scholarly journals Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets

2019 ◽  
Author(s):  
Frédéric Pont ◽  
Marie Tosolini ◽  
Qing Gao ◽  
Marion Perrier ◽  
Miguel Madrid-Mencía ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Single Cell ◽  
Open Source ◽  
Open Source Software ◽  
Healthy Donor ◽  
Large Datasets ◽  
Integrated Analysis ◽  
Functional Maturation ◽  
Healthy Donors ◽  
User Friendly

ABSTRACTThe development of single cell transcriptomic technologies yields large datasets comprising multimodal informations such as transcriptomes and immunophenotypes. Currently however, there is no software to easily and simultaneously analyze both types of data. Here, we introduce Single-Cell Virtual Cytometer, an open-source software for flow cytometry-like visualization and exploration of multi-omics single cell datasets. Using an original CITE-seq dataset of PBMC from an healthy donor, we illustrate its use for the integrated analysis of transcriptomes and phenotypes of functional maturation in peripheral T lymphocytes from healthy donors. So this free and open-source algorithm constitutes a unique resource for biologists seeking for a user-friendly analytic tool for multimodal single cell datasets.

scholarly journals Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Frédéric Pont ◽  
Marie Tosolini ◽  
Qing Gao ◽  
Marion Perrier ◽  
Miguel Madrid-Mencía ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Single Cell ◽  
Open Source ◽  
Open Source Software ◽  
Healthy Donor ◽  
Large Datasets ◽  
Integrated Analysis ◽  
Functional Maturation ◽  
User Friendly ◽  
Cell Data

Abstract The development of single-cell transcriptomic technologies yields large datasets comprising multimodal informations, such as transcriptomes and immunophenotypes. Despite the current explosion of methods for pre-processing and integrating multimodal single-cell data, there is currently no user-friendly software to display easily and simultaneously both immunophenotype and transcriptome-based UMAP/t-SNE plots from the pre-processed data. Here, we introduce Single-Cell Virtual Cytometer, an open-source software for flow cytometry-like visualization and exploration of pre-processed multi-omics single cell datasets. Using an original CITE-seq dataset of PBMC from an healthy donor, we illustrate its use for the integrated analysis of transcriptomes and epitopes of functional maturation in human peripheral T lymphocytes. So this free and open-source algorithm constitutes a unique resource for biologists seeking for a user-friendly analytic tool for multimodal single cell datasets.

scholarly journals FlowCal: A User-Friendly, Open Source Software Tool for Automatically Converting Flow Cytometry Data from Arbitrary to Calibrated Units

2016 ◽  
Vol 5 (7) ◽  
pp. 774-780 ◽  
Author(s):  
Sebastian M. Castillo-Hair ◽  
John T. Sexton ◽  
Brian P. Landry ◽  
Evan J. Olson ◽  
Oleg A. Igoshin ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Open Source ◽  
Open Source Software ◽  
Software Tool ◽  
Flow Cytometry Data ◽  
User Friendly

scholarly journals Integrated open-source software for multiscale electrophysiology

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Konstantinos Nasiotis ◽  
Martin Cousineau ◽  
François Tadel ◽  
Adrien Peyrache ◽  
Richard M. Leahy ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Analysis Data ◽  
Open Science ◽  
Dense Array ◽  
Unrestricted Access ◽  
Research Transparency ◽  
Programming Skills ◽  
User Friendly

Abstract The methods for electrophysiology in neuroscience have evolved tremendously over the recent years with a growing emphasis on dense-array signal recordings. Such increased complexity and augmented wealth in the volume of data recorded, have not been accompanied by efforts to streamline and facilitate access to processing methods, which too are susceptible to grow in sophistication. Moreover, unsuccessful attempts to reproduce peer-reviewed publications indicate a problem of transparency in science. This growing problem could be tackled by unrestricted access to methods that promote research transparency and data sharing, ensuring the reproducibility of published results. Here, we provide a free, extensive, open-source software that provides data-analysis, data-management and multi-modality integration solutions for invasive neurophysiology. Users can perform their entire analysis through a user-friendly environment without the need of programming skills, in a tractable (logged) way. This work contributes to open-science, analysis standardization, transparency and reproducibility in invasive neurophysiology.

scholarly journals Open-source software for mouse-tracking in Qualtrics to measure category competition

2018 ◽  
Author(s):  
Maya B Mathur ◽  
David Reichling
Keyword(s):  
Data Collection ◽  
Open Source ◽  
Real Time ◽  
Cognitive Processes ◽  
Open Source Software ◽  
Online Survey ◽  
Mouse Tracking ◽  
Crowdsourced Data ◽  
Programming Skills ◽  
User Friendly

Mouse-tracking is a sophisticated tool for measuring rapid, dynamic cognitive processes in real time, particularly in experiments investigating competition between perceptual or cognitive categories. We provide user-friendly, open-source software (https://osf.io/st2ef/) for designing and analyzing such experiments online using the Qualtrics survey platform. The software consists of a Qualtrics template with embedded Javascript and CSS along with R code to clean, parse, and analyze the data. No special programming skills are required to use this software. As we discuss, this software could be readily modified for use with other online survey platforms that allow the addition of custom Javascript. We empirically validate the provided software by benchmarking its performance on previously tested stimuli in a standard category-competition experiment with realistic crowdsourced data collection.

Traffic Simulation with Open-Source and Commercial Traffic Microsimulators: A Case Study

2022 ◽  
Vol 24 (2) ◽  
pp. E49-E62
Author(s):  
Nelson Baza-Solares ◽  
Ruben Velasquez-Martínez ◽  
Cristian Torres-Bohórquez ◽  
Yerly Martínez-Estupiñán ◽  
Cristian Poliziani
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Transport Modeling ◽  
Graphical Interface ◽  
Urban Centers ◽  
Output Data ◽  
Computational Tools ◽  
Input And Output ◽  
User Friendly

The analysis of traffic problems in large urban centers often requires the use of computational tools, which give the possibility to make a more detailed analysis of the issue, suggest solutions, predict behaviors and, above all, support efficient decision-making. Transport microsimulation software programs are a handy set of tools for this type of analysis. This research paper shows a case study where functions and limitations of Aimsun version 8.2.0, a commercial-like European software and Sumo version 1.3.1, a European open-source software, are presented. The input and output data are similar in both software and the interpretation of results is quite intuitive for both, as well. However, Aimsun's graphical interface interprets results more user-friendly, because Sumo is an open-access software presented as an effective alternative tool for transport modeling.

scholarly journals New Capabilities of EvoBot: A Modular, Open-Source Liquid-Handling Robot

2017 ◽  
Vol 22 (5) ◽  
pp. 500-506 ◽  
Author(s):  
Farzad Nejatimoharrami ◽  
Andres Faina ◽  
Kasper Stoy
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Low Cost ◽  
Integrated Analysis ◽  
Experiment Data ◽  
Time Interaction ◽  
Modeling Software ◽  
Offline Processing ◽  
Liquid Handling Robot

We introduce a robot developed to perform feedback-based experiments, such as droplet experiments, a common type of experiments in artificial chemical life research. These experiments are particularly well suited for automation because they often stretch over long periods of time, possibly hours, and often require that the human takes action in response to observed events such as changes in droplet size, count, shape, or clustering or declustering of multiple droplets. Our robot is designed to monitor long-term experiments and, based on the feedback from the experiment, interact with it. The combination of precise automation, accurately collected experiment data, and integrated analysis and modeling software makes real-time interaction with the experiment feasible, as opposed to traditional offline processing of experiments. Last but not least, we believe the low cost of our platform can promote artificial life research. Furthermore, prevalently, findings from an experiment will inspire redesign for novel experiments. In addition, the robot’s open-source software enables easy modification of experiments. We will cover two case studies for application of our robot in feedback-based experiments and demonstrate how our robot can not only automate these experiments, collect data, and interact with the experiments intelligently but also enable chemists to perform formerly infeasible experiments.

scholarly journals ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR

2021 ◽  
Author(s):  
Ankush Sharma ◽  
Akshay Akshay ◽  
Marie Rogne ◽  
Ragnhild Eskeland
Keyword(s):  
Single Cell ◽  
Open Source ◽  
Cell Fate ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Data Accessibility ◽  
Shiny App ◽  
User Friendly ◽  
Collaborative Efforts ◽  
Accessible Chromatin

Motivation: Mapping of chromatin accessibility landscapes in single-cells and the integration with gene expression enables a better understanding of gene regulatory mechanisms defining cell identities and cell-fate determination in development and disease. Generally, raw data generated from single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) are deposited in reposito-ries that are inaccessible due to lack of in-depth knowledge of computational programming. Results: We have developed ShinyArchR.UiO, an R-based shiny app, that facilitates scATAC-seq data accessibility and visualisation in a user-friendly, interactive, and open-source web interface. ShinyArchR.UiO is a tool that can streamline collaborative efforts for interpretation of massive chro-matin accessible data and promotes open access data sharing for wider audiences.

scholarly journals RadioPharmaDose, a java-based open-source software for estimating and reporting internal radiation doses

2018 ◽  
Vol 16 (1/2) ◽  
pp. 259-266
Author(s):  
Jaafar EL Bakkali ◽  
Hamid Mansouri ◽  
Abderrahim Doudouh
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Radiation Dosimetry ◽  
Absorbed Dose ◽  
Radiological Protection ◽  
Internal Radiation ◽  
Dosimetric Data ◽  
Sqlite Database ◽  
User Friendly ◽  
Friendly Graphical User Interface

In this work, a user-friendly Java-based open-source software has been developed for internal radiation dosimetry. Based on values published by the International Commission on Radiological Protection (ICRP), the software calculates the estimated absorbed dose for each organ and also the estimated effective dose, this for about forty of the most known radioactive drugs. In addition, the present software offers many features which include: 1) a very friendly graphical user-interface (GUI) designed to facilitate the process of selecting mandatory input data such as radiopharmaceutical product, administered activity and patient's data, 2) a tool for generating a medical report, which can be exported as PDF file or printed directly and then incorporated into the patient's record, 3) a SQLite database for storing patient's specific and dosimetric data. We believe that the present software can be a useful tool for nuclear medicine workers. It is freely available for download on GitHub (https://github.com/EL-Bakkali-Jaafar/RadioPharmaDose).

scholarly journals Image Processing Filters for Grids of Cells Analogous to Filters Processing Grids of Pixels

2021 ◽  
Vol 3 ◽  
Author(s):  
Robert Haase
Keyword(s):  
Image Processing ◽  
Open Source ◽  
Open Source Software ◽  
Image Data ◽  
Tissue Level ◽  
General Purpose ◽  
Cellular Processes ◽  
Microscopy Image ◽  
Programming Skills ◽  
User Friendly

Intra- and extra-cellular processes shape tissues together. For understanding how neighborhood relationships between cells play a role in this process, having image processing filters based on these relationships would be beneficial. Those operations are known and their application to microscopy image data typically requires programming skills. User-friendly general purpose tools for pursuing image processing on a level of neighboring cells were yet missing. In this manuscript I demonstrate image processing filters which process grids of cells on tissue level and the analogy to their better known counter parts processing grids of pixels. The tools are available as part of free and open source software in the ImageJ/Fiji and napari ecosystems and their application does not require any programming experience.

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