Related papers: Triander: A new program for visual analysis of nuc…
Tracking many cells in time-lapse 3D image sequences is an important challenging task of bioimage informatics. Motivated by a study of brain-wide 4D imaging of neural activity in C. elegans, we present a new method of multi-cell tracking.…
Sophisticated visualization tools are essential for the presentation and exploration of human neuroimaging data. While two-dimensional orthogonal views of neuroimaging data are conventionally used to display activity and statistical…
Tracers provide users with useful information about program executions. In this article, we propose a ``tracer driver''. From a single tracer, it provides a powerful front-end enabling multiple dynamic analysis tools to be easily…
Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in…
Nanopore sequencing offers the ability for real-time analysis of long DNA sequences at a low cost, enabling new applications such as early detection of cancer. Due to the complex nature of nanopore measurements and the high cost of…
Braidlab is a Matlab package for analyzing data using braids. It was designed to be fast, so it can be used on relatively large problems. It uses the object-oriented features of Matlab to provide a class for braids on punctured disks and a…
Ray tracing 3D Gaussian particles enables realistic effects such as depth of field, refractions, and flexible camera modeling for novel-view synthesis. However, existing methods trace Gaussians through proxy geometry, which requires…
We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holographic microscopy. Our program detects the…
We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to i) spend less time on data management and processing, ii)…
Software frameworks for neural networks play a key role in the development and application of deep learning methods. In this paper, we introduce the Chainer framework, which intends to provide a flexible, intuitive, and high performance…
Seglearn is an open-source python package for machine learning time series or sequences using a sliding window segmentation approach. The implementation provides a flexible pipeline for tackling classification, regression, and forecasting…
Visualizations have become an indispensable part of the scientific process. A vibrant ecosystem of visualization tools exists, catering to a wide variety of different needs. Real-time visualizations of numerical simulations offer scientists…
This report describes an NLP assistant for the collaborative development environment Clide, that supports the development of NLP applications by providing easy access to some common NLP data structures. The assistant visualizes text…
SIMD||DNA is a model of DNA strand displacement allowing parallel in-memory computation on DNA storage. We show how to simulate an arbitrary 3-symbol space-bounded Turing machine with a SIMD||DNA program, giving a more direct and efficient…
We present BrainPainter, a software that automatically generates images of highlighted brain structures given a list of numbers corresponding to the output colours of each region. Compared to existing visualisation software (i.e.…
Punzo et al. (2015) recently reported on the state of the art for visualisation of H I data cubes. I here briefly describe another program, FRELLED, specifically designed for dealing with H I data. Unlike many 3D viewers, FRELLED can handle…
RNA-Seq analysis has revolutionized researchers' understanding of the transcriptome in biological research. Assessing the differences in transcriptomic profiles between tissue samples or patient groups enables researchers to explore the…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
This paper proposes a new mathematical framework that can be applied to biological problems such as analysis of the structures of proteins and protein complexes. In particular, it gives a new method for encoding the three-dimensional…
Understanding the behavior of software in execution is a key step in identifying and fixing performance issues. This is especially important in high performance computing contexts where even minor performance tweaks can translate into large…