and Cancer
The Institute of Cancer Research
15 Cotswold Road
SM2 5NG, Surrey
Contact: shan.raza@icr.ac.uk