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As image generation techniques mature, there is a growing interest in explainable representations that are easy to understand and intuitive to manipulate. In this work, we turn to co-occurrence statistics, which have long been used for…
Spatial transcriptomics is a modern sequencing technology that allows the measurement of the activity of thousands of genes in a tissue sample and map where the activity is occurring. This technology has enabled the study of the so-called…
The histological assessment of human tissue has emerged as the key challenge for detection and treatment of cancer. A plethora of different data sources ranging from tissue microarray data to gene expression, proteomics or metabolomics data…
Tissue stiffness is related to soft tissue pathologies and can be assessed through palpation or via clinical imaging systems, e.g., ultrasound or magnetic resonance imaging. Typically, the image based approaches are not suitable during…
Artificial intelligence may assist healthcare systems in meeting increasing demand for pathology services while maintaining diagnostic quality and reducing turnaround time and costs. We aimed to investigate the performance of an…
Target identification, one of the steps of drug discovery, aims at identifying biomolecules whose function should be therapeutically altered in order to cure the considered pathology. This work proposes an algorithm for in silico target…
The interactions between tumor cells and the tumor microenvironment (TME) dictate therapeutic efficacy of radiation and many systemic therapies in breast cancer. However, to date, there is not a widely available method to reproducibly…
Automating white blood cell classification for diagnosis of leukaemia is a promising alternative to time-consuming and resource-intensive examination of cells by expert pathologists. However, designing robust algorithms for classification…
In the field of image-based drug discovery, capturing the phenotypic response of cells to various drug treatments and perturbations is a crucial step. However, existing methods require computationally extensive and complex multi-step…
Rheumatoid Arthritis (RA) is a chronic, autoimmune disease which primarily affects the joint's synovial tissue. It is a highly heterogeneous disease, with wide cellular and molecular variability observed in synovial tissues. Over the last…
Microscopic examination of tissues or histopathology is one of the diagnostic procedures for detecting colorectal cancer. The pathologist involved in such an examination usually identifies tissue type based on texture analysis, especially…
Topological data analysis (TDA) has emerged as one of the most promising techniques to reconstruct the unknown shapes of high-dimensional spaces from observed data samples. TDA, thus, yields key shape descriptors in the form of persistent…
Progress in digital pathology is hindered by high-resolution images and the prohibitive cost of exhaustive localized annotations. The commonly used paradigm to categorize pathology images is patch-based processing, which often incorporates…
Calcium imaging has emerged as a workhorse method in neuroscience to investigate patterns of neuronal activity. Instrumentation to acquire calcium imaging movies has rapidly progressed and has become standard across labs. Still, algorithms…
Deep learning techniques have proven high accuracy for identifying melanoma in digitised dermoscopic images. A strength is that these methods are not constrained by features that are pre-defined by human semantics. A down-side is that it is…
The process of digitising histology slides involves multiple factors that can affect a whole slide image's (WSI) final appearance, including the staining protocol, scanner, and tissue type. This variability constitutes a domain shift and…
Digital pathology has made significant advances in tumor diagnosis and segmentation, but image variability due to differences in organs, tissue preparation, and acquisition - known as domain shift - limits the effectiveness of current…
The overexpression of human epidermal growth factor receptor 2 (HER2) has been established as a therapeutic target in multiple types of cancers, such as breast and gastric cancers. Immunohistochemistry (IHC) is employed as a basic HER2 test…
Histopathology images; microscopy images of stained tissue biopsies contain fundamental prognostic information that forms the foundation of pathological analysis and diagnostic medicine. However, diagnostics from histopathology images…
The accurate classification of lymphoma subtypes using hematoxylin and eosin (H&E)-stained tissue is complicated by the wide range of morphological features these cancers can exhibit. We present LymphoML - an interpretable machine learning…