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.

scholarly journals TraCurate: efficiently curating cell tracks

2020 ◽  
Author(s):  
S. Wagner ◽  
K. Thierbach ◽  
T. Zerjatke ◽  
I. Glauche ◽  
I. Roeder ◽  
...  
Keyword(s):  
Open Source Software ◽  
Cell Tracking ◽  
User Interaction ◽  
Software Tool ◽  
Time Lapse ◽  
Tracking Data ◽  
Cellular Behavior ◽  
Data Source ◽  
Complete Cell

AbstractTraCurate is an open-source software tool to curate and manually annotate cell tracking data from time-lapse microscopy. Although many studies of cellular behavior require high-quality, long-term observations across generations of cells, automated cell tracking is often imperfect and typically yields fragmented results that still contain many errors. TraCurate provides the functionality for the curation and correction of cell tracking data with minimal user interaction and expenditure of time and supports the extraction of complete cell tracks and cellular genealogies from experimental data. Source code and binary packages for Linux, macOS and Windows are available at https://tracurate.gitlab.io/, as well as all other complementary tools described herein.

scholarly journals Tibanna: software for scalable execution of portable pipelines on the cloud

2019 ◽  
Vol 35 (21) ◽  
pp. 4424-4426 ◽  
Author(s):  
Soohyun Lee ◽  
Jeremy Johnson ◽  
Carl Vitzthum ◽  
Koray Kırlı ◽  
Burak H Alver ◽  
...  
Keyword(s):  
Open Source Software ◽  
Source Code ◽  
Software Tool ◽  
Application Programming Interface ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Description Language ◽  
Amazon Web Services ◽  
Application Programming ◽  
Programming Interface

Abstract Summary We introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (CWL), Workflow Description Language (WDL) and Docker. It adopts a strategy of isolation and optimization of individual executions, combined with a serverless scheduling approach. Pipelines are executed and monitored using local commands or the Python Application Programming Interface (API) and cloud configuration is automatically handled. Tibanna is well suited for projects with a range of computational requirements, including those with large and widely fluctuating loads. Notably, it has been used to process terabytes of data for the 4D Nucleome (4DN) Network. Availability and implementation Source code is available on GitHub at https://github.com/4dn-dcic/tibanna. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

2015 ◽  
Vol 14 ◽  
pp. CIN.S26470 ◽  
Author(s):  
Richard P. Finney ◽  
Qing-Rong Chen ◽  
Cu V. Nguyen ◽  
Chih Hao Hsu ◽  
Chunhua Yan ◽  
...  
Keyword(s):  
Graphical User Interface ◽  
Reference Genome ◽  
Source Code ◽  
Software Tool ◽  
Command Line ◽  
Sequencing Data ◽  
Genome Data ◽  
Command Line Tool ◽  
Portable Software ◽  
Microsoft Windows

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview . The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview .

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.

scholarly journals Temporal network alignment via GoT-WAVE

2019 ◽  
Vol 35 (18) ◽  
pp. 3527-3529 ◽  
Author(s):  
David Aparício ◽  
Pedro Ribeiro ◽  
Tijana Milenković ◽  
Fernando Silva
Keyword(s):  
User Interface ◽  
State Of The Art ◽  
Source Code ◽  
Network Alignment ◽  
Supplementary Information ◽  
Temporal Network ◽  
Temporal Networks ◽  
Supplementary Data ◽  
Node Similarity ◽  
User Friendly

Abstract Motivation Network alignment (NA) finds conserved regions between two networks. NA methods optimize node conservation (NC) and edge conservation. Dynamic graphlet degree vectors are a state-of-the-art dynamic NC measure, used within the fastest and most accurate NA method for temporal networks: DynaWAVE. Here, we use graphlet-orbit transitions (GoTs), a different graphlet-based measure of temporal node similarity, as a new dynamic NC measure within DynaWAVE, resulting in GoT-WAVE. Results On synthetic networks, GoT-WAVE improves DynaWAVE’s accuracy by 30% and speed by 64%. On real networks, when optimizing only dynamic NC, the methods are complementary. Furthermore, only GoT-WAVE supports directed edges. Hence, GoT-WAVE is a promising new temporal NA algorithm, which efficiently optimizes dynamic NC. We provide a user-friendly user interface and source code for GoT-WAVE. Availability and implementation http://www.dcc.fc.up.pt/got-wave/ Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation

2019 ◽  
Vol 35 (17) ◽  
pp. 3146-3147 ◽  
Author(s):  
Adrien L S Jacquin ◽  
Duncan T Odom ◽  
Margus Lukk
Keyword(s):  
Open Source Software ◽  
Software Tool ◽  
Supplementary Information ◽  
Small Scale ◽  
Genome Sequences ◽  
Guide Rnas ◽  
Genome Modification ◽  
Order Of Magnitude ◽  
Sgrna Design ◽  
Reference Genomes

Abstract Summary CRISPR/Cas9 system requires short guide RNAs (sgRNAs) to direct genome modification. Most currently available tools for sgRNA design operate only with standard reference genomes, and are best suited for small-scale projects. To address these limitations, we developed Crisflash, a software tool for fast sgRNA design and potential off-target discovery, built for performance and flexibility. Crisflash can rapidly design CRISPR guides against any sequenced genome or genome sequences, and can optimize guide accuracy by incorporating user-supplied variant data. Crisflash is over an order of magnitude faster than comparable tools, even using a single CPU core, and efficiently and robustly scores the potential off-targeting of all possible candidate CRISPR guide oligonucleotides. Availability and implementation https://github.com/crisflash Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals DamageProfiler: Fast damage pattern calculation for ancient DNA

2021 ◽  
Author(s):  
Judith Neukamm ◽  
Alexander Peltzer ◽  
Kay Nieselt
Keyword(s):  
Ancient Dna ◽  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Central Importance ◽  
Command Line Interface ◽  
Analysis Pipeline ◽  
File Formats ◽  
Programming Knowledge ◽  
User Friendly

Abstract Motivation In ancient DNA research, the authentication of ancient samples based on specific features remains a crucial step in data analysis. Because of this central importance, researchers lacking deeper programming knowledge should be able to run a basic damage authentication analysis. Such software should be user-friendly and easy to integrate into an analysis pipeline. Results DamageProfiler is a Java based, stand-alone software to determine damage patterns in ancient DNA. The results are provided in various file formats and plots for further processing. DamageProfiler has an intuitive graphical as well as command line interface that allows the tool to be easily embedded into an analysis pipeline. Availability All of the source code is freely available on GitHub (https://github.com/Integrative-Transcriptomics/DamageProfiler). Supplementary information Supplementary data are available at Bioinformatics online.

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 MOSGA: Modular Open-Source Genome Annotator

2020 ◽  
Author(s):  
Roman Martin ◽  
Thomas Hackl ◽  
Georges Hattab ◽  
Matthias G Fischer ◽  
Dominik Heider
Keyword(s):  
Open Source ◽  
Source Code ◽  
Supplementary Information ◽  
Web Interface ◽  
Fully Integrated ◽  
Sequencing Technologies ◽  
A Genome ◽  
Wide Range ◽  
User Friendly ◽  
Eukaryotic Genomes

Abstract Motivation The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies—a crucial step toward unlocking the biology of the organism of interest—has remained a complex challenge that often requires advanced bioinformatics expertise. Results Here, we present MOSGA (Modular Open-Source Genome Annotator), a genome annotation framework for eukaryotic genomes with a user-friendly web-interface that generates and integrates annotations from various tools. The aggregated results can be analyzed with a fully integrated genome browser and are provided in a format ready for submission to NCBI. MOSGA is built on a portable, customizable and easily extendible Snakemake backend, and thus, can be tailored to a wide range of users and projects. Availability and implementation We provide MOSGA as a web service at https://mosga.mathematik.uni-marburg.de and as a docker container at registry.gitlab.com/mosga/mosga: latest. Source code can be found at https://gitlab.com/mosga/mosga Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals PolishEM: image enhancement in FIB–SEM

2020 ◽  
Vol 36 (12) ◽  
pp. 3947-3948
Author(s):  
Jose-Jesus Fernandez ◽  
Teobaldo E Torres ◽  
Eva Martin-Solana ◽  
Gerardo F Goya ◽  
Maria-Rosario Fernandez-Fernandez
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Source Code ◽  
Software Tool ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Efficient Processing ◽  
Scanning Electron

Abstract Summary We have developed a software tool to improve the image quality in focused ion beam–scanning electron microscopy (FIB–SEM) stacks: PolishEM. Based on a Gaussian blur model, it automatically estimates and compensates for the blur affecting each individual image. It also includes correction for artifacts commonly arising in FIB–SEM (e.g. curtaining). PolishEM has been optimized for an efficient processing of huge FIB–SEM stacks on standard computers. Availability and implementation PolishEM has been developed in C. GPL source code and binaries for Linux, OSX and Windows are available at http://www.cnb.csic.es/%7ejjfernandez/polishem. Supplementary information Supplementary data are available at Bioinformatics online.

Sign in / Sign up

Export Citation Format

Share Document