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Nowadays, the amount of heterogeneous biomedical data is increasing more and more thanks to novel sensing techniques and high-throughput technologies. In reference to biomedical image analysis, the advances in image acquisition modalities…
Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…
BlenderProc is a modular procedural pipeline, which helps in generating real looking images for the training of convolutional neural networks. These can be used in a variety of use cases including segmentation, depth, normal and pose…
The quantification of synapses is instrumental to measure the evolution of synaptic densities of neurons under the effect of some physiological conditions, neuronal diseases or even drug treatments. However, the manual quantification of…
Authors of biomedical publications often use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a way to concisely communicate such findings,…
Imaging Mueller polarimetry has already proved its potential for metrology, remote sensing and biomedicine. The real-time applications of this modality require both video rate image acquisition and fast data post-processing algorithms.…
We propose a software platform that integrates methods and tools for multi-objective parameter auto- tuning in tissue image segmentation workflows. The goal of our work is to provide an approach for improving the accuracy of nucleus/cell…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
Medical imaging is the technique used to create images of the human body or parts of it for clinical purposes. Medical images always have large sizes and they are commonly corrupted by single or multiple noise type at the same time, due to…
Interactive computing notebooks, such as Jupyter notebooks, have become a popular tool for developing and improving data-driven models. Such notebooks tend to be executed either in the user's own machine or in a cloud environment, having…
Our work aims at using quantitative imaging tools to complement the limitation of noise encountered by high resolution fluorescence microscopy methods. Several cycles of fluorophore activation, imaging and deactivation produce a sequence of…
Computer models of humans are ubiquitous throughout computer animation and computer vision. However, these models rarely represent the dynamics of human motion, as this requires adding a complex layer that solves body motion in response to…
A program execution monitor is a program that collects and abstracts information about program executions. The "collect" operator is a high level, general purpose primitive which lets users implement their own monitors. "Collect" is built…
Cells are the fundamental unit of biological organization, and identifying them in imaging data - cell segmentation - is a critical task for various cellular imaging experiments. While deep learning methods have led to substantial progress…
Medical image processing is often limited by the computational cost of the involved algorithms. Whereas dedicated computing devices (GPUs in particular) exist and do provide significant efficiency boosts, they have an extra cost of use in…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
Cell tracking and segmentation assist biologists in extracting insights from large-scale microscopy time-lapse data. Driven by local accuracy metrics, current tracking approaches often suffer from a lack of long-term consistency and the…
We introduce Biomaker CA: a Biome Maker project using Cellular Automata (CA). In Biomaker CA, morphogenesis is a first class citizen and small seeds need to grow into plant-like organisms to survive in a nutrient starved environment and…
Histopathology, the microscopic study of diseased tissue, is increasingly digitized, enabling improved visualization and streamlined workflows. An important task in histopathology is the segmentation of cells and glands, essential for…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…