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Tissue Image Analytics (TIA) Centre

TIA Centre: Publications

For publications from 2020 onwards, please visit the Team and click on individual Core Faculty members and Research Fellows to see their 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]
  • S. Javed, A. Mahmood, N. Werghi & N. M. Rajpoot, “Deep Multiresolution Cellular Communities for Semantic Segmentation of Multi-Gigapixel Histology Images,” 2019 IEEE/CVF International Conference on Computer Vision Workshop (ICCVW) Seoul, Korea (South), 2019, vol. 10581, p. 342–351. [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]
  • S. Javed, M. M. Fraz, D. Epstein, D. Snead, & N. M. Rajpoot, “Cellular community detection for tissue phenotyping in histology images,” in MICCAI Workshop Computational Pathology and Ophthalmic Medical Image Analysis, Sep. 2018, pp. 120–129. [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]