Related papers: Software for Microscopy Workshop White Paper
The software development process has evolved with respect to the problems in developing large and complex applications. There is a paradigm shift towards collaborative development, which necessitates the need to evaluate this approach. A…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
One of the goals of software design is to model a system in such a way that it is easily understandable. Nowadays the tendency for software development is changing from manual coding to automatic code generation; it is becoming model-based.…
Software engineering research benefited for decades from openly available tools, accessible systems, and problems that could be studied at modest scale. Today, many of the most relevant software systems are large, proprietary, and embedded…
The landscape of workflow systems for scientific applications is notoriously convoluted with hundreds of seemingly equivalent workflow systems, many isolated research claims, and a steep learning curve. To address some of these challenges…
The vast majority of the long tail of scientific software, the myriads of tools that implement the many analysis and visualization methods for different scientific fields, is highly specialized, purpose-built for a research project, and has…
Using machine learning in clinical practice poses hard requirements on explainability, reliability, replicability and robustness of these systems. Therefore, developing reliable software for monitoring critically ill patients requires close…
Scientific workflows are a cornerstone of modern scientific computing, and they have underpinned some of the most significant discoveries of the last decade. Many of these workflows have high computational, storage, and/or communication…
In the past decade, enormous progress has been made in advancing the state-of-the-art in bioimage analysis - a young computational field that works in close collaboration with the life sciences on the quantitative analysis of scientific…
A low cost remote imaging platform for biological applications was developed. The "Picroscope" is a device that allows the user to perform longitudinal imaging studies on multi-well cell culture plates. Here we present the network…
Workflows in biomolecular science are very important as they are intricately intertwined with the scientific outcomes, as well as algorithmic and methodological innovations. The use and effectiveness of workflow tools to meet the needs of…
High-quality research software is a cornerstone of modern scientific progress, enabling researchers to analyze complex data, simulate phenomena, and share reproducible results. However, creating such software requires adherence to best…
Research software -- specialist software used to support or undertake research -- is of huge importance to researchers. It contributes to significant advances in the wider world and requires collaboration between people with diverse skills…
{\mu}Manager, an open-source microscopy acquisition software, has been an essential tool for many microscopy experiments over the past 15 years, but is not easy to use for experiments in which image acquisition and analysis are closely…
This report summarizes insights from the 2025 Workshop on Next-Generation Ecosystems for Scientific Computing: Harnessing Community, Software, and AI for Cross-Disciplinary Team Science, which convened more than 40 experts from national…
We pose that microscopy offers an ideal real-world experimental environment for the development and deployment of active Bayesian and reinforcement learning methods. Indeed, the tremendous progress achieved by machine learning (ML) and…
Microscopes are vital pieces of equipment in much of biological research and medical diagnostics. However, access to a microscope can represent a bottleneck in research, especially in lower-income countries. `Smart' computer controlled…
The adoption of DevOps practices in embedded systems and firmware development is emerging as a response to the growing complexity of modern hardware--software co-designed products. Unlike cloud-native applications, embedded systems…
Research software plays a crucial role in advancing scientific knowledge, but ensuring its sustainability, maintainability, and long-term viability is an ongoing challenge. To address these concerns, the Sustainable Research Software…
Software is foundationally important to scientific and social progress, however, traditional acknowledgment of the use of others' work has not adapted in step with the rapid development and use of software in research. This report outlines…