CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data.


BACKGROUND:Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been missing is a single open-source software package to visualize standard tracking output (from software like CellProfiler) in a way that allows convenient assessment of track quality, especially for researchers tuning tracking parameters for high-content time-lapse experiments. This makes quality assessment and algorithm adjustment a substantial challenge, particularly when dealing with hundreds of time-lapse movies collected in a high-throughput manner. RESULTS:We present CellProfiler Tracer, a free and open-source tool that complements the object tracking functionality of the CellProfiler biological image analysis package. Tracer allows multi-parametric morphological data to be visualized on object tracks, providing visualizations that have already been validated within the scientific community for time-lapse experiments, and combining them with simple graph-based measures for highlighting possible tracking artifacts. CONCLUSIONS:CellProfiler Tracer is a useful, free tool for inspection and quality control of object tracking data, available from http://www.cellprofiler.org/tracer/.


BMC Bioinformatics


BMC bioinformatics


Bray MA,Carpenter AE




Has Abstract


2015-11-04 00:00:00










  • Partitioning of functional gene expression data using principal points.

    abstract:BACKGROUND:DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene function over a period of time. Temporal gene expression curves can be treated as functional data s...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Kim J,Kim H

    更新日期:2017-10-12 00:00:00

  • Bioinformatics approach to predict target genes for dysregulated microRNAs in hepatocellular carcinoma: study on a chemically-induced HCC mouse model.

    abstract:BACKGROUND:Hepatocellular carcinoma (HCC) is an aggressive epithelial tumor which shows very poor prognosis and high rate of recurrence, representing an urgent problem for public healthcare. MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNAs that attract great attention because of their role in regulation of...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Del Vecchio F,Gallo F,Di Marco A,Mastroiaco V,Caianiello P,Zazzeroni F,Alesse E,Tessitore A

    更新日期:2015-12-10 00:00:00

  • Predicting variant deleteriousness in non-human species: applying the CADD approach in mouse.

    abstract:BACKGROUND:Predicting the deleteriousness of observed genomic variants has taken a step forward with the introduction of the Combined Annotation Dependent Depletion (CADD) approach, which trains a classifier on the wealth of available human genomic information. This raises the question whether it can be done with less ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Groß C,de Ridder D,Reinders M

    更新日期:2018-10-12 00:00:00

  • πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.

    abstract:BACKGROUND:Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular evolutionary processes, supports a wide array of evolutionary models, but lacked ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Bielejec F,Lemey P,Carvalho LM,Baele G,Rambaut A,Suchard MA

    更新日期:2014-05-07 00:00:00

  • Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses.

    abstract:BACKGROUND:Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as the defa...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Ong E,Xie J,Ni Z,Liu Q,Sarntivijai S,Lin Y,Cooper D,Terryn R,Stathias V,Chung C,Schürer S,He Y

    更新日期:2017-12-21 00:00:00

  • Development and tuning of an original search engine for patent libraries in medicinal chemistry.

    abstract:BACKGROUND:The large increase in the size of patent collections has led to the need of efficient search strategies. But the development of advanced text-mining applications dedicated to patents of the biomedical field remains rare, in particular to address the needs of the pharmaceutical & biotech industry, which inten...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Pasche E,Gobeill J,Kreim O,Oezdemir-Zaech F,Vachon T,Lovis C,Ruch P

    更新日期:2014-01-01 00:00:00

  • Robustness of signal detection in cryo-electron microscopy via a bi-objective-function approach.

    abstract:BACKGROUND:The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cryo-EM data analysis. Template-based particle picking by an objective function using fast local corre...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Wang WL,Yu Z,Castillo-Menendez LR,Sodroski J,Mao Y

    更新日期:2019-04-03 00:00:00

  • Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis.

    abstract:BACKGROUND:In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorith...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Yang C,He Z,Yu W

    更新日期:2009-01-06 00:00:00

  • Automating dChip: toward reproducible sharing of microarray data analysis.

    abstract:BACKGROUND:During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dC...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Li C

    更新日期:2008-05-08 00:00:00

  • MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles.

    abstract:BACKGROUND:The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Shaw GT,Pao YY,Wang D

    更新日期:2016-11-25 00:00:00

  • Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration.

    abstract:BACKGROUND:The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Brown J,Phillips AR,Lewis DA,Mans MA,Chang Y,Tanguay RL,Peterson ES,Waters KM,Tilton SC

    更新日期:2019-05-17 00:00:00

  • Recursive model for dose-time responses in pharmacological studies.

    abstract:BACKGROUND:Clinical studies often track dose-response curves of subjects over time. One can easily model the dose-response curve at each time point with Hill equation, but such a model fails to capture the temporal evolution of the curves. On the other hand, one can use Gompertz equation to model the temporal behaviors...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Dhruba SR,Rahman A,Rahman R,Ghosh S,Pal R

    更新日期:2019-06-20 00:00:00

  • CellSim: a novel software to calculate cell similarity and identify their co-regulation networks.

    abstract:BACKGROUND:Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct reprogramming from an original cell to target cell type needs the cell similarity and cell specific regu...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Li L,Che D,Wang X,Zhang P,Rahman SU,Zhao J,Yu J,Tao S,Lu H,Liao M

    更新日期:2019-03-04 00:00:00

  • Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins.

    abstract:BACKGROUND:Molecular docking is a widely-employed method in structure-based drug design. An essential component of molecular docking programs is a scoring function (SF) that can be used to identify the most stable binding pose of a ligand, when bound to a receptor protein, from among a large set of candidate poses. Des...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Ashtawy HM,Mahapatra NR

    更新日期:2015-01-01 00:00:00

  • Molecular evolution of dihydrouridine synthases.

    abstract:BACKGROUND:Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Kasprzak JM,Czerwoniec A,Bujnicki JM

    更新日期:2012-06-28 00:00:00

  • Pre-processing Agilent microarray data.

    abstract:BACKGROUND:Pre-processing methods for two-sample long oligonucleotide arrays, specifically the Agilent technology, have not been extensively studied. The goal of this study is to quantify some of the sources of error that affect measurement of expression using Agilent arrays and to compare Agilent's Feature Extraction ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Zahurak M,Parmigiani G,Yu W,Scharpf RB,Berman D,Schaeffer E,Shabbeer S,Cope L

    更新日期:2007-05-01 00:00:00

  • Multi-label literature classification based on the Gene Ontology graph.

    abstract:BACKGROUND:The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of t...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Jin B,Muller B,Zhai C,Lu X

    更新日期:2008-12-08 00:00:00

  • A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data.

    abstract:BACKGROUND:Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order t...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Corradi L,Fato M,Porro I,Scaglione S,Torterolo L

    更新日期:2008-11-13 00:00:00

  • InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams.

    abstract:BACKGROUND:Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited. RESULTS:We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams includin...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Heberle H,Meirelles GV,da Silva FR,Telles GP,Minghim R

    更新日期:2015-05-22 00:00:00

  • Novel domain expansion methods to improve the computational efficiency of the Chemical Master Equation solution for large biological networks.

    abstract:BACKGROUND:Numerical solutions of the chemical master equation (CME) are important for understanding the stochasticity of biochemical systems. However, solving CMEs is a formidable task. This task is complicated due to the nonlinear nature of the reactions and the size of the networks which result in different realizat...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Kosarwal R,Kulasiri D,Samarasinghe S

    更新日期:2020-11-11 00:00:00

  • Natural computation meta-heuristics for the in silico optimization of microbial strains.

    abstract:BACKGROUND:One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metabolic phenotype which typically means having a high yield/productivity. This challenge is not only du...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Rocha M,Maia P,Mendes R,Pinto JP,Ferreira EC,Nielsen J,Patil KR,Rocha I

    更新日期:2008-11-27 00:00:00

  • SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

    abstract:BACKGROUND:There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage, environmental condition, or disease state. Accurate analysis of microarray expression data and des...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Kahn AB,Ryan MC,Liu H,Zeeberg BR,Jamison DC,Weinstein JN

    更新日期:2007-03-05 00:00:00

  • On pairwise distances and median score of three genomes under DCJ.

    abstract::In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a re...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Aganezov S Jr,Alekseyev MA

    更新日期:2012-01-01 00:00:00

  • FocAn: automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy.

    abstract:BACKGROUND:Phosphorylated histone H2AX, also known as γH2AX, forms μm-sized nuclear foci at the sites of DNA double-strand breaks (DSBs) induced by ionizing radiation and other agents. Due to their specificity and sensitivity, γH2AX immunoassays have become the gold standard for studying DSB induction and repair. One o...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Memmel S,Sisario D,Zimmermann H,Sauer M,Sukhorukov VL,Djuzenova CS,Flentje M

    更新日期:2020-01-28 00:00:00

  • DraGnET: software for storing, managing and analyzing annotated draft genome sequence data.

    abstract:BACKGROUND:New "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Duncan S,Sirkanungo R,Miller L,Phillips GJ

    更新日期:2010-02-22 00:00:00

  • MTAP: the motif tool assessment platform.

    abstract:BACKGROUND:In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences. As the number of software packages increases, it becomes more important to identify the tools with ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Quest D,Dempsey K,Shafiullah M,Bastola D,Ali H

    更新日期:2008-08-12 00:00:00

  • Bayesian neural networks for detecting epistasis in genetic association studies.

    abstract:BACKGROUND:Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. RESULTS:A non-parametric Bayesian ap...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Beam AL,Motsinger-Reif A,Doyle J

    更新日期:2014-11-21 00:00:00

  • Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts.

    abstract:BACKGROUND:Word sense disambiguation (WSD) attempts to solve lexical ambiguities by identifying the correct meaning of a word based on its context. WSD has been demonstrated to be an important step in knowledge-based approaches to automatic summarization. However, the correlation between the accuracy of the WSD methods...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Plaza L,Jimeno-Yepes AJ,Díaz A,Aronson AR

    更新日期:2011-08-26 00:00:00

  • Scuba: scalable kernel-based gene prioritization.

    abstract:BACKGROUND:The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can h...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Zampieri G,Tran DV,Donini M,Navarin N,Aiolli F,Sperduti A,Valle G

    更新日期:2018-01-25 00:00:00

  • TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas.

    abstract:BACKGROUND:Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Cumbo F,Fiscon G,Ceri S,Masseroli M,Weitschek E

    更新日期:2017-01-03 00:00:00