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Here we report on a set of programs developed at the ZMBH Bio-Imaging Facility for tracking real-life images of cellular processes. These programs perform 1) automated tracking; 2) quantitative and comparative track analyses of different…
The field of computer graphics was revolutionized by models such as Neural Radiance Fields and 3D Gaussian Splatting, displacing triangles as the dominant representation for photogrammetry. In this paper, we argue for a triangle comeback.…
Parcellations are fundamental tools in neuroanatomy, allowing researchers to place functional imaging and molecular data within a structural context in the brain. Visualizing these parcellations is critical to guide biological understanding…
Methods for Novel View Synthesis (NVS) have recently found traction in the field of LiDAR simulation and large-scale 3D scene reconstruction. While solutions for faster rendering or handling dynamic scenes have been proposed, LiDAR specific…
Movies of human induced pluripotent stem cell (hiPSC)-derived engineered cardiac tissue (microbundles) contain abundant information about structural and functional maturity. However, extracting these data in a reproducible and…
As deep neural networks are increasingly used in solving high-stake problems, there is a pressing need to understand their internal decision mechanisms. Visualization has helped address this problem by assisting with interpreting complex…
Research is an incremental, iterative process, with new results relying and building upon previous ones. Scientists need to find, retrieve, understand, and verify results in order to confidently extend them, even when the results are their…
RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent…
We present SNID-SAGE (SuperNova IDentification-Spectral Analysis and Guided Exploration), a framework for supernova spectral classification with both a fully interactive graphical interface and a scriptable command-line pipeline for…
Graph Neural Networks (GNNs) have emerged as the leading paradigm for learning over graph-structured data. However, their performance is limited by issues inherent to graph topology, most notably oversquashing and oversmoothing. Recent…
Hydrodynamical simulations are increasingly able to accurately model physical systems on stellar, galactic, and cosmological scales, however, the utility of these simulations is often limited by our ability to directly compare them with the…
Image-based experiments can yield many thousands of individual measurements describing each object of interest, such as cells in microscopy screens. CellProfiler Analyst is a free, open-source software package designed for the exploration…
Data visualisation is a key tool in data mining for understanding big datasets. Many visualisation methods have been proposed, including the well-regarded state-of-the-art method t-Distributed Stochastic Neighbour Embedding. However, the…
Software engineering education and training have obstacles caused by a lack of basic knowledge about a process of program execution. The article is devoted to the development of special tools that help to visualize the process. We analyze…
The task of understanding and interpreting the complex information encoded within genomic sequences remains a grand challenge in biological research and clinical applications. In this context, recent advancements in large language model…
Training and testing supervised object detection models require a large collection of images with ground truth labels. Labels define object classes in the image, as well as their locations, shape, and possibly other information such as…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
Tensors (also commonly seen as multi-linear operators or as multi-dimensional arrays) are ubiquitous in scientific computing and in data science, and so are the software efforts for tensor operations. Particularly in recent years, we have…
Upcoming HI surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize HI objects is imperative. In this context,…
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…