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Image processing holds immense potential for societal benefit, yet its full potential is often accessible only to tech-savvy experts. Bridging this knowledge gap and providing accessible tools for users of all backgrounds remains an…
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…
Research in ultrasound imaging is limited in reproducibility by two factors: First, many existing ultrasound pipelines are protected by intellectual property, rendering exchange of code difficult. Second, most pipelines are implemented in…
Fast, incremental evolution of physics instrumentation raises the question of efficient software abstraction and transferability of algorithms across similar technologies. This contribution aims to provide an answer by introducing Track…
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…
This paper is an overview of Image Processing and Analysis using Scilab, a free prototyping environment for numerical calculations similar to Matlab. We demonstrate the capabilities of SIP -- the Scilab Image Processing Toolbox -- which…
Medical image computing software is essential for identifying imaging biomarkers that can support diagnosis, prognosis, treatment planning, and clinical research. However, the lack of standardized, user-friendly, and reproducible software…
Modern bioimage analysis approaches are data hungry, making it necessary for researchers to scavenge data beyond those collected within their (bio)imaging facilities. In addition to scale, bioimaging datasets must be accompanied with…
We present an open source software package SpectroLab a Matlab-based tool developed in 2018 for the analysis of spectroscopic data. In this package, there are tools for derivative analysis, stacked energy contours, stacked plots for theory,…
Image-based experiments can yield many thousands of individual measurements describing each object of interest, such as cells in microscopy screens. CellProfiler Analyst is a free, open-source software package designed for the exploration…
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…
Epileptic Seizure is an abnormal neuronal exertion in the brain, affecting nearly 70 million of the world's population (Ngugi et al., 2010). So many open-source neuroimaging tools are used for metabolism checkups and analysis purposes. The…
With the development of high-speed electron detectors, four-dimensional scanning transmission electron microscopy (4D-STEM) has emerged as a powerful tool for characterizing microstructures in material science and life science. However, the…
Medical image registration is an active research topic and forms a basis for many medical image analysis tasks. Although image registration is a rather general concept specialized methods are usually required to target a specific…
CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…
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…
Unprocessed RAW data is a highly valuable image format for image editing and computer vision. However, since the file size of RAW data is huge, most users can only get access to processed and compressed sRGB images. To bridge this gap, we…
One major challenge in science is to make all results potentially reproducible. Thus, along with the raw data, every step from basic processing of the data, evaluation, to the generation of the figures, has to be documented as clearly as…
Medical imaging is an invaluable resource in medicine as it enables to peer inside the human body and provides scientists and physicians with a wealth of information indispensable for understanding, modelling, diagnosis, and treatment of…