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Cell boundary information is crucial for analyzing cell behaviors from time-lapse microscopy videos. Existing supervised cell segmentation tools, such as ImageJ, require tuning various parameters and rely on restrictive assumptions about…
Cell state discovery is crucial for understanding biological systems and enhancing medical outcomes. A key aspect of this process is identifying distinct biomarkers that define specific cell states. However, difficulties arise from the…
Tracking single molecules is instrumental for quantifying the transport of molecules and nanoparticles in biological samples, e.g., in brain drug delivery studies. Existing intensity-based localisation methods are not developed for imaging…
Creating the best possible conditions is essential for proper cell growth. Incubators, a type of biotechnological instrument, are used to simulate this condition and maintain the cells within them. The processes involved in creating a…
This paper presents a Matlab toolbox to perform basic image processing and visualization tasks, particularly designed for medical image processing. The functionalities available are similar to basic functions found in other non-Matlab…
Recent advances in high-throughput electron microscopy imaging enable detailed study of centrosome aberrations in cancer cells. While the image acquisition in such pipelines is automated, manual detection of centrioles is still necessary to…
Visualisations drive all aspects of the Machine Learning (ML) Development Cycle but remain a vastly untapped resource by the research community. ML testing is a highly interactive and cognitive process which demands a human-in-the-loop…
Due to the increased complexity of parallel and distributed programs, debugging of them is considered to be the most difficult and time consuming part of the software lifecycle. Tool support is hence a crucial necessity to hide complexity…
ImageJ is a graphical user interface (GUI) driven, public domain, Java-based, software package for general image processing traditionally used mainly in life sciences fields. The image processing capabilities of ImageJ are useful and…
Semantic understanding of programs has attracted great attention in the community. Inspired by recent successes of large language models (LLMs) in natural language understanding, tremendous progress has been made by treating programming…
In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the…
ImageJ is a graphical user interface (GUI) driven, public domain, Java-based, software package for general image processing traditionally used mainly in life sciences fields. The image processing capabilities of ImageJ are useful and…
In this paper, we propose a new approach for building cellular automata to solve real-world segmentation problems. We design and train a cellular automaton that can successfully segment high-resolution images. We consider a colony that…
BioImageLoader (BIL) is a python library that handles bioimage datasets for machine learning applications, easing simple workflows and enabling complex ones. BIL attempts to wrap the numerous and varied bioimages datasets in unified…
Label-free cell classification is advantageous for supplying pristine cells for further use or examination, yet existing techniques frequently fall short in terms of specificity and speed. In this study, we address these limitations through…
The automated segmentation of cells in microscopic images is an open research problem that has important implications for studies of the developmental and cancer processes based on in vitro models. In this paper, we present the approach for…
Microbiomes are a vital part of the human body, engaging in tasks like food digestion and immune defense. Their structure and function must be understood in order to promote host health and facilitate swift recovery during disease. Due to…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Multiplex tissue immunostaining is a technology of growing relevance as it can capture in situ the complex interactions existing between the elements of the tumor microenvironment. The existence and availability of large, annotated image…
Biomedical data harmonization is essential for enabling exploratory analyses and meta-studies, but the process of schema matching - identifying semantic correspondences between elements of disparate datasets (schemas) - remains a…