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TIA Lab: Publications

2019

  • S. Graham, Q. Dang, S. E A. Raza, A. Azam, Y.-W Tsang, J. T. Kwak, N.M. Rajpoot, “Hover-Net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images,” Medical Image Analysis, Dec. 2019, vol. 58, p. 101563. [Abstract] [doi] [Data]
  • M. Shaban, A. Mahmood, S. A. Al-Maadeed & N. M. Rajpoot, “An Information Fusion Framework for Person Localization Via Body Pose in Spectator Crowds,” Information Fusion, Nov. 2019, vol. 51, p. 178–188. [Abstract] [doi]
  • N. Kumar, R. Verma, D. Anand, Y. Zhou, O. F. Onder, E. Tsougenis, H. Chen, P. A. Heng, J. Li, Z. Hu, Y. Wang, N. A. Koohbanani, M. Jahanifar, N. Z. Tajeddin, A. Gooya, N. Rajpoot, X. Ren, S. Zhou, Q. Wang, D. Shen, C. K. Yang, C. H. Weng, W. H. Yu, C. Y. Yeh, S. Yang, S. Xu, P. H. Yeung, P. Sun, A. Mahbod, G. Schaefer, I. Ellinger, R. Ecker, O. Smedby, C. Wang, B. Chidester, T. V. Ton, M. T. Tran, J. Ma, M. N. Do, S. Graham, Q. D. Vu, J. T. Kwak, A. Gunda, R. Chunduri, C. Hu, X. Zhou, D. Lotfi, R. Safdari, A. Kascenas, A. O'Neil, D. Eschweiler, J. Stegmaier, Y. Cui, B. Yin, K. Chen, X. Tian, P. Gruening, E. Barth, E. Arbel, I. Remer, A. Ben-Dor, E. Sirazitdinova, M. Kohl, S. Braunewell, Y. Li, X. Xie, L. Shen, J. Ma, K. D. Baksi, M. A. Khan, J. Choo, A. Colomer, V. Naranjo, L. Pei, K. M. Iftekharuddin, K. Roy, D. Bhattacharjee, A. Pedraza, M. G. Bueno, S. Devanathan, S. Radhakrishnan, P. Koduganty, Z. Wu, G. Cai, X. Liu, Y. Wang, A. Sethi, “A Multi-organ Nucleus Segmentation Challenge.,” IEEE Transactions on Medical Imaging (TMI), Oct. 2019, p. 1. [Abstract] [doi]
  • M. Shaban, S.A. Khurram, M.M. Fraz, N. Alsubaie, I. Masood, S. Mushtaq, M. Hassan, A. Loya, N. M. Rajpoot, “A Novel Digital Score for Abundance of Tumour Infiltrating Lymphocytes Predicts Disease Free Survival in Oral Squamous Cell Carcinoma,” Nature Scientific Reports, Sep. 2019, vol. 9, p. 13341. [Abstract] [doi]
  • H. Lin, H. Chen, S. Graham, Q. Dou, N. M. Rajpoot, P.-A Heng, “Fast scannet: Fast and dense analysis of multi-gigapixel whole-slide images for cancer metastasis detection,” IEEE Transactions on Medical Imaging (TMI), Aug. 2019, vol. 38(8), p. 1948–1958. [Abstract] [doi]
  • T. Qaiser, Y.-W Tsang, D. Taniyama, N. Sakamoto, K. Nakane, D. Epstein, N. M. Rajpoot, “Fast and Accurate Tumor Segmentation of Histology Images using Persistent Homology and Deep Convolutional Features,” Medical Image Analysis, Jul. 2019, vol. 55, p. 1–14. [Abstract] [doi]
  • S. Graham, D. Epstein & N. M. Rajpoot, “Rota-Net: Rotation Equivariant Network for Simultaneous Gland and Lumen Segmentation in Colon Histology Images,” European Congress on Digital Pathology, Jul. 2019, vol. 10581, p. 109–116. [Abstract] [doi]
  • T. Qaiser, M. Pugh, S. Margielewska, R. Hollows, P. Murray, N. M. Rajpoot, “Digital Tumor-Collagen Proximity Signature Predicts Survival in Diffuse Large B-Cell Lymphoma,” European Congress on Digital Pathology, Jul. 2019, vol. 11435, p. 163–171. [Abstract] [doi]
  • J. Gamper, N. A. Koohbanani, K. Benet, A. Khuram, N. M. Rajpoot, “PanNuke: An Open Pan-Cancer Histology Dataset for Nuclei Instance Segmentation and Classification,” European Congress on Digital Pathology, Jul. 2019, vol. 11435, p. 11–19. [Abstract] [doi]
  • T. Qaiser, M. Pugh, S. Margielewska, R. Hollows, P. Murray, N. M. Rajpoot, “Tumor-collagen digital proximity signature to indicate prognosis in diffuse large B-cell lymphoma,” Journal Clinical Oncology, Jun. 2019, e19073. [Abstract] [doi]
  • M. Veta, Y. J. Heng, N. Stathonikos, B. E. Bejnordi, F. Beca, T. Wollmann, K. Rohr, M. A. Shah, D. Wang, M. Rousson, M. Hedlund, D. Tellez, F. Ciompi, E. Zerhouni, D. Lanyi, M. Viana, V. Kovalev, V. Liauchuk, H. A. Phoulady, T. Qaiser, S. Graham, N. M. Rajpoot, E. Sjöblom, J. Molin, K. Paengo, S. Hwang, S. Park, Z. Jia, EI-C. Chang, Y. Xu, A. H. Beck, P. J. van Diest, J. P. W. Pluim, “Predicting breast tumor proliferation from whole-slide images: The TUPAC16 challenge,” Medical Image Analysis, May. 2019, vol. 54, p. 111–121. [Abstract] [doi]
  • R. Colling, H. Pitman, K. Oien, N.M. Rajpoot, P. Macklin, CM-Path AI in Histopathology Working Group, D. Snead, T. Sackville, C. Verrill, “Artificial intelligence in digital pathology: a roadmap to routine use in clinical practice,” Journal of Pathology, May. 2019, vol. 249(2), p. 143–150. [Abstract] [doi]
  • R. Pell, K. Oien, M. Robinson, H. Pitman, N. M. Rajpoot, J. Rittscher, D. Snead, C. Verrill, CM-Path, “The use of digital pathology and image analysis in clinical trials,” The Journal of Pathology: Clinical Research, Apr. 2019, vol. 5(2), p. 81–90. [Abstract] [doi]
  • Q. D. Vu, S. Graham, T. Kurc, M. N. To, M. Shaban, T. Qaiser, N. A. Koohbanani, S. A. Khurram, T. Kurc, K. Farahani, T. Zhao, R. Gupta, J. T. Kwak, N. M. Rajpoot, J. Saltz, “Methods for segmentation and classification of digital microscopy tissue images,” Frontiers in bioengineering and biotechnology, Apr. 2019, vol. 7, p. 53. [Abstract] [doi]
  • M Shapcott, K Hewitt & N. M. Rajpoot, “Deep Learning with Sampling for Colon Cancer Histology Images,” Frontiers of Bioengineering and Biotechnology, Mar. 2019, vol. 7, p. 52. [Abstract] [doi]
  • T. Qaiser & N.M. Rajpoot, “Learning Where to See: A Novel Attention Model for Automated Immunohistochemical Scoring,” IEEE Transactions on Medical Imaging (TMI), Mar. 2019, vol. , p. 1–1. [Abstract] [doi][Data]
  • S. Graham, H. Chen, J. Gamper, H. Chen, J. Gamper, Q. Dou, P.-A Heng, D. Snead, Y.-W Tsang, N. M. Rajpoot, “MILD-Net: Minimal information loss dilated network for gland instance segmentation in colon histology images,” Medical Image Analysis, Feb. 2019, vol. 52, p. 199–211. [Abstract] [doi] [Data]

2018

  • L. Maier-Hein, M. Eisenmann, A. Reinke, S. Onogur, M. Stankovic, P. Scholz, T. Arbel, H. Bogunovic, A. P. Bradley, A. Carass, C. Feldmann, A. F. Frangi, P. M. Full, B. van Ginneken, A. Hanbury, K. Honauer, M. Kozubek, B. A. Landman, K. März, O. Maier, K. Maier-Hein, B. H. Menze, H. Müller, P. F. Neher, W. Niessen, N. M. Rajpoot, G. C. Sharp, K. Sirinukunwattana, S. Speidel, C. Stock, D. Stoyanov, A. A. Taha, F. van der Sommen, C.-W Wang, M.-A Weber, G. Zheng, P. Jannin, A. Kopp-Schneider, “Why rankings of biomedical image analysis competitions should be interpreted with care,” Nature Communications, Dec. 2018, vol. 9, p. 5217. [Abstract] [doi]
  • S. E. A. Raza, L. Cheung, M. Shaban, S. Graham, D. Epstein, S. Pelengaris, M. Khan, N. M. Rajpoot, “Micro-Net: A unified model for segmentation of various objects in microscopy images,” Medical Image Analysis, Dec. 2018, vol. 52, p. 160–173. [Abstract] [doi] [Data]
  • T.-H. Song, V. Sanchez, H. ElDaly & N. M. Rajpoot, “Simultaneous Cell Detection and Classification in Bone Marrow Histology Images,” IEEE Journal of Biomedical and Health Informatics, Oct. 2018, vol. 23 (4), p. 1469 – 1476. [Abstract] [doi]
  • K. Sirinukunwattana, D. Snead, D. Epstein, Z. Aftab, I. Mujeeb, Y.-W. Tsang, I. Cree, N. M. Rajpoot, “Novel digital signatures of tissue phenotypes for predicting distant metastasis in colorectal cancer,” Nature Scientific Reports, Sep. 2018, vol. 8, p. 13692. [Abstract] [doi]
  • R. Awan & N. Rajpoot, “Deep Autoencoder Features for Registration of Histology Images,” Annual Conference on Medical Image Understanding and Analysis, Jun 2018, p. 371–378. [Abstract] [doi]
  • M. Shaban, S. A. Khurram, M. Hassan, S. Mushtaq, A. Loya, N. M. Rajpoot, “Prognostic significance of automated score of tumor infiltrating lymphocytes in oral cancer,” Journal of Clinical Oncology, Jun. 2018, p. e18036. [Abstract] [doi]
  • N. A. Koohababni, M. Jahanifar, A. Gooya, N.M.Rajpoot, “Nuclei detection using mixture density networks.,” International Workshop on Machine Learning in Medical Imaging, Sep. 2018, vol. 11046, p. 241–248. [Abstract] [doi]
  • S. Graham, H. Chen, P.-A. Heng, N. M. Rajpoot, “MILD-Net: Minimal Information Loss Dilated Network for Gland Instance Segmentation in Colon Histology Images,” Medical Imaging with Deep Learning (MIDL) , Jul. 2018. [Abstract] [doi]
  • R. Awan, N. A. Koohbanani, M. Shaban, A. Lisowska, N. M. Rajpoot, “Context-aware learning using transferable features for classification of breast cancer histology images,” International Conference Image Analysis and Recognition, 2018, p. 788–795. [Abstract] [doi]
  • S. Graham & N.M. Rajpoot, “Sams-net: Stain-aware multi-scale network for instance-based nuclei segmentation in histology images,” IEEE International Symposium on Biomedical Imaging, May. 2018, p. 590–594. [Abstract] [doi]
  • S. Graham, M. Shaban, T. Qaiser, N. A. Koohababni, S. A. Khurram, N. M. Rajpoot, “Classification of lung cancer histology images using patch-level summary statistics,” SPIE Medical Imaging, Mar. 2018, vol. 10581, p. 1058119. [Abstract] [doi]
  • T. Qaiser, A. Mukherjee, C. Reddy Pb, S. D. Munugoti, V. Tallam, T. Pitkäaho, T. Lehtimäki, T. Naughton, M. Berseth, A. Pedraza, R. Mukundan, M. Smith, A. Bhalerao, E. Rodner, M. Simon, J. Denzler, C.-H Huang, G. Bueno, D. Snead, I. Ellis, M. Ilyas, N. M. Rajpoot, “HER2 challenge contest: a detailed assessment of automated HER2 scoring algorithms in whole slide images of breast cancer tissues,” Histopathology, Jan. 2018, vol. 72(2), p. 227–238. [Abstract] [doi][Data]
  • A. Ahmad, A. Asif, N. M. Rajpoot, M. Arif, F. Minhas, “Correlation Filters for Detection of Cellular Nuclei in Histopathology Images,” Journal of Medical Systems, Jan. 2018, vol. 42, p. 7. [Abstract] [doi]
  • J. van der Laak, N. M. Rajpoot, D. Vossen, “The Promise of Computational Pathology,” The Pathologist, Jan. 2018, vol. 38, p. 16–26. [Magazine article]

2017

  • B. E. Bejnordi, M. Veta, P. J. van Diest, B van Ginneken, N Karssemeijer, G Litjens, JAWM van der Laak, M. Hermsen, Q. F. Manson, M. Balkenhol, O. Geessink, N. Stathonikos, M. CRF van Dijk, P. Bult, F. Beca, A. H. Beck, D. Wang, A. Khosla, R. Gargeya, H. Irshad, A. Zhong, Q. Dou, Q. Li, H. Chen, H.-J. Lin, P.-A. Heng, C. Haß, E. Bruni, Q. Wong, U. Halici, M. Ü. Öner, R. Cetin-Atalay, M. Berseth, V. Khvatkov, A. Vylegzhanin, O. Kraus, M. Shaban, N. M. Rajpoot, R. Awan, K. Sirinukunwattana, T. Qaiser, Y.-W. Tsang, D. Tellez, J. Annuscheit, P. Hufnagl, M. Valkonen, K. Kartasalo, L. Latonen, P. Ruusuvuori, K. Liimatainen, S. Albarqouni, B. Mungal, A. George, S. Demirci, N. Navab, S. Watanabe, S. Seno, Y. Takenaka, H. Matsuda, H. A. Phoulady, V. Kovalev, A. Kalinovsky, V. Liauchuk, G. Bueno, M. M. Fernandez-Carrobles, I. Serrano, O. Deniz, D. Racoceanu, R. Venâncio, “Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer,” Journal of the American Medical Association (JAMA), Dec. 2017, vol. 318(22), p. 2199–2210. [Abstract] [doi]
  • R. Awan, K. Sirinukunwattana, D. Epstein, S. Jefferyes, U. Qidwai, Z. Aftab, I. Mujeeb, D. Snead, N. M. Rajpoot, “Glandular morphometrics for objective grading of colorectal adenocarcinoma histology images,” Nature Scientific Reports, Dec. 2017, vol. 7(1), p. 16852. [Abstract] [doi]
  • T.-H. Song, V. Sanchez, H. Eldaly & N. M. Rajpoot, “Dual-Channel Active Contour Model for Megakaryocytic Cell Segmentation in Bone Marrow Trephine Histology Images,” IEEE Transactions on Biomedical Engineering, Dec. 2017, vol. 64(12), p. 2913–2923. [Abstract] [doi]
  • E. Rezk, Z. Awan, F. Islam, A. Jaoua, S. AlMaadeed, N. Zhang, G. Das, N. M. Rajpoot, “Conceptual data sampling for breast cancer histology image classification,” Computers in Biology and Medicine, Oct. 2017, vol. 89, p. 59–67. [Abstract] [doi]
  • M. Xue, A. Shafie, T. Qaiser, N. M. Rajpoot, G. Kaltsas, S. James, K. Gopalakrishnan, A. Fisk, G. K. Dimitriadis, D. K. Grammatopoulos, N. Rabbani, P. J. Thornalley, M. O. Weickert, “Glyoxalase 1 copy number variation in patients with well differentiated gastro-entero-pancreatic neuroendocrine tumours (GEP-NET).,” Oncotarget, Sep. 2017, vol. 8(44), p. 76961–76973. [Abstract] [doi]
  • N. Trahearn, D. Epstein, I. Cree, D. R. J. Snead, N. M. Rajpoot, “Hyper-Stain Inspector: A Framework for Robust Registration and Localised Co-Expression Analysis of Multiple Whole-Slide Images of Serial Histology Sections,” Nature Scientific Reports, Jul. 2017, vol. 7, p. 5641. [Abstract] [doi]
  • N. Trahearn, Y.-W . Tsang, I. Cree, D. R. J. Snead, D. B. A. Epstein, N. M. Rajpoot, “Simultaneous Automatic Scoring and Co-Registration of Hormone Receptors in Tumour Areas in Whole Slide Images of Breast Cancer Tissue Slides,” Cytometry: Part A special issue on Computer-Aided Diagnostics in Digital Pathology, Jun. 2017, vol. 91(6), p. 585–594. [Abstract] [doi]
  • T. Qaiser, Y.-W. Tsang, D. Epstein, N. M. Rajpoot, “Tumor segmentation in whole slide images using persistent homology and deep convolutional features.,” In Medical Image Understanding and Analysis (MIUA), Jul. 2017, vol. 723, p. 320–329. [Abstract] [doi]
  • 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), Jul. 2017, pp. 698–706. [Abstract] [doi]
  • 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,” IEEE International Symposium on Biomedical Imaging (ISBI), Apr. 2017, p. 337-340. [Abstract] [doi]
  • 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, Jan. 2017, vol. 37, p. 91–100. [Abstract] [doi]
  • N. Alsubaie, N. Trahearn, S.E.A. Raza, D. R. J. Snead, N. M. Rajpoot, “Stain Deconvolution Using Statistical Analysis of Multi-Resolution Stain Colour Representation,” PLoS One, Jan. 2017, vol. 12, no. 1, p.e0169875. [Abstract] [doi]
  • K. Sirinukunwattana, J. P. W. Pluim, H. Chen, X. Qi, P-A Heng, Y. B. Guo, L. Y. Wang, B. J. Matuszewski, E. Bruni, U. Sanchez, A. Böhm, O. Ronneberger, B. B. Cheikh, D. Racoceanu, P. Kainz, M. Pfeiffer, M. Urschler, D. R. J. Snead, N. M. Rajpoot, “Gland Segmentation in Colon Histology Images: The GlaS Challenge Contest,” Medical Image Analysis, Jan. 2017, vol. 35, p. 489–502. [Abstract] [doi] [Data]

2016

  • T. Qaiser, K. Sirinukunwattana, K. Nakane, Y.-W Tsang, D. B. A. Epstein, N. M. Rajpoot, “Persistent Homology for Fast Tumor Segmentation in Whole Slide Histology Images,” Procedia Computer Science, Dec. 2016, vol. 90, p.119-124. [Abstract] [doi]
  • A. Mahmood, M. Small, S. Al-Maadeed, N. M. Rajpoot, “Using Geodesic Space Density Gradients for Network Community Detection,” IEEE Transactions on Knowledge and Data Engineering, Nov. 2016, vol. PP, no.99, p.1-1. [Abstract] [doi]
  • V. N. Kovacheva, N. M. Rajpoot, “Subcellular protein expression models for microsatellite instability in colorectal adenocarcinoma tissue images,” BMC Bioinformatics, Oct. 2016, vol. 17:430. [Abstract] [doi]
  • V. N. Kovacheva, D. Snead, N. M. Rajpoot, “A model of the spatial tumour heterogeneity in colorectal adenocarcinoma tissue,” BMC Bioinformatics, Jun. 2016, vol. 17:25. [Abstract] [doi]
  • T. Qaiser, K. Sirinukunwattana, & N.M. Rajpoot, “An Integrated Environment For Tissue Morphometrics And Analytics.,” Diagnostic Pathology, Jun. 2016, vol. 1(8). [Abstract] [doi]
  • N. Alsubaie, S. E. A. Raza, and N. M. Rajpoot, “Stain Deconvoloution of Histology Images via Independent Component Analysis in the Wavelet Domain,” IEEE International Symposium on Biomedical Imaging (ISBI), Apr. 2016, p. 803-806. [Abstract] [doi]
  • M. N. Kashif, S.E.A. Raza, K. Sirinukunwattana, M. Arif, N. M. Rajpoot, “Handcrafted features with convolutional neural networks for detection of tumor cells in histology images,” IEEE International Symposium on Biomedical Imaging (ISBI), Apr. 2016, p. 1029-1032. [Abstract] [doi]
  • S. E. A. Raza, D. Langenkämper, K. Sirinukunwattana, D. B. A. Epstein, T. W. Nattkemper, and N. M. Rajpoot, “Robust Normalization Protocols for Multiplexed Fluorescence Bioimage Analysis,” BMC Biodata Min., Mar. 2016, vol. 9:11. [Abstract] [doi]
  • K. Sirinukunwattana, S.E.A. Raza, Y.-W. Tsang, D. Snead, I. Cree, and N.M. Rajpoot, “Locality Sensitive Deep Learning for Detection and Classification of Nuclei in Routine Colon Cancer Histology Images,” IEEE Transactions on Medical Imaging (TMI), pp. 1–1, Jan. 2016. [Abstract] [doi] [Data]

2015

  • G. Li, V. Sanchez, P. C. S. B. Nagaraj, S. Khan, and N. M. Rajpoot, “A novel multitarget tracking algorithm for Myosin VI protein molecules on actin filaments in TIRFM sequences,” Journal of Microscopy, vol. 260, no. 3, pp. 312–325, Dec. 2015. [Abstract] [doi]
  • K. Sirinukunwattana, S. E. A.Raza, Y.-W. Tsang, D. Snead, I. Cree, and N.M. 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, Oct. 2015, pp. 154–162. [Abstract] [doi]
  • G. Li, S. E. A. Raza, and N.M. 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, Oct. 2015, pp. 172–179. [Abstract] [doi]
  • D. R. Snead, Y.-W. Tsang, A. Meskiri, P. K. Kimani, R. Crossman, N. M. Rajpoot, E. Blessing, K. Chen, K. Gopalakrishnan, P. Matthews, N. Momtahan, S. Read-Jones, S. Sah, E. Simmons, B. Sinha, S. Suortamo, Y. Yeo, H. El Daly, and I. A. Cree, “Validation of digital pathology imaging for primary histopathological diagnosis,” Histopathology, Sep. 2015. [Abstract] [doi]
  • A. M. Khan, K. Sirinukunwattana, and N.M. Rajpoot, “A Global Covariance Descriptor for Nuclear Atypia Scoring in Breast Histopathology Images,” IEEE Journal of Biomedical and Health Informatics, vol. 19, no. 5, pp. 1637–1647, Sep. 2015. [Abstract] [doi]
  • K. Rajpoot, A. Riaz, W. Majeed, and N.M. Rajpoot, “Functional Connectivity Alterations in Epilepsy from Resting-State Functional MRI,” PLoS One, vol. 10, no. 8, p. e0134944, Aug. 2015. [Abstract] [doi]
  • 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, vol. 48, pp. 2119–2128, Jul. 2015. [Abstract] [doi][Software]
  • S. E. A. Raza and N. M. Rajpoot, “Cell Nuclei Segmentation in Variable Intensity Fluorescence Microscopy Images,” in Medical Image Understanding and Analysis, Jul. 2015, pp. 28–33. [Abstract] [doi]
  • 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, Jul. 2015, pp. 132–137. [Abstract] [doi]
  • K. Sirinukunwattana, A. M. Khan, and N. M. Rajpoot, “Cell words: Modelling the visual appearance of cells in histopathology images,” Computerized Medical Imaging and Graphics on Breakthrough Technologies in Digital Pathology, vol. 42, pp. 16–24, Jun. 2015. [Abstract] [doi][Software]
  • G. Li, V. Sanchez, G. Patel, S. Quenby, and N.M. Rajpoot, “Localisation of luminal epithelium edge in digital histopathology images of IHC stained slides of endometrial biopsies,” Comput. Med. Imaging Graph., vol. 42, pp. 56–64, Jun. 2015. [Abstract] [doi]
  • K. Sirinukunwattana, D. Snead, and N.M. Rajpoot, “A Stochastic Polygons Model for Glandular Structures in Colon Histology Images,” IEEE Transactions on Medical Imaging (TMI), vol. 0062, no. c, pp. 1–1, May 2015. [Abstract] [doi]
  • V. N. Kovacheva, D. Snead, and N. M. Rajpoot, “A model of the spatial microenvironment of the colonic crypt,” in IEEE 12th International Symposium on Biomedical Imaging (ISBI), Apr. 2015, pp. 172–176. [Abstract] [doi]
  • K. Sirinukunwattana, D. R. J. Snead, and N. M. Rajpoot, “A random polygons model of glandular structures in colon histology images,” in IEEE 12th International Symposium on Biomedical Imaging (ISBI), Apr. 2015, pp. 1526–1529. [Abstract] [doi]
  • 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, Apr. 2015. [Abstract] [doi]
  • 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, Feb. 2015, vol. 9420, p. 942005. [Abstract] [doi]
  • N. Trahearn, D. Snead, I. Cree, and N.M. Rajpoot, “Multi-class stain separation using independent component analysis,” in SPIE Medical Imaging, Feb. 2015, vol. 9420, p. 94200J. [Abstract] [doi]
  • T.-H. Song, V. Sanchez, H. EIDaly, and N. M. Rajpoot, “A circumscribing active contour model for delineation of nuclei and membranes of megakaryocytes in bone marrow trephine biopsy images,”in SPIE Medical Imaging, Feb. 2015, vol. 9420, p. 94200T. [Abstract] [doi]
  • K. Sirinukunwattana, D. R. Snead, and N. M. Rajpoot, “A novel texture descriptor for detection of glandular structures in colon histology images,”in SPIE Medical Imaging, Feb. 2015, vol. 9420, p. 94200S. [Abstract] [doi]
  • M. Veta, P. J. van Diest, S. M. Willems, H. Wang, A. Madabhushi, A. Cruz-Roa, F. Gonzalez, A. B. L. Larsen, J. S. Vestergaard, A. B. Dahl, D. C. Cirean, J. Schmidhuber, A. Giusti, L. M. Gambardella, F. B. Tek, T. Walter, C.-W. Wang, S. Kondo, B. J. Matuszewski, F. Precioso, V. Snell, J. Kittler, T. E. de Campos, A. M. Khan, N. M. Rajpoot, E. Arkoumani, M. M. Lacle, M. A. Viergever, J. P. W. Pluim, “Assessment of algorithms for mitosis detection in breast cancer histopathology images,” Medical Image Analysis, Feb. 2015, vol. 20, no. 1, pp. 237–248. [Abstract] [doi]

2014

  • A.M. Khan, N.M. Rajpoot, D. Treanor, D. Magee, “A Non-Linear Mapping Approach to Stain Normalisation in Digital Histopathology Images using Image-Specific Colour Deconvolution,” IEEE Transactions on Biomedical Engineering, Jun. 2014, vol. 61 no. 6 p. 1729-1738. [Abstract] [doi][Software]
  • A.M. Khan, S.E.A. Raza, M. Khan, N. M. Rajpoot, “Cell Phenotyping in Multi-Tag Fluorescent Bioimages,” Neurocomputing, Jun. 2014, vol. 134 no. 1 p. 254-261. [Abstract] [doi]
  • S.E.A Raza, H. Smith, G.J.J. Clarkson, G. Taylor, A. J. Thompson, J. Clarkson, N. M. Rajpoot, “Automatic Detection of Regions in Spinach Canopies Responding to Soil Moisture Deficit Using Combined Visible and Thermal Imagery,” PLoS ONE, Jun. 2014, vol. 9 no. 6 p. e97612. [Abstract] [doi]
  • V.N. Kovacheva, A.M. Khan, M. Khan, D. B. A. Epstein, N. M. Rajpoot, “DiSWOP: A Novel Measure for Cell-Level Protein Network Analysis in Localised Proteomics Image Data,” Bioinformatics, Mar. 2014, vol. 30 no. 3 p. 420-427. [Abstract] [doi]
  • V.N. Kovacheva, D.B.A. Epstein, N.M. Rajpoot, “Advances in Discovery of Complex Biomarkers for Colorectal Cancer Using Multiplexed Proteomics Imaging,” Oncolongy News, Jan. 2014, vol. 8 no. 6 p. 191-193. [Abstract] [doi]

2013

  • K. Sirinukunwattana, R.S. Savage, M.F. Bari, D. R. J. Snead, N. M. Rajpoot, “Bayesian Hierarchical Clustering for Studying Cancer Gene Expression Data with Unknown Statistics,” PLoS ONE, Oct. 2013, vol. 8 no. 10 p. e75748. [Abstract] [doi][Software]
  • A.M. Khan, H. El-Daly, N.M. Rajpoot, “A Gamma-Gaussian Mixture Model for Detection of Mitotic Cells in Breast Cancer Histopathology Images,” Journal of Pathology Informatics, Mar. 2013, vol. 4 no. 11. [Abstract] [doi]
  • A.M. Khan, H. El-Daly, E. Simmons, N. M. Rajpoot, “HyMaP: A hybrid magnitude-phase approach to unsupervised segmentation of tumor areas in breast cancer histology images,” Journal of Pathology Informatics, Mar. 2013, vol. 4 no. 1. [Abstract] [doi]

2012

  • R. Evans, U. Naidu, N.M. Rajpoot, et al. “Toponome imaging system: multiplex biomarkers in oncology,” Trends in Molecular Medicine Cell, Dec. 2012, vol. 18 no. 12, p. 723-731. [Abstract] [doi]
  • N.M. Rajpoot, I.T. Butt, “A Multiresolution Framework for Local Similarity based Image Denoising,” Pattern Recognition, Aug. 2012, vol. 45 no. 8, p. 2938-2951. [Abstract] [doi]
  • L. Zhou, S. Pelengaris, S. Abouna, et al., “Re-expression of IGF-II is important for beta cell regeneration in adult mice.,” PloS one, Sep. 2012, vol. 7(9), p. e43623. [Abstract] [doi]
  • S. Khan, T.S. Reese, N.M. Rajpoot, et al., “Spatiotemporal Maps of CaMKII in Dendritic Spines,” Journal of Computational Neuroscience, Aug. 2012, vol. 33 no. 1, p. 123-139. [Abstract] [doi]
  • S.J. McKenna, D. Magee, N.M. Rajpoot, “Special issue on microscopy image analysis for biomedical applications,” Machine Vision and Applications, Jun. 2012, vol. 23 no. 4, p. 603-605. [doi]
  • S.E.A. Raza, A. Humayun, S. Abouna, et al., “RAMTaB: Robust Alignment of Multi-Tag Bioimages,” PLoS ONE, Feb. 2012, vol. 7 no. 2, p. e30894. [Abstract] [doi][Software]
  • M. Kuse, Y.F. Wang, V. Kalassannavar, et al., “Local Isotropic Phase Symmetry for Detection of beta Cells and Lymphocytes,” Journal of Pathology Informatics, Jan. 2012, vol. 2 no. 2. [Abstract] [doi][Software]

2011

  • A. Humayun, S.E.A. Raza, C. Waddington, S. Abouna, M. Khan, N. M. Rajpoot, “A Framework for Molecular Co-Expression Pattern Analysis in Multi-Channel Toponome Fluorescence Images,” Proceedings Microscopy Image Analysis with Applications in Biology (MIAAB), Sep. 2011, Heidelberg, Germany. [Abstract] [doi]
  • S. Qureshi, A. Mirza, N.M. Rajpoot, M. Arif, “Hybrid Diversification Operator Based Evolutionary Approach towards Tomographic Image Reconstruction,” IEEE Transactions on Image Processing, Jul. 2011, vol. 27 no. 7, p. 1977–1990. [Abstract] [doi]
  • C. Loyek, N.M. Rajpoot, M. Khan, T. W. Nattkemper, “BioIMAX: A Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data,” BMC Bioinformatics, Jul. 2011, vol. 12, p. 297–297. [Abstract] [doi]
  • M. Arif, N.M. Rajpoot, T.W. Nattkemper, U. Technow, T. Chakraborty, N. Fische, N. Jensen, K. Niehaus, “Quantification of Cell Infection Caused by Listeria monocytogenes Invasion,” Journal of Biotechnology, Jun. 2011, vol. 154, p. 76–83. [Abstract] [doi][Software]
  • D. Langenkamper, J. Kolling, A. Humayun, S. Abouna, D. Epstein, M. Khan, N. M. Rajpoot, TW Nattkemper, “Towards Protein Network Analysis Using TIS Imaging and Exploratory Data Analysis,” Proceedings Workshop on Computational Systems Biology (WCSB), Zürich, Switzerland, Jun. 2011. [Abstract] [doi]

2010

  • S. Bhattacharya, G. Mathew, E. Ruban, E. Ruban, D. Epstein, A. Krusche, R. Hillert, W. Schubert, M. Khan, “Toponome imaging system: in situ protein network mapping in normal and cancerous colon from the same patient reveals more than five-thousand cancer specific protein clusters and their subcellular annotation by using a three symbol code.,” Journal of proteome research, Sep. 2010, vol. 9(12), p. 6112–6125. [Abstract] [doi]
  • S. Abouna, R. W. Old, S. Pelengaris, D. Epstein, V. Ifandi, I. Sweeney & M. Khan, “Non-β-cell progenitors of β-cells in pregnant mice.,” Organogenesis , Apr. 2010, vol. 6(2), p. 6112–6125. [Abstract] [doi]
  • L. Wang, G. Zhao, N. M. Rajpoot, M. Nixon, “Special issue on new advances in video-based gait analysis and applications: challenges and solutions,” IEEE Transactions on Systems, Man and Cybernetics, Part B: Cybernetics, Aug. 2010, vol. 40, p. 982-985. [doi]

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  • pin Our full list of publications is available here.
  • pin Prof Rajpoot to lead the computational arm of the recently awarded £15m PathLAKE centre of excellence for AI in Pathology (Nov 2018)
  • pin Prof Rajpoot and Prof Snead to co-chair the European Congress on Digital Pathology at Warwick (Apr 2019)
  • new.gifWe extend a warm welcome to Dr Young Saeng Park, Dr Hadi Saki, and Dr Noorul Wahab who have joined the PathLAKE project (1 Nov 2019)
  • new.gifWe are delighted to welcome Dr Fayyaz Minhas as a new faculty in the group (11 Oct 2019)
  • newWelcome to Miss Wenqi Lu who started with us as a Research Fellow today (16 Sep 2019)
  • new.gifKudos to Simon on the publication of his jointly first-authored paper on HoVer-Net in Medical Image Analysis (16 Sep 2019)
  • new.gifWe welcome Dr Nima Hatami and Dr Mohsin Bilal as postdoc fellows in the lab (19 Aug 2019)
  • newCongrats to Shaban on the acceptance of his paper on a novel score of TIL abudance for predicting disease-free survival in oral cancer in Nature Sci Rep (31 July 2019)
  • newWe welcome Dr Shan Raza as Assistant Professor in the group (1 Jun 2019)
  • Congrats to Mary and Simon for the publication of their articles in Frontiers Bioengineering & Biotechnology (Apr 2019)
  • Kudos to Talha on the acceptance of his paper on persistent homology for tumor segmentation in Medical Image Analysis (30 Mar 2019)
  • Congrats to Talha on the acceptance of his paper on visual attention in computational pathology accepted for publication in IEEE Transactions on Medical Imaging (13 Mar 2019)
  • Congrats to Shan and Simon on the acceptance of his Micro-Net paper in Medical Image Analysis (Feb 2019)
  • Kudos to Huangjang (CUHK) and Simon for their paper on ScanNet accepted for publication in IEEE TMI (2 Jan 2019)
  • Kudos to Shan and Simon for the acceptance of their paper on Micro-Net for publication in Medical Image Analysis (16 Dec 2018)
  • Congrats to Simon and Shaban for the acceptance of their papers on MILD-Net and Deep Head Detector in Medical Image Analysis and Information Fusion, respectively (14 Dec 2018)
  • Vacancy for Assistant Prof in Computational Pathology (see here for details; deadline for applications 13 Dec)
  • Our lab is proud to host the European Congress on Digital Pathology at Warwick in 2019 (previously held in Helsinki in 2018 and Berlin in 2016)
  • Congrats to Najah on successfully defending her PhD thesis (Nov 2018)
  • Two MRC funded postdoc positions available in our lab - see the job ad (application deadline 20 Nov 2018)
  • Congrats to Mike Song on the acceptance of his paper on simultaneous detection and classification of cells in bone marrow histology images in IEEE JBHI (Oct 2018)
  • Kudos to Korsuk on the acceptance of his paper on digital tissue phenotype based signatures for distant metastasis in colorectal cancer in Nature Scientific Reports (Sep 2018)
  • Congrats to Sajid, Moazam, Navid, and Saad on the acceptance of their papers in the MICCAI COMPAY workshop (20 July, 2018)
  • Congratulations to Navid on the acceptance of his paper in the MICCAI MLMI workshop (18 July, 2018)
  • Congrats to Simon on the acceptance of his paper for presentation at MIDL Amsterdam (16 May, 2018)
  • Congrats to Najah, Ruqayya, and Moazam on the acceptance of their papers in MIUA (12 Apr, 2018)
  • Kudos to Shaban on the acceptance of his abstract at the Annual ASCO meeting (2 Apr, 2018)
  • Congrats to Ruqayya, Navid, Shaban, and Ania on the acceptance of their paper on breast cancer image classification in ICIAR (2 Apr, 2018)
  • Congrats to Kat, Ruqayya, Najah, Ania, Navid, Shaban, Simon, and Talha for the acceptance of their abstracts for presentation at the ECDP (29 Mar, 2018)
  • RA position in AI/ML for cancer pathology (24 months) - deadline 5 Mar 2018; Click here to apply [CLOSED]
  • Congrats to Shaban, Ruqayya, Korsuk and Talha for the publication of the CAMELYON contest paper in JAMA (12 Dec, 2017)
  • Kudos to Ruqayya & Korsuk for the acceptance of their paper in Nature Scientific Reports (Nov 14, 2017)
  • Congrats to Najah and Simon on the acceptance of their papers on NSCLC image analysis for presentation at the SPIE Digital Pathology 2018 (Oct 6, 2017)
  • Kudos to Talha on the acceptance of his paper on Her2 Scoring Contest (held with PathSoc 2016) in the Histopathology journal (July 30, 2017)
  • Special congrats to Korsuk (now at the Harvard Med School) on the award of Science Faculty Best Thesis Prize 2017 (July 13, 2017)
  • Kudos to Nick (now at the Inst Cancer Research) on the acceptance of his paper on a Hyper-Stain Inspector for publication in Nature Scientific Reports (May 31, 2017)
  • Congrats to Mike Song, Talha Qaiser and Shan Raza on the acceptance of their papers in MIUA 2017 (Apr 24, 2017)
  • Congrats to Mike Song on the acceptance of his paper in IEEE Transactions on Biomedical Engineering (Mar 24, 2017)
  • Postdoc research fellow position available (deadline for applications Mar 30, 2017)
  • Warwick to lead new research on cancer image analytics (Feb 2, 2017)
  • Kudos to Guannan on his PhD graduation and to Guannan and Shan on the acceptance of their paper on luminal epithelium segmentation in the Medical Image Analysis journal (Jan 20, 2017)
  • Congrats to Shan and Mike on the acceptance of their papers for presentation at IEEE ISBI 2017 (Jan 10, 2017)
  • Congrats to Najah on the acceptance of her paper on wavelets based stain deconvolution in the PLoS ONE journal (Dec 30, 2016)
  • Kudos to Nick on the successful defense of his PhD thesis (Nov 24, 2016)
  • Congrats to Nick on the acceptance of his paper on simultaneous ER/PR scoring in Cytometry Part A (Nov 21, 2016)
  • Warwick to conduct breakthrough research on oral cancers in Pakistan (Oct 6, 2016)
  • Kudos to Violet on the acceptance of her paper on protein expression models in BMC Bioinformatics (Sep 7, 2016)
  • Congrats to Korsuk on the acceptance of his GlaS challenge contest paper in the Medical Image Analysis journal (Aug 30, 2016)
  • Funded PhD studentship available (deadline 1 Sep, 2016)
  • Kudos to Talha on winning the Best Paper Award at the MIUA 2016 (July 8, 2016)
  • Congrats to Nick & Violet on winning the Intel code acceleration contest held on campus (Apr 19, 2016)
  • Congrats to Dr Korsuk Sirinukunwattana on successfully defending his PhD thesis (Mar 30, 2016)
  • Kudos to Talha on the acceptance of his paper for Oral presentation at the European Congress on Digital Pathology to be held in Berlin in May (March 10, 2016)
  • Congrats to Shan for the acceptance of his paper on normalization protocols for multiplexed bioimage data for publication in the BMC Biodata Mining (Feb 2, 2016)
  • Congrats to Dr Guannan Li on successfully defending his PhD thesis (Jan 27, 2016)
  • Kudos to Korsuk for the acceptance of his paper on cell detection and labeling in standard H&E images for publication in the IEEE Transactions on Medical Imaging (Jan 16, 2016)
  • Congrats to Najah, Korsuk, and Shan for the acceptance of their papers for presentation at the IEEE ISBI (Dec 23, 2015)
  • Congrats to Dr Violeta Kovacheva on the successful defense of her PhD thesis (Dec 2, 2015)
  • Kudos to Korsuk for winning the Best Paper award at the MICCAI Patch-MI workshop (Oct 9, 2015)
  • Congrats to Korsuk and Guannan for the acceptance of their papers on epithelium analysis for presentation at the MICCAI Patch-MI workshop (August 8, 2015)
  • Kudos to Guannan for the acceptance of his paper on Myosin spot tracking in the Journal of Microscopy (July 10, 2015) [DOI]
  • Kudos to Korsuk and Adnan for the acceptance of their paper on nuclear atypia scoring in the IEEE Journal of Biomedical and Health Informatics (June 13, 2015) [DOI]
  • Kudos to Adnan for winning the Computer Science Faculty Thesis prize 2015 (May 28, 2015)
  • Congratulations to Najah and Shan for the acceptance of their papers in MIUA'2015 (May 22, 2015)
  • Kudos to Korsuk on the acceptance of his paper on gland segmentation in the IEEE Transactions on Medical Imaging (May 12, 2015) [DOI]
  • We are organizing the Gland Segmentation (GlaS) challenge contest at MICCAI'2015. Check out the contest website here (Apr 21, 2015)
  • Kudos to Violeta and Korsuk for the acceptance of their papers at the IEEE ISBI'2015 conference (Jan 24, 2015)
  • Congrats to Dr Sam Jefferyes on the successful defense of his PhD thesis (Dec 8, 2014)
  • Kudos to Shan, Korsuk, Mike Song, and Nick for the acceptance of their papers for presentation at the SPIE Digital Pathology 2015 conference (Oct 24, 2014)
  • Congrats to Dr Adnan Khan on the successful defense of his PhD thesis (Sep 22, 2014)
  • Kudos to Adnan Khan and Korsuk Sirinukunwattana for winning the MITOS-ATYPIA challenge contest held at ICPR'2014 in Stockholm (Aug 24, 2014)
  • Kudos to Korsuk Sirinukunwattana and Guannan Li for the acceptance of extended version of their papers presented at the ECDP'2014 (Paris) in a special issue of CMIG on Breakthrough Technologies in Digital Pathology (August, 2014)
  • Congrats to Dr Shan-e-Ahmed Raza on the successful defense of his PhD thesis (Feb 18, 2014)
  • BBSRC-funded postdoc position (deadline 22 Nov, 2013)
  • Our submission to the AMIDA challenge contest held at MICCAI'2013 ranked 3rd in terms of the average F1-score (Sep 22, 2013)
  • RA position (deadline expired)
  • CASE PhD Studentship (deadline expired)