Related papers: Software for Microscopy Workshop White Paper
We design the imaging data calibration and reduction software for MICADO, the First Light near-IR instrument on the Extremely Large Telescope. In this process we have hit the limit of what can be achieved with a detailed software design…
The use of embedded software is advancing in modern medical devices, so does its capabilities and complexity. This paradigm shift brings many challenges such as an increased rate of medical device failures due to software faults. In this…
In the field of computational science and engineering, workflows often entail the application of various software, for instance, for simulation or pre- and postprocessing. Typically, these components have to be combined in arbitrarily…
Scientific open-source software (OSS) has greatly benefited research communities through its transparent and collaborative nature. Given its critical role in scientific research, ensuring the sustainability of such software has become…
Real time computer control is an essential feature of scanning probe microscopes, which have become essential tools for the characterization and investigation of nanometer scale samples. Most commercial (and some open-source) scanning probe…
Developing software to undertake complex, compute-intensive scientific processes requires a challenging combination of both specialist domain knowledge and software development skills to convert this knowledge into efficient code. As…
As spatial and temporal resolutions of scientific instruments improve, the explosion in the volume of data produced is becoming a key challenge. It can be a critical bottleneck for integration between scientific instruments at the edge and…
Many microscopy applications are limited by the total amount of usable light and are consequently challenged by the resulting levels of noise in the acquired images. This problem is often addressed via (supervised) deep learning based…
Software production research is quickly evolving on two parallel approaches: conventional and bio-inspired. The bio-inspired approaches are generally developed and presented as enhancements of the conventional ones. However the conventional…
Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, an open-source software package that enables to simulate operational light-sheet microscopes by combining data…
The profile of research software engineering has been greatly enhanced by developments at institutions around the world to form groups and communities that can support effective, sustainable development of research software. We observe,…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
Modern systems are increasingly connected and more integrated with other existing systems, giving rise to \textit{systems-of-systems} (SoS). An SoS consists of a set of independent, heterogeneous systems that interact to provide new…
This work-in-progress paper describes a vision, i.e., that of fast and reliable software user experience studies conducted with the help from the crowd. Commonly, user studies are controlled in-lab activities that require the instruction,…
What is the impact of software engineering research on current practices in industry? In this paper, I report on my direct experience as a PhD/post-doc working in software engineering research projects, and then spending the following five…
Understanding different types of users' needs can even be more critical in today's data visualization field, as exploratory visualizations for novice users are becoming more widespread with an increasing amount of data sources. The…
Despite the growing availability of tools designed to support scholarly knowledge extraction and organization, many researchers still rely on manual methods, sometimes due to unfamiliarity with existing technologies or limited access to…
The advancement of software sustainability encounters notable challenges, underscoring the necessity for understanding these challenges to facilitate significant progress and pave the way for effective solutions to advance software…
Software plays an ever increasing role in complex system development and prototyping, and in recent years, MIT Lincoln Laboratory has sought to improve both the effectiveness and culture surrounding software engineering in execution of its…
Containers as the unit of application delivery are the 'next big thing' in the software development world. They enable developers to create an executable image containing an application bundled with all its dependencies which a user can run…