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Live cell culture is crucial in biomedical studies for analyzing cell properties and dynamics in vitro. This study focuses on segmenting unstained live cells imaged with bright-field microscopy. While many segmentation approaches exist for…
Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the…
Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a…
Medical image classification plays a crucial role in computer-aided clinical diagnosis. While deep learning techniques have significantly enhanced efficiency and reduced costs, the privacy-sensitive nature of medical imaging data…
The discovery of disease subtypes is an essential step for developing precision medicine, and disease subtyping via omics data has become a popular approach. While promising, subtypes obtained from conventional approaches may not be…
Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer…
Pure and homogeneous biological macromolecules (i.e. proteins, nucleic acids, protein-protein or protein-nucleic acid complexes, and functional assemblies such as ribosomes and viruses) are the key for consistent and reliable biochemical…
Quality control in molecular optical sectioning microscopy is indispensable for transforming acquired digital images from qualitative descriptions to quantitative data. Although numerous tools, metrics, and phantoms have been developed,…
The living body is composed of innumerable fine and complex structures and although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these…
The ethical and legal imperative to share research data without causing harm requires careful attention to privacy risks. While mounting evidence demonstrates that data sharing benefits science, legitimate concerns persist regarding the…
This thesis centres on the development of multidimensional fluorescence imaging tools, with a particular emphasis on fluorescence lifetime imaging (FLIM) microscopy for application to biological research. The key aspects of this thesis are…
Automated identification of DICOM image series is essential for large-scale medical image analysis, quality control, protocol harmonization, and reliable downstream processing. However, DICOM series classification remains challenging due to…
Accurate localization of organ boundaries is critical in medical imaging for segmentation, registration, surgical planning, and radiotherapy. While deep convolutional networks (ConvNets) have advanced general-purpose edge detection to…
Mass spectrometry is a widely used method to study molecules and processes in medicine, life sciences, chemistry, catalysis, and industrial product quality control, among many other applications. One of the main features of some mass…
Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that…
MR imaging is a valuable diagnostic tool allowing to non-invasively visualize patient anatomy and pathology with high soft-tissue contrast. However, MRI acquisition is typically time-consuming, leading to patient discomfort and increased…
For personalized medicines, very crucial intrinsic information is present in high dimensional omics data which is difficult to capture due to the large number of molecular features and small number of available samples. Different types of…
Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks…
{\it ' Seeing is believing '} \cite{north06}- is the fundamental philosophy of optical imaging based on light microscopy \cite{ntziachristos10}. Since the pioneering works of Antonie van Leeuwenhoek and Robert Hooke in the 17th century,…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…