Related papers: Cellulyzer - Automated analysis and interactive vi…
We here propose an automated pipeline for the microscopy image-based characterization of catalytically active inclusion bodies (CatIBs), which includes a fully automatic experimental high-throughput workflow combined with a hybrid approach…
The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and…
The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…
Cellular and molecular imaging techniques and models have been developed to characterize single stages of viral proliferation after focal infection of cells in vitro. The fast and automatic classification of cell imaging data may prove…
Biofilms are communities of microorganisms that grow on virtually all surfaces with sufficient nutrients including aquatic and industrial water systems and medical devices. Biofilms are complex, structured communities where the interplay of…
We introduce Trialstreamer, a living database of clinical trial reports. Here we mainly describe the evidence extraction component; this extracts from biomedical abstracts key pieces of information that clinicians need when appraising the…
By their very nature microscopy images of cells and tissues consist of a limited number of object types or components. In contrast to most natural scenes, the composition is known a priori. Decomposing biological images into semantically…
Cell tracking remains a pivotal yet challenging task in biomedical research. The full potential of deep learning for this purpose is often untapped due to the limited availability of comprehensive and varied training data sets. In this…
Whole-slide multiplex imaging of brain tissue generates massive information-dense images that are challenging to analyze and require custom software. We present an alternative query-driven programming-free strategy using a multiplex visual…
Program synthesis -- the automatic generation of code given a specification -- is one of the most fundamental tasks in artificial intelligence (AI) and the dream of many programmers. Numerous synthesizers have been developed for program…
Cell tracking algorithms which automate and systematise the analysis of time lapse image data sets of cells are an indispensable tool in the modelling and understanding of cellular phenomena. In this study we present a theoretical framework…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
Unified multimodal models (UMMs) have shown impressive capabilities in generating natural images and supporting multimodal reasoning. However, their potential in supporting computer-use planning tasks, which are closely related to our…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
Lineage tracing, the tracking of living cells as they move and divide, is a central problem in biological image analysis. Solutions, called lineage forests, are key to understanding how the structure of multicellular organisms emerges. We…
As software systems grow in complexity, data and tools that provide valuable insights for easier program comprehension become increasingly important. OpenTelemetry has become a standard for the collection of monitoring data. In this work we…
Image simulation remains under-exploited for the most widely used biological phase microscopy methods, because of difficulties in simulating partially coherent illumination. We describe an open-source toolbox, microlith…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
We present TrialsSummarizer, a system that aims to automatically summarize evidence presented in the set of randomized controlled trials most relevant to a given query. Building on prior work, the system retrieves trial publications…
With the rapid advancement of Big Data platforms such as Hadoop, Spark, and Dataflow, many tools are being developed that are intended to provide end users with an interactive environment for large-scale data analysis (e.g., IQmulus).…