ABSTRACT
BACKGROUND AND OBJECTIVE: Cell migration is essential for many biological phenomena with direct impact on human health and disease. One conventional approach to study cell migration involves the quantitative analysis of individual cell trajectories recorded by time-lapse video microscopy. Dedicated software tools exist to assist the automated or semi-automated tracking of cells and translate these into coordinate positions along time. However, cell biologists usually bump into the difficulty of plotting and computing these data sets into biologically meaningful figures and metrics. METHODS: This report describes MigraR, an intuitive graphical user interface executed from the RStudioTM (via the R package Shiny), which greatly simplifies the task of translating coordinate positions of moving cells into measurable parameters of cell migration (velocity, straightness, and direction of movement), as well as of plotting cell trajectories and migration metrics. One innovative function of this interface is that it allows users to refine their data sets by setting limits based on time, velocity and straightness. RESULTS: MigraR was tested on different data to assess its applicability. Intended users of MigraR are cell biologists with no prior knowledge of data analysis, seeking to accelerate the quantification and visualization of cell migration data sets delivered in the format of Excel files by available cell-tracking software. CONCLUSIONS: Through the graphics it provides, MigraR is an useful tool for the analysis of migration parameters and cellular trajectories. Since its source code is open, it can be subject of refinement by expert users to best suit the needs of other researchers. It is available at GitHub and can be easily reproduced.
Subject(s)
Cell Tracking , Software , Cell Movement , HumansABSTRACT
Cardiovascular disease is the leading cause of death in the world, and its early detection is a key to improving long-term health outcomes. The auscultation of the heart is still an important method in the medical process because it is very simple and cheap. To detect possible heart anomalies at an early stage, an automatic method enabling cardiac health low-cost screening for the general population would be highly valuable. By analyzing the phonocardiogram signals, it is possible to perform cardiac diagnosis and find possible anomalies at an early-term. Therefore, the development of intelligent and automated analysis tools of the phonocardiogram is very relevant. In this work, we use simultaneously collected electrocardiograms and phonocardiograms from the Physionet Challenge database with the main objective of determining whether a phonocardiogram corresponds to a "normal" or "abnormal" physiological state. Our main contribution is the methodological combination of time domain features and frequency domain features of phonocardiogram signals to improve cardiac disease automatic classification. This novel approach is developed using both features. First, the phonocardiogram signals are segmented with an algorithm based on a logistic regression hidden semi-Markov model, which uses electrocardiogram signals as a reference. Then, two groups of features from the time and frequency domain are extracted from the phonocardiogram segments. One group is based on motifs and the other on Mel-frequency cepstral coefficients. After that, we combine these features into a two-dimensional time-frequency heat map representation. Lastly, a binary classifier is applied to both groups of features to learn a model that discriminates between normal and abnormal phonocardiogram signals. In the experiments, three classification algorithms are used: Support Vector Machines, Convolutional Neural Network, and Random Forest. The best results are achieved when both time and Mel-frequency cepstral coefficients features are considered using a Support Vector Machines with a radial kernel.
