Shan E Ahmed Raza
YOU?
Author Swipe
View article: Star-Motifs: Revealing Single-Cell Spatiotypes from Routine Histology Using Star-Convex Neighborhoods
Star-Motifs: Revealing Single-Cell Spatiotypes from Routine Histology Using Star-Convex Neighborhoods Open
The tumor microenvironment (TME) is a dynamic interplay among cancer, immune, and stromal cells that profoundly influences tumor growth, progression, and treatment response. Although recent spatial transcriptomics and multiplex imaging tec…
View article: CORE -- A Cell-Level Coarse-to-Fine Image Registration Engine for Multi-stain Image Alignment
CORE -- A Cell-Level Coarse-to-Fine Image Registration Engine for Multi-stain Image Alignment Open
Accurate and efficient registration of whole slide images (WSIs) is essential for high-resolution, nuclei-level analysis in multi-stained tissue slides. We propose a novel coarse-to-fine framework CORE for accurate nuclei-level registratio…
View article: From traditional to deep learning approaches in whole slide image registration: A methodological review
From traditional to deep learning approaches in whole slide image registration: A methodological review Open
Whole slide image (WSI) registration is an essential task for analyzing the tumor microenvironment (TME) in histopathology. It involves the alignment of spatial information between WSIs of the same section or serial sections of a tissue sa…
View article: Pan-Cancer Profiling of Mitotic Topology & Mitotic Errors: Insights into Prognosis, Genomic Alterations, and Immune Landscape
Pan-Cancer Profiling of Mitotic Topology & Mitotic Errors: Insights into Prognosis, Genomic Alterations, and Immune Landscape Open
SUMMARY Mitotic activity and mitotic errors are critical biomarkers of cancer proliferation and progression. While the role of mitosis count in diverse cancer types has been studied, its characterization through organizational patterns in …
View article: Development and validation of an artificial intelligence-based pipeline for predicting oral epithelial dysplasia malignant transformation
Development and validation of an artificial intelligence-based pipeline for predicting oral epithelial dysplasia malignant transformation Open
View article: CellOMaps: A compact representation for robust classification of lung adenocarcinoma growth patterns
CellOMaps: A compact representation for robust classification of lung adenocarcinoma growth patterns Open
Lung adenocarcinoma (LUAD) is a morphologically heterogeneous disease, characterized by five primary histological growth patterns. The classification of such patterns is crucial due to their direct relation to prognosis but the high subjec…
View article: Domain Generalization in Computational Pathology: Survey and Guidelines
Domain Generalization in Computational Pathology: Survey and Guidelines Open
Deep learning models have exhibited exceptional effectiveness in Computational Pathology (CPath) for various tasks on multi-gigapixel histology images. Nevertheless, the presence of out-of-distribution data (stemming from different sources…
View article: Tumor-infiltrating lymphocytes in breast cancer through artificial intelligence: biomarker analysis from the results of the TIGER challenge
Tumor-infiltrating lymphocytes in breast cancer through artificial intelligence: biomarker analysis from the results of the TIGER challenge Open
The prognostic significance of tumor-infiltrating lymphocytes (TILs) in breast cancer has been recognized for over a decade. Although histology-based scoring recommendations exist to standardize visual TILs assessment, interobserver agreem…
View article: From Traditional to Deep Learning Approaches in Whole Slide Image Registration: A Methodological Review
From Traditional to Deep Learning Approaches in Whole Slide Image Registration: A Methodological Review Open
Whole slide image (WSI) registration is an essential task for analysing the tumour microenvironment (TME) in histopathology. It involves the alignment of spatial information between WSIs of the same section or serial sections of a tissue s…
View article: Gland Segmentation Using SAM With Cancer Grade as a Prompt
Gland Segmentation Using SAM With Cancer Grade as a Prompt Open
Cancer grade is a critical clinical criterion that can be used to determine the degree of cancer malignancy. Revealing the condition of the glands, a precise gland segmentation can assist in a more effective cancer grade classification. In…
View article: Deep Learning Based Segmentation of Blood Vessels from H&E Stained Oesophageal Adenocarcinoma Whole-Slide Images
Deep Learning Based Segmentation of Blood Vessels from H&E Stained Oesophageal Adenocarcinoma Whole-Slide Images Open
Blood vessels (BVs) play a critical role in the Tumor Micro-Environment (TME), potentially influencing cancer progression and treatment response. However, manually quantifying BVs in Hematoxylin and Eosin (H&E) stained images is challengin…
View article: CellOMaps: A Compact Representation for Robust Classification of Lung Adenocarcinoma Growth Patterns
CellOMaps: A Compact Representation for Robust Classification of Lung Adenocarcinoma Growth Patterns Open
Lung adenocarcinoma (LUAD) is a morphologically heterogeneous disease, characterized by five primary histological growth patterns. The classification of such patterns is crucial due to their direct relation to prognosis but the high subjec…
View article: A novel AI-based score for assessing the prognostic value of intra-epithelial lymphocytes in oral epithelial dysplasia
A novel AI-based score for assessing the prognostic value of intra-epithelial lymphocytes in oral epithelial dysplasia Open
View article: Characterization of Breast Cancer Intra-Tumor Heterogeneity Using Artificial Intelligence
Characterization of Breast Cancer Intra-Tumor Heterogeneity Using Artificial Intelligence Open
Intra-tumor heterogeneity (ITH) is a fundamental characteristic of breast cancer (BC), influencing tumor progression, prognosis, and therapeutic responses. However, the complexity of ITH in BC makes its accurate characterization challengin…
View article: Development and Validation of an Artificial Intelligence-based Pipeline for Predicting Oral Epithelial Dysplasia Malignant Transformation
Development and Validation of an Artificial Intelligence-based Pipeline for Predicting Oral Epithelial Dysplasia Malignant Transformation Open
Oral epithelial dysplasia (OED) is a potentially malignant histopathological diagnosis given to lesions of the oral cavity that are at risk of progression to malignancy. Manual grading of OED is subject to substantial variability and does …
View article: Table S1 from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma
Table S1 from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma Open
Differentially expressed genes in TCGA LUSC and LUAD patients with high versus low S_intra/immune
View article: Data from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma
Data from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma Open
Beyond tertiary lymphoid structures, a significant number of immune rich areas without germinal center-like structures are observed in non-small cell lung cancer. Here, we integrated transcriptomic data and digital pathology images to stud…
View article: Supplementary Data from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma
Supplementary Data from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma Open
Table S3 and Fig. S1-S10
View article: Supplementary Data from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma
Supplementary Data from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma Open
Table S3 and Fig. S1-S10
View article: Table S2 from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma
Table S2 from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma Open
Lists of TCGA LUSC and LUAD cases in the discovery and validation cohort
View article: Table S1 from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma
Table S1 from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma Open
Differentially expressed genes in TCGA LUSC and LUAD patients with high versus low S_intra/immune
View article: Table S2 from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma
Table S2 from Spatial positioning of immune hotspots reflects the interplay between B and T cells in lung squamous cell carcinoma Open
Lists of TCGA LUSC and LUAD cases in the discovery and validation cohort
View article: A fully automated and explainable algorithm for predicting malignant transformation in oral epithelial dysplasia
A fully automated and explainable algorithm for predicting malignant transformation in oral epithelial dysplasia Open
View article: An Attention Based Pipeline for Identifying Pre-Cancer Lesions in Head and Neck Clinical Images
An Attention Based Pipeline for Identifying Pre-Cancer Lesions in Head and Neck Clinical Images Open
Early detection of cancer can help improve patient prognosis by early intervention. Head and neck cancer is diagnosed in specialist centres after a surgical biopsy, however, there is a potential for these to be missed leading to delayed di…
View article: Nuclei-Location Based Point Set Registration of Multi-Stained Whole Slide Images
Nuclei-Location Based Point Set Registration of Multi-Stained Whole Slide Images Open
Whole Slide Images (WSIs) provide exceptional detail for studying tissue architecture at the cell level. To study tumour microenvironment (TME) with the context of various protein biomarkers and cell sub-types, analysis and registration of…
View article: A Novel AI-based Score for Assessing the Prognostic Value of Intra-Epithelial Lymphocytes in Oral Epithelial Dysplasia
A Novel AI-based Score for Assessing the Prognostic Value of Intra-Epithelial Lymphocytes in Oral Epithelial Dysplasia Open
Oral epithelial dysplasia (OED) poses a significant clinical challenge due to its potential for malignant transformation and the lack of reliable prognostic markers. Current grading systems for OED may not be reliable for prediction of mal…
View article: Mitosis detection, fast and slow: Robust and efficient detection of mitotic figures
Mitosis detection, fast and slow: Robust and efficient detection of mitotic figures Open
Counting of mitotic figures is a fundamental step in grading and prognostication of several cancers. However, manual mitosis counting is tedious and time-consuming. In addition, variation in the appearance of mitotic figures causes a high …
View article: TIAViz: A Browser-based Visualization Tool for Computational Pathology Models
TIAViz: A Browser-based Visualization Tool for Computational Pathology Models Open
Digital pathology has gained significant traction in modern healthcare systems. This shift from optical microscopes to digital imagery brings with it the potential for improved diagnosis, efficiency, and the integration of AI tools into th…
View article: Artificial Intelligence-Based Mitosis Scoring in Breast Cancer: Clinical Application
Artificial Intelligence-Based Mitosis Scoring in Breast Cancer: Clinical Application Open
In recent years, artificial intelligence (AI) has demonstrated exceptional performance in mitosis identification and quantification. However, the implementation of AI in clinical practice needs to be evaluated against the existing methods.…
View article: CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting
CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting Open