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Many creative ideas are being proposed for image sensor designs, and these may be useful in applications ranging from consumer photography to computer vision. To understand and evaluate each new design, we must create a corresponding image…
The Core Imaging Library (CIL) is an open-source versatile Python framework for solving inverse problems with special emphasis on imaging applications such as computed tomography (CT), using a plug-in architecture for data and operators,…
With the increasing amount of data and use of computation in science, software has become an important component in many different domains. Computing is now being used more often and in more aspects of scientific work including data…
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…
We have prototyped a "spreadsheet component repository" Web site, from which users can copy "components" into their own Excel or Google spreadsheets. Components are collections of cells containing formulae: in real life, they would do…
PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0):…
High-quality visualizations are an essential part of robotics research, enabling clear communication of results through figures, animations, and demonstration videos. While Blender is a powerful and freely available 3D graphics platform,…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
Systematic exploration of hypotheses is a major part of any empirical research. In software engineering, we often produce unique tools for experiments and evaluate them independently on different data sets. In this paper, we present…
We propose to automatically create capsule wardrobes. Given an inventory of candidate garments and accessories, the algorithm must assemble a minimal set of items that provides maximal mix-and-match outfits. We pose the task as a subset…
Natural language processing is used for solving a wide variety of problems. Some scholars and interest groups working with language resources are not well versed in programming, so there is a need for a good graphical framework that allows…
A major bottleneck of interdisciplinary computer vision (CV) research is the lack of a framework that eases the reuse and abstraction of state-of-the-art CV models by CV and non-CV researchers alike. We present here BU-CVKit, a computer…
Large-scale biological discovery requires integrating massive, heterogeneous datasets like those from the JUMP Cell Painting consortium, but technical batch effects and a lack of generalizable models remain critical roadblocks. To address…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
We present Synthesizer, a fast, flexible, modular and extensible platform for modelling synthetic astrophysical observables. Synthesizer can be used for a number of applications, but is predominantly designed for generating mock observables…
Bright-field microscopy, a cost-effective solution for live-cell culture, is often the only resource available, along with standard CPUs, for many low-budget labs. The inherent challenges of bright-field images -- their noisiness, low…
Spectropolarimetry, the observation of polarization and intensity as a function of wavelength, is a powerful tool in stellar astrophysics. It is particularly useful for characterizing stars and circumstellar material, and for tracing the…
Application containers, such as Docker containers, have recently gained popularity as a solution for agile and seamless deployment of applications. These light-weight virtualization environments run applications that are packed together…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modelling. Microtubule and actin filaments are well characterized, and the associated proteins are often known, as well as their abundance and…