Related papers: BioSig - An application of Octave
BioImageLoader (BIL) is a python library that handles bioimage datasets for machine learning applications, easing simple workflows and enabling complex ones. BIL attempts to wrap the numerous and varied bioimages datasets in unified…
Benchmarking, which involves collecting reference datasets and demonstrating method performances, is a requirement for the development of new computational tools, but also becomes a domain of its own to achieve neutral comparisons of…
This paper presents a digital signal processing tool developed using MatlabTM, which provides a very low-cost and effective strategy for analog-to-digital conversion of legated paper biomedical maps without requiring dedicated hardware.…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
Scientific Computing relies on executing computer algorithms coded in some programming languages. Given a particular available hardware, algorithms speed is a crucial factor. There are many scientific computing environments used to code…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Engineered image-based biomarkers offer a clinically interpretable alternative to black-box AI in computational pathology, yet their discovery remains largely intuition-driven, guided by fragmented literature rather than rigorous biological…
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)…
A key goal of bioinformatics is to create database systems and software platforms capable of storing and analysing large sets of biological data. Hundreds of biological databases are now available and provide access to huge amount of…
Live time-lapse microscopy is essential for a wide range of biological applications. Software-based automation is the gold standard for the operation of hardware accessories necessary for image acquisition. Given that current software…
The growing demand for continuous physiological monitoring and human-machine interaction in real-world settings calls for wearable platforms that are flexible, low-power, and capable of on-device intelligence. This work presents…
BCI algorithm development has long been hampered by two major issues: small sample sets and a lack of reproducibility. We offer a solution to both of these problems via a software suite that streamlines both the issues of finding and…
Biomedical research increasingly relies on heterogeneous, high-dimensional datasets, yet effective visualization remains hindered by fragmented code resources, steep programming barriers, and limited domain-specific guidance. Bizard is an…
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking, and dependency management. To manage these processes, a diverse set…
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
Automated debugging, long pursued in a variety of fields from software engineering to cybersecurity, requires a framework that offers the building blocks for a programmable debugging workflow. However, existing debuggers are primarily…
DeepReg (https://github.com/DeepRegNet/DeepReg) is a community-supported open-source toolkit for research and education in medical image registration using deep learning.
This work describes the setup of an advanced technical infrastructure for collaborative software development (CDE) in large, distributed projects based on GitLab. We present its customization and extension, additional features and processes…
Most particle induced X-ray emission (PIXE) data analysis codes are not focused on handling multilayered samples. We have developed an open-source library called "LibCPIXE", for PIXE data analysis. It is written in standard C and implements…
JISA is a software library, written in Java, aimed at providing an easy, flexible and standardised means of creating experimental control software for physical sciences researchers. Specifically, with an emphasis on enabling measurement…