QuArray: an application for tissue array whole slide image export and signal analysis

2021 ◽  
Author(s):  
Callum Arthurs ◽  
Aamir Ahmed
Keyword(s):  
Graphical User Interface ◽  
Signal Analysis ◽  
Tissue Array ◽  
Integrated Analysis ◽  
Whole Slide Imaging ◽  
Output Data ◽  
Slide Image ◽  
Disease Stratification ◽  
Downstream Analysis ◽  
User Friendly

Abstract Motivation Tissue array (TA) staining, combined with whole slide imaging (WSI) methods facilitate discovery of biomarkers for diagnosis, prognostication and disease stratification. A key impediment in TA WSI analysis is handling missing tissue and artefacts when identifying tissue cores before quantitative, standardized downstream analysis. There is a need for an open access, user friendly, integrated analysis of the WSI generated using TAs in clinical and scientific research laboratories. Results We have developed QuArray (Quantitative Array Application) for image export and signal analysis of TAs using WSI. The application input is a WSI and a corresponding TA configuration file. QuArray identifies and exports core images and analyses chromogen staining in a simple graphical user interface. Output data is saved to file for further analysis including indexed data. Availabilityand implementation Available for download from https://github.com/c-arthurs/QuArray under an MIT licence.

scholarly journals MuSA: a graphical user interface for multi-OMICs data integration in radiogenomic studies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mario Zanfardino ◽  
Rossana Castaldo ◽  
Katia Pane ◽  
Ornella Affinito ◽  
Marco Aiello ◽  
...  
Keyword(s):  
User Interface ◽  
Data Integration ◽  
Graphical User Interface ◽  
Data Science ◽  
Heterogeneous Data ◽  
Biological Information ◽  
Omics Data ◽  
Correlation Clustering ◽  
Downstream Analysis ◽  
Omics Data Integration

AbstractAnalysis of large-scale omics data along with biomedical images has gaining a huge interest in predicting phenotypic conditions towards personalized medicine. Multiple layers of investigations such as genomics, transcriptomics and proteomics, have led to high dimensionality and heterogeneity of data. Multi-omics data integration can provide meaningful contribution to early diagnosis and an accurate estimate of prognosis and treatment in cancer. Some multi-layer data structures have been developed to integrate multi-omics biological information, but none of these has been developed and evaluated to include radiomic data. We proposed to use MultiAssayExperiment (MAE) as an integrated data structure to combine multi-omics data facilitating the exploration of heterogeneous data. We improved the usability of the MAE, developing a Multi-omics Statistical Approaches (MuSA) tool that uses a Shiny graphical user interface, able to simplify the management and the analysis of radiogenomic datasets. The capabilities of MuSA were shown using public breast cancer datasets from TCGA-TCIA databases. MuSA architecture is modular and can be divided in Pre-processing and Downstream analysis. The pre-processing section allows data filtering and normalization. The downstream analysis section contains modules for data science such as correlation, clustering (i.e., heatmap) and feature selection methods. The results are dynamically shown in MuSA. MuSA tool provides an easy-to-use way to create, manage and analyze radiogenomic data. The application is specifically designed to guide no-programmer researchers through different computational steps. Integration analysis is implemented in a modular structure, making MuSA an easily expansible open-source software.

GEView (Gene Expression View) Tool for Intuitive and High Accessible Visualization of Expression Data for Non-Programmer Biologists

2020 ◽  
pp. 580-592
Author(s):  
Libi Hertzberg ◽  
Assif Yitzhaky ◽  
Metsada Pasmanik-Chor
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
User Interface ◽  
High Throughput ◽  
Graphical User Interface ◽  
Differential Expression Analysis ◽  
Biological Data ◽  
Expression Data ◽  
Batch Correction ◽  
User Friendly

This article describes how the last decade has been characterized by the production of huge amounts of different types of biological data. Following that, a flood of bioinformatics tools have been published. However, many of these tools are commercial, or require computational skills. In addition, not all tools provide intuitive and highly accessible visualization of the results. The authors have developed GEView (Gene Expression View), which is a free, user-friendly tool harboring several existing algorithms and statistical methods for the analysis of high-throughput gene, microRNA or protein expression data. It can be used to perform basic analysis such as quality control, outlier detection, batch correction and differential expression analysis, through a single intuitive graphical user interface. GEView is unique in its simplicity and highly accessible visualization it provides. Together with its basic and intuitive functionality it allows Bio-Medical scientists with no computational skills to independently analyze and visualize high-throughput data produced in their own labs.

scholarly journals MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos

2019 ◽  
Author(s):  
A Trullo ◽  
J Dufourt ◽  
M Lagha
Keyword(s):  
Graphical User Interface ◽  
Transcriptional Activation ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Automatic Image Analysis ◽  
Lineage Tree ◽  
Automatic Software ◽  
Integrated Software ◽  
Lineage Tracking ◽  
User Friendly

Abstract Motivation During development, progenitor cells undergo multiple rounds of cellular divisions during which transcriptional programs must be faithfully propagated. Investigating the timing of transcriptional activation, which is a highly stochastic phenomenon, requires the analysis of large amounts of data. In order to perform automatic image analysis of transcriptional activation, we developed a software that segments and tracks both small and large objects, leading the user from raw data up to the results in their final form. Results MitoTrack is a user-friendly open-access integrated software that performs the specific dual task of reporting the precise timing of transcriptional activation while keeping lineage tree history for each nucleus of a living developing embryo. The software works automatically but provides the possibility to easily supervise, correct and validate each step. Availability and implementation MitoTrack is an open source Python software, embedded within a graphical user interface (download here). Supplementary information Supplementary data are available at Bioinformatics online.

Shoreline Bioremediation Model (SBM) - A Graphical User Interface for Simulating the Biodegradation of Beached Oil

2014 ◽  
Vol 2014 (1) ◽  
pp. 1099-1112
Author(s):  
Jagadish Torlapati ◽  
Xiaolong Geng ◽  
Tom King ◽  
Michel Boufadel ◽  
Kenneth Lee
Keyword(s):  
Decision Making ◽  
User Interface ◽  
Numerical Model ◽  
Graphical User Interface ◽  
Biodegradation Rate ◽  
Worst Case ◽  
Oil Concentration ◽  
Oil Components ◽  
User Friendly ◽  
Friendly Graphical User Interface

ABSTRACT We developed a user-friendly numerical model, Shoreline Bioremediation Model (SBM), to simulate the biodegradation and bioremediation of oil entrapped within shorelines. The model takes oil properties and environmental conditions as input and produces variation of oil concentration with time, up to several years from the time of the spill. SBM is equipped with a user-friendly graphical user interface (GUI). The accessibility and easy-to-use interface allow the user to quickly produce several biodegradation and bioremediation scenarios before they are implemented at the contaminated shoreline. The model has been calibrated to predict the biodegradation rate of saturates and aromatics, but it can be also used to predict the biodegradation rates of individual oil components and to decide on bioremediation studies in shorelines based on the enhancement due to biostimulation (addition of nutrients) or bioaugmentation (addition of hydrocarbon degrading organisms). The GUI provides the oil concentration with time along with best case and worst case scenarios, which is commonly needed for decision making.

CellTracker (not only) for dummies

2015 ◽  
Vol 32 (6) ◽  
pp. 955-957 ◽  
Author(s):  
Filippo Piccinini ◽  
Alexa Kiss ◽  
Peter Horvath
Keyword(s):  
Graphical User Interface ◽  
Open Source Software ◽  
Phase Contrast ◽  
Cell Tracking ◽  
Source Code ◽  
Software Tool ◽  
Time Lapse ◽  
Supplementary Information ◽  
Differential Interference Contrast ◽  
User Friendly

Abstract Motivation: Time-lapse experiments play a key role in studying the dynamic behavior of cells. Single-cell tracking is one of the fundamental tools for such analyses. The vast majority of the recently introduced cell tracking methods are limited to fluorescently labeled cells. An equally important limitation is that most software cannot be effectively used by biologists without reasonable expertise in image processing. Here we present CellTracker, a user-friendly open-source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. Availability and implementation: CellTracker is written in MATLAB (The MathWorks, Inc., USA). It works with Windows, Macintosh and UNIX-based systems. Source code and graphical user interface (GUI) are freely available at: http://celltracker.website/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

A graphical robot language developed in Japan

Robotica ◽  
1997 ◽  
Vol 15 (1) ◽  
pp. 99-103 ◽  
Author(s):  
Tamio Arai ◽  
Toshiyuki Itoko ◽  
Hidetoshi Yago
Keyword(s):  
Graphical User Interface ◽  
Arc Welding ◽  
Industrial Robots ◽  
Robot Programming ◽  
Prototype System ◽  
Programming System ◽  
Graphical Interface ◽  
Welding Robot ◽  
Batch Production ◽  
User Friendly

A graphical robot programming system has been developed. This system with a graphical interface is user-friendly and easy-to-learn for low-skill users. It has been developed as a prototype system under a project by the Japan Robot Association (JARA) since 1994. The system runs on a personal computer and consists of a graphical user interface and an editing system. It is designed for programming an arc welding robot in small batch production and is expected to provide low-skill users with a means to use industrial robots with ease.

A Python-based interface to examine motions in time series of solar images

2016 ◽  
Vol 12 (S327) ◽  
pp. 25-27
Author(s):  
J. I. Campos-Rozo ◽  
S. Vargas Domínguez
Keyword(s):  
Time Series ◽  
Graphical User Interface ◽  
Solar Physics ◽  
Velocity Fields ◽  
Proper Motions ◽  
Local Correlation ◽  
Scientific Analysis ◽  
User Friendly ◽  
Selection Of ◽  
Analysis Of Time Series

AbstractPython is considered to be a mature programming language, besides of being widely accepted as an engaging option for scientific analysis in multiple areas, as will be presented in this work for the particular case of solar physics research. SunPy is an open-source library based on Python that has been recently developed to furnish software tools to solar data analysis and visualization. In this work we present a graphical user interface (GUI) based on Python and Qt to effectively compute proper motions for the analysis of time series of solar data. This user-friendly computing interface, that is intended to be incorporated to the Sunpy library, uses a local correlation tracking technique and some extra tools that allows the selection of different parameters to calculate, vizualize and analyze vector velocity fields of solar data, i.e. time series of solar filtergrams and magnetograms.

siGnum: Graphical user interface for EMG signal analysis

2014 ◽  
Vol 39 (1) ◽  
pp. 19-25 ◽  
Author(s):  
Manvinder Kaur ◽  
Shilpi Mathur ◽  
Dinesh Bhatia ◽  
Suresh Verma
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Signal Analysis ◽  
Emg Signal

LEADME: An Educational Software for Composite Laminate Analysis and Design

2015 ◽  
Vol 1115 ◽  
pp. 578-581
Author(s):  
J.S. Mohamed Ali ◽  
Abeid Abeid Rubeya
Keyword(s):  
User Interface ◽  
Structural Analysis ◽  
Graphical User Interface ◽  
Composite Laminate ◽  
Educational Software ◽  
Laminated Composite ◽  
Educational Tool ◽  
Analysis And Design ◽  
Mechanics Analysis ◽  
User Friendly

LEADME ( Laminate Analysis and Design Made Easy ), an educational software useful for the analysis and design of laminated composite structure has been developed. The software encompasses both the micro and macro mechanics analysis of lamina and laminate. The highlight of this software is that, apart from usual laminate analysis, the software is capable to solve practical laminate applications such as analysis of beams and also a design module is included. The software has been developed using MATLAB-Graphical User Interface (GUI) which makes it very user friendly. The results obtained from this software have been validated. It is expected that this software will serve as an educational tool complementing textbooks for students to gain better understanding of composite structural analysis.

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