Article
Engineering, Biomedical
Ariel Hernan Curiale, Agustin Bernardo, Rodrigo Cardenas, German Mato
Summary: This paper introduces an open-source application CardIAc as an alternative to commercial software for left ventricle myocardial strain quantification. It provides a useful extension for myocardial strain analysis that promotes easy modification and adjustment to different motion tracking strategies for improved accuracy. The software is intended for research use and allows users to tailor the program's performance to their scientific or clinical requirements.
INTERNATIONAL JOURNAL OF COMPUTER ASSISTED RADIOLOGY AND SURGERY
(2021)
Article
Computer Science, Information Systems
Raul Marticorena-Sanchez, Carlos Lopez-Nozal, Yi Peng Ji, Carlos Pardo-Aguilar, Alvar Arnaiz-Gonzalez
Summary: This paper introduces UBUMonitor, an open-source desktop application that monitors student activity and performance by downloading data from the Moodle platform. The application organizes and summarizes the data in customizable charts for visual analysis. The paper also discusses various approaches to e-teaching improvement through real case studies, including access analysis, statistical analysis, error detection, teacher activity check, and comparisons between online and blended learning profiles.
Article
Plant Sciences
Feiyu Zhu, Puneet Paul, Waseem Hussain, Kyle Wallman, Balpreet K. Dhatt, Jaspreet Sandhu, Larissa Irvin, Gota Morota, Hongfeng Yu, Harkamal Walia
Summary: Accurate measurement of seed size parameters is crucial for breeding and basic research. The open-source SeedExtractor software efficiently processes images, demonstrating adaptability and accuracy in determining key yield-related traits in crops.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Zhe Dong, William Mau, Yu Feng, Zachary T. Pennington, Lingxuan Chen, Yosif Zaki, Kanaka Rajan, Tristan Shuman, Daniel Aharoni, Denise J. Cai
Summary: Miniature microscopes are widely used for in vivo calcium imaging in freely behaving animals. However, the computation complexity of extracting calcium signals from raw videos remains a challenge. In order to overcome this bottleneck, a user-friendly and low memory demand analysis pipeline called Minian has been developed, which allows researchers to extract cell locations, calcium traces, and deconvolved neural activities.
Article
Computer Science, Interdisciplinary Applications
Nirbhaya Shaji, Florbela Nunes, M. Ines Rocha, Elsa Ferreira Gomes, Helena Castro
Summary: This report introduces a graphical user interface called MigraR, which translates the coordinate positions of moving cells into measurable parameters of cell migration, and plots cell trajectories and migration metrics. By simplifying the data analysis process, this interface helps cell biologists without data analysis experience to quantify and visualize cell migration datasets.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Editorial Material
Environmental Sciences
Isamar M. Cortes
Summary: Isamar Cortes discusses the usage of Python-based open-source software for processing satellite data.
NATURE REVIEWS EARTH & ENVIRONMENT
(2023)
Article
Ecology
Sam Lapp, Tessa Rhinehart, Louis Freeland-Haynes, Jatin Khilnani, Alexandra Syunkova, Justin Kitzes
Summary: Landscape-scale bioacoustic projects are popular for biodiversity monitoring, utilizing passive acoustic monitoring recordings combined with automated detection to monitor sound-producing species' occupancy and phenology. However, technological barriers in data analysis remain a bottleneck for extracting biological insights from bioacoustic datasets. In this study, we provide an open-source Python toolkit, OpenSoundscape, that offers access to automated acoustic detection, classification, and localization methods, along with extensive documentation and tutorials to facilitate the analysis of bioacoustic data.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Computer Science, Interdisciplinary Applications
Henry Martin, Ye Hong, Nina Wiedemann, Dominik Bucher, Martin Raubal
Summary: Over the past decade, scientific studies utilizing large tracking datasets have advanced our understanding of human mobility behavior. However, standardized data processing pipelines for different data collection methods are lacking, hindering reproducibility, comparability, and transferability of methods and results in quantitative human mobility analysis. This paper presents Trackintel, an open-source Python library that standardizes human mobility analysis using a compatible data model for different tracking data types. The library covers the entire life-cycle of human mobility analysis and includes processing steps, read and write interfaces, and analysis functions. A case study with four tracking datasets demonstrates the effectiveness of Trackintel in standardizing mobility data analysis and promoting transparency and comparability in novel human mobility research. The library is available open-source at https://github.com/mie-lab/trackintel.
COMPUTERS ENVIRONMENT AND URBAN SYSTEMS
(2023)
Article
Neurosciences
A. -Sophie Dubarry, Catherine Liegeois-Chauvel, Agnes Trebuchon, Christian Benar, F. -Xavier Alario
Summary: In this study, the researchers developed and tested a user-friendly and efficient open-source toolbox for Multi Patient Intracranial data Analysis (MIA). They demonstrated that MIA can be used to analyze event-related iEEG signals, apply robust statistics, and assess the similarity of time courses across patients or contacts within anatomical regions.
Article
Construction & Building Technology
Eugenio Rodrigues, Marco S. Fernandes, David Carvalho
Summary: Mathematical morphing is commonly used to generate future weather files for building energy simulation, but current tools have limitations in accuracy and availability. This paper presents an open-source morphing tool that can generate future hourly weather data for building performance simulation. The tool was applied to an office building in Portugal, showing significant reductions in thermal energy needs for heating and increases for cooling. The study concluded that HVAC energy needs may decrease in heating-dominated climates.
BUILDING AND ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Matthew W. Flood, Bernd Grimm
Summary: Entropy has been increasingly used in various research fields to quantify the regularity, variability, and randomness of time series and image data, yet there is a lack of validated, open-source software tools. EntropyHub is an open-source toolkit that provides a wide range of functions for estimating various entropy methods, aiming to make advanced entropic time series analysis straightforward and reproducible.
Article
Biochemical Research Methods
Mikolaj Rogalski, Piotr Zdankowski, Maciej Trusiak
Summary: Fourier ptychographic microscopy (FPM) is a computational microscopy technique that enables large field of view and high-resolution microscopic imaging of biological samples. Researchers have developed an open-source application called the FPM app to address the lack of capable software for FPM, improving the reconstruction process and making it more automatic, noise-robust, and faster.
Article
Neurosciences
Jessie Benedict, Robert H. Cudmore
Summary: In the past two decades, there has been an increase in conducting behavioral assays in rodents in neuroscience labs. However, the equipment used for collecting this data can be expensive and possess limitations. To address these issues, an open-source and inexpensive behavior assay system called PiE has been introduced. The PiE system includes a custom-built behavior box, software for continuous video recording, and remote control through a web browser. It also offers the ability to scale up experiments and streamline the scoring process with a standalone desktop application.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Neurosciences
Tulio Fernandes De Almeida, Bruno Guedes Spinelli, Ramon Hypolito Lima, Maria Carolina Gonzalez, Abner Cardoso Rodrigues
Summary: PyRAT is an open-source Python library for analyzing and tracking data to classify behaviors, estimate traveled distance, speed, and area occupancy. It utilizes unsupervised algorithms for behavior classification and clustering, and allows for the association of behaviors with synchronized neural data and visualization in the pixel space.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Ecology
Jakub Nowosad
Summary: The study introduces an R package called motif for pattern-based spatial analysis, which includes functions for geomorphon classification, land cover change detection, and spatial pattern clustering. The tool supports cross-platform usage and handling of large datasets beyond RAM capacity.