2023

Vu, Quoc Dang, Rajpoot, Kashif, Raza, Shan E. Ahmed and Rajpoot, Nasir M. (Nasir Mahmood) (2023) Handcrafted Histological Transformer (H2T) : unsupervised representation of whole slide images. Medical Image Analysis, 85 . p. 102743. 102743. doi:10.1016/j.media.2023.102743 ISSN 1361-8415.

Awan, Ruqayya, Raza, Shan-e-Ahmed, Lotz, Johannes, Weiss, Nick and Rajpoot, Nasir M. (2023) Deep feature based cross-slide registration. Computerized Medical Imaging and Graphics, 104 . 102162. doi:10.1016/j.compmedimag.2022.102162 ISSN 0895-6111.

Graham, Simon, Vu, Quoc Dang, Jahanifar, Mostafa, Raza, Shan E. Ahmed, Minhas, Fayyaz ul Amir Afsar, Snead, David and Rajpoot, Nasir M. (Nasir Mahmood) (2023) One model is all you need : multi-task learning enables simultaneous histology image segmentation and classification. Medical Image Analysis, 83 . 102685. doi:10.1016/j.media.2022.102685 ISSN 13618415.

Albusayli, Rawan, Graham, J. Dinny, Pathmanathan, Nirmala, Shaban, Muhammad, Raza, Shan E. Ahmed, Minhas, Fayyaz ul Amir Afsar, Armes, Jane E. and Rajpoot, Nasir M. (Nasir Mahmood) (2023) Artificial intelligence‐based digital scores of stromal tumour‐infiltrating lymphocytes and tumour‐associated stroma predict disease‐specific survival in triple‐negative breast cancer. The Journal of Pathology . doi:10.1002/path.6061 ISSN 0022-3417. (In Press)

2022

Pocock, Johnathan, Graham, Simon, Vu, Quoc Dang, Jahanifar, Mostafa, Deshpande, Srijay, Hadjigeorghiou, Giorgos, Shephard, Adam, Bashir, Raja Muhammad Saad, Bilal, Mohsin, Lu, Wenqi, Epstein, D. B. A., Minhas, Fayyaz ul Amir Afsar, Rajpoot, Nasir M. and Raza, Shan-e-Ahmed (2022) TIAToolbox as an end-to-end library for advanced tissue image analytics. Communications Medicine, 2 (1). 120. doi:10.1038/s43856-022-00186-5 ISSN 2730-664X.

Pan, Xiaoxi, Zhang, Hanyun, Grapa, Anca-Ioana, AbdulJabbar, Khalid, Raza, Shan E. Ahmed, Cheung, Ho Kwan Alvin, Karasaki, Takahiro, Quesne, John Le, Moore, David A., Swanton, Charles and Yuan, Yinyin (2022) Cross-stream interactions : segmentation of lung adenocarcinoma growth patterns. In: CMMCA 2022: Computational Mathematics Modeling in Cancer Analysis, Singapore, 18 Sep 2022. Published in: Proceedings of the International Workshop on Computational Mathematics Modeling in Cancer Analysis, 13574 pp. 78-90. doi:10.1007/978-3-031-17266-3_8 ISSN 0302-9743.

Gunesli, Gozde, Jewsbury, Robert, Raza, Shan E. Ahmed and Rajpoot, Nasir M. (Nasir Mahmood) (2022) Morph-Net : end-to-end prediction of nuclear morphological features from histology images. In: Huo, Y. and Millis, B. A. and Zhou, Y. and Wang, X. and Harrison, A. P. and Xu, Z., (eds.) Medical Optical Imaging and Virtual Microscopy Image Analysis. Lecture Notes in Computer Science, 13578 . Cham: Springer, pp. 136-144. ISBN 9783031169601

Bashir, Raja Muhammad Saad, Shaban, Muhammad, Raza, Shan E. Ahmed, Khurram, Syed Ali and Rajpoot, Nasir M. (Nasir Mahmood) (2022) A novel framework for coarse-grained semantic segmentation of whole-slide images. In: Yang, G. and Aviles-Rivero, A. and Roberts, M. and Schönlieb, C. B., (eds.) Medical Image Understanding and Analysis.MIUA 2022. Lecture Notes in Computer Science , 13413 . Cham: Springer International Publishing, pp. 425-439. ISBN 9783031120527

Nederlof, I., Hajizadeh, S., Sobhani, F., Raza, Shan-e-Ahmed, AbdulJabbar, K., Harkes, R., van de Vijver, M. J., Salgado, R., Desmedt, C., Kok, M., Yuan, Y. and Horlings, H. M. (2022) Spatial interplay of lymphocytes and fibroblasts in estrogen receptor-positive HER2-negative breast cancer. npj Breast Cancer, 8 (1). 56. doi:10.1038/s41523-022-00416-y ISSN 2374-4677.

Qureshi, Shahzad Ahmad, Raza, Shan E. Ahmed, Hussain, Lal, Malibari, Areej A., Nour, Mohamed K., Rehman, Aziz ul, Al-Wesabi, Fahd N. and Hilal, Anwer Mustafa (2022) Intelligent ultra-light deep learning model for multi-class brain tumor detection. Applied Sciences, 12 (8). e3715. doi:10.3390/app12083715 ISSN 2076-3417.

Shaban, Muhammad, Raza, Shan E. Ahmed, Hassan, Mariam, Jamshed, Arif, Mushtaq, Sajid, Loya, Asif, Batis, Nikolaos, Brooks, Jill, Nankivell, Paul, Sharma, Neil, Robinson, Max, Mehanna, Hisham, Khurram, Syed Ali and Rajpoot, Nasir M. (Nasir Mahmood) (2022) A digital score of tumour‐associated stroma infiltrating lymphocytes predicts survival in head and neck squamous cell carcinoma. The Journal of Pathology, 256 (2). pp. 174-185. doi:10.1002/path.5819 ISSN 0022-3417.

2021

Bilal, Mohsin, Raza, Shan-e-Ahmed, Azam, Ayesha, Graham, Simon, Ilyas, Mohammad, Cree, Ian A., Snead, David, Minhas, Fayyaz ul Amir Afsar and Rajpoot, Nasir M. (2021) Development and validation of a weakly supervised deep learning framework to predict the status of molecular pathways and key mutations in colorectal cancer from routine histology images : a retrospective study. The Lancet Digital Health, 3 (12). e763-e772. doi:10.1016/S2589-7500(21)00180-1 ISSN 2589-7500.

Winfield, Jessica M., Wakefield, Jennifer C., Brenton, James D., AbdulJabbar, Khalid, Savio, Antonella, Freeman, Susan, Pace, Erika, Lutchman-Singh, Kerryn , Vroobel, Katherine M., Yuan, Yinyin, Banerjee, Susana, Porta, Nuria, Raza, Shan-e-Ahmed and deSouza, Nandita M. (2021) Biomarkers for site-specific response to neoadjuvant chemotherapy in epithelial ovarian cancer : relating MRI changes to tumour cell load and necrosis. British Journal of Cancer, 124 . pp. 1130-1137. doi:10.1038/s41416-020-01217-5 ISSN 0007-0920.

Narayanan, Priya Lakshami, Raza, Shan-e-Ahmed, Hall, Allison H., Marks, Jeffrey R. , King, Lorraine , West, Robert B. , Hernandez, Lucia , Guppy, Naomi , Dowsett, Mitch , Gusterson, Barry , Maley, Carlo , Hwang, E. Shelley and Yuan, Yinyin (2021) Unmasking the immune microecology of ductal carcinoma in situ with deep learning. npj Breast Cancer , 7 . 19. doi:10.1038/s41523-020-00205-5 ISSN 2374-4677.

2020

(2020) Immune surveillance in clinical regression of pre-invasive squamous cell lung cancer. Cancer Discovery . doi:10.1158/2159-8290.CD-19-1366 ISSN 2159-8274.

TRACERx Consortium (Including:

). (2020) Geospatial immune variability illuminates differential evolution of lung adenocarcinoma. Nature Medicine, 26 . pp. 1054-1062. doi:10.1038/s41591-020-0900-x ISSN 1078-8956.

2019

Graham, Simon, Vu, Quoc Dang, Raza, Shan E. Ahmed, Azam, Ayesha, Tsang, Yee Wah, Kwak, Jin Tae and Rajpoot, Nasir M. (Nasir Mahmood) (2019) Hover-Net : simultaneous segmentation and classification of nuclei in multi-tissue histology images. Medical Image Analysis, 58 . 101563. doi:10.1016/j.media.2019.101563 ISSN 1361-8415.

Zormpas-Petridis, Konstantinos , Failmezger, Henrik , Raza, Shan E. Ahmed, Roxanis, Ioannis , Jamin, Yann and Yuan, Yinyin (2019) Superpixel-based conditional random fields (SuperCRF) : incorporating global and local context for enhanced deep learning in melanoma histopathology. Frontiers in Oncology, 9 . 1045. doi:10.3389/fonc.2019.01045 ISSN 2234-943X.

Raza, Shan-e-Ahmed, Cheung, Linda, Shaban, Muhammad, Graham, Simon, Epstein, D. B. A., Pelengaris, Stella, Khan, Michael and Rajpoot, Nasir M. (2019) Micro-Net : a unified model for segmentation of various objects in microscopy images. Medical Image Analysis, 52 . pp. 160-173. doi:10.1016/j.media.2018.12.003 ISSN 1361-8415.

2017

Li, Guannan, Raza, Shan-e-Ahmed and Rajpoot, Nasir M. (2017) Multi-resolution cell orientation congruence descriptors for epithelium segmentation in endometrial histology images. Medical Image Analysis, 37 . pp. 91-100. doi:10.1016/j.media.2017.01.006 ISSN 1361-8415.

Alsubaie, Najah, Trahearn, Nicholas, Raza, Shan-e-Ahmed, Snead, David and Rajpoot, Nasir M. (2017) Stain deconvolution using statistical analysis of multi-resolution stain colour representation. PLoS One, 12 (1). e0169875. doi:10.1371/journal.pone.0169875 ISSN 1932-6203.

2016

Sirinukunwattana, Korsuk, Raza, Shan-e-Ahmed, Tsang, Yee-Wah, Snead, David, Cree, Ian A. and Rajpoot, Nasir M. (2016) Locality sensitive deep learning for detection and classification of nuclei in routine colon cancer histology images. IEEE Transactions on Medical Imaging, 35 (5). 1196 -1206. doi:10.1109/TMI.2016.2525803 ISSN 0278-0062.

Raza, Shan-e-Ahmed, Langenkämper, Daniel, Sirinukunwattana, Korsuk, Epstein, D. B. A., Nattkemper, Tim W. and Rajpoot, Nasir M. (2016) Robust normalization protocols for multiplexed fluorescence bioimage analysis. BioData Mining, 9 (11). pp. 1-13. doi:10.1186/s13040-016-0088-2 ISSN 1756-0381 .

2015

Raza, Shan-e-Ahmed, Sanchez Silva, Victor, Prince, Gillian, Clarkson, John P. and Rajpoot, Nasir M. (2015) Registration of thermal and visible light images of diseased plants using silhouette extraction in the wavelet domain. Pattern Recognition, Volume 48 (Number 7). pp. 2119-2128. doi:10.1016/j.patcog.2015.01.027 ISSN 0031-3203.

Raza, Shan-e-Ahmed, Prince, Gillian, Clarkson, John P. and Rajpoot, Nasir M. (2015) Automatic detection of diseased tomato plants using thermal and stereo visible light images. PLoS One, Volume 10 (Number 4). Article number e0123262. doi:10.1371/journal.pone.0123262 ISSN 1932-6203.

2014

Khan, Adnan M., Raza, Shan-e-Ahmed, Khan, Michael and Rajpoot, Nasir M. (2014) Cell phenotyping in multi-tag fluorescent bioimages. Neurocomputing , Volume 134 . pp. 254-261. doi:10.1016/j.neucom.2013.08.043 ISSN 0925-2312.

Raza, Shan-e-Ahmed, Smith, Hazel K., Clarkson, Graham J. J., Taylor, Gail, Thompson, Andrew J., Clarkson, John P. and Rajpoot, Nasir M. (Nasir Mahmood) (2014) Automatic detection of regions in spinach canopies responding to soil moisture deficit using combined visible and thermal imagery. PLoS One, Volume 9 (Number 6). Article number e97612. doi:10.1371/journal.pone.0097612 ISSN 1932-6203.

Raza, Shan-e-Ahmed (2014) Multi-variate image analysis for detection of biomedical anomalies. PhD thesis, University of Warwick.

2012

Raza, Shan-e-Ahmed, Humayun, Ahmad, Abouna, Sylvie, Nattkemper, Tim W., Epstein, D. B. A., Khan, Michael and Rajpoot, Nasir M. (Nasir Mahmood) (2012) RAMTaB : robust alignment of multi-tag bioimages. PLoS One, Vol.7 (No.2). e30894. doi:10.1371/journal.pone.0030894 ISSN 1932-6203.

2011

Humayun, A., Raza, Shan-e-Ahmed, Waddington, C., Abouna, Sylvie, Khan, Michael and Rajpoot, Nasir M. (Nasir Mahmood) (2011) A novel framework for molecular co-expression pattern analysis in multi-channel toponome fluorescence images. In: MIAAB 2011 (Microscopic Image Analysis with Applications in Biology), Heidelberg, Germany, 2 Sep 2011. Published in: Proceedings of the 2011 Microscopic Image Analysis with Applications in Biology (Submitted)