Rapid and fully automated blood vasculature analysis in 3D light-sheet image volumes of different organs.

Light-sheet fluorescence microscopy (LSFM) can produce high-resolution tomograms of tissue vasculature with high accuracy. However, data processing and analysis is laborious due to the size of the datasets. Here, we introduce VesselExpress, an automated software that reliably analyzes six characteristic vascular network parameters including vessel diameter in LSFM data on average computing hardware. VesselExpress is ∼100 times faster than other existing vessel analysis tools, requires no user interaction, and integrates batch processing and parallelization. Employing an innovative dual Frangi filter approach, we show that obesity induces a large-scale modulation of brain vasculature in mice and that seven other major organs differ strongly in their 3D vascular makeup. Hence, VesselExpress transforms LSFM from an observational to an analytical working tool.

Open-source analysis and visualization of segmented vasculature datasets with VesselVio.

Vascular networks are fundamental components of biological systems. Quantitative analysis and observation of the features of these networks can improve our understanding of their roles in health and disease. Recent advancements in imaging technologies have enabled the generation of large-scale vasculature datasets, but barriers to analyzing these datasets remain. Modern analysis options are mainly limited to paid applications or open-source terminal-based software that requires programming knowledge with high learning curves. Here, we describe VesselVio, an open-source application developed to analyze and visualize pre-binarized vasculature datasets and pre-constructed vascular graphs. Vasculature datasets and graphs can be loaded with annotations and processed with custom parameters. Here, the program is tested on ground-truth datasets and is compared with current pipelines. The utility of VesselVio is demonstrated by the analysis of multiple formats of 2D and 3D datasets acquired with several imaging modalities, including annotated mouse whole-brain vasculature volumes.

An Open Source-Based BCI Application for Virtual World Tour and Its Usability Evaluation.

Brain-computer interfaces can provide a new communication channel and control functions to people with restricted movements. Recent studies have indicated the effectiveness of brain-computer interface (BCI) applications. Various types of applications have been introduced so far in this field, but the number of those available to the public is still insufficient. Thus, there is a need to expand the usability and accessibility of BCI applications. In this study, we introduce a BCI application for users to experience a virtual world tour. This software was built on three open-source environments and is publicly available through the GitHub repository. For a usability test, 10 healthy subjects participated in an electroencephalography (EEG) experiment and evaluated the system through a questionnaire. As a result, all the participants successfully played the BCI application with 96.6% accuracy with 20 blinks from two sessions and gave opinions on its usability (e.g., controllability, completeness, comfort, and enjoyment) through the questionnaire. We believe that this open-source BCI world tour system can be used in both research and entertainment settings and hopefully contribute to open science in the BCI field.

Analysis of Selected Methods Use for Calculation of the Coefficients of Adsorption Isotherms and Simplified Equations of Adsorption Dynamics with the Use of IZO Application.

The purpose of this paper is to present the IZO application that calculates and visualizes coefficients of adsorption isotherms according to Freundlich, Langmuir, and BET in a classic and linear system, in a simple communicative way. The application also calculates the working time of the adsorption bed based on the transformation of the mass balance equation, and according to the Zuchowicki, Zabiezinski, Tichonow, and the Bohart-Adams equations. The laboratory tests of the adsorption process of leachate from a municipal landfill on selected active coals ORGANOSORB 10, DESOTEK, and BA-10, were conducted to check the program for accuracy. Results of tests confirm that the linearization method of the calculation of adsorption isotherms coefficients, used in the IZO application, gives sufficient accuracy and may be used as an alternative of, e.g., the nonlinear estimation method.