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










  • Prediction of dinucleotide-specific RNA-binding sites in proteins.

    abstract:BACKGROUND:Regulation of gene expression, protein synthesis, replication and assembly of many viruses involve RNA-protein interactions. Although some successful computational tools have been reported to recognize RNA binding sites in proteins, the problem of specificity remains poorly investigated. After the nucleotide...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Fernandez M,Kumagai Y,Standley DM,Sarai A,Mizuguchi K,Ahmad S

    更新日期:2011-01-01 00:00:00

  • Predicting blood pressure from physiological index data using the SVR algorithm.

    abstract:BACKGROUND:Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effective prevention and control measures for blood pressure diseases. Traditional blood pressure measure...

    journal_title:BMC bioinformatics

    pub_type: 临床试验,杂志文章


    authors: Zhang B,Ren H,Huang G,Cheng Y,Hu C

    更新日期:2019-02-28 00:00:00

  • CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes.

    abstract:BACKGROUND:It is now well established that nearly 20% of human cancers are caused by infectious agents, and the list of human oncogenic pathogens will grow in the future for a variety of cancer types. Whole tumor transcriptome and genome sequencing by next-generation sequencing technologies presents an unparalleled opp...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Borozan I,Wilson S,Blanchette P,Laflamme P,Watt SN,Krzyzanowski PM,Sircoulomb F,Rottapel R,Branton PE,Ferretti V

    更新日期:2012-08-17 00:00:00

  • Localizing triplet periodicity in DNA and cDNA sequences.

    abstract:BACKGROUND:The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues. Such periodicity is usually not observed in introns and intergenic regions. If a DNA sequence is d...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Wang L,Stein LD

    更新日期:2010-11-08 00:00:00

  • Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences.

    abstract:BACKGROUND:Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune sup...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Ammari M,McCarthy FM,Nanduri B,Pinchuk LM

    更新日期:2010-10-07 00:00:00

  • RECOVIR: an application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses.

    abstract:BACKGROUND:Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is essential for epidemiology, diagnostics, and vaccine development. Strain recognition based on similar...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Zhu D,Fox GE,Chakravarty S

    更新日期:2007-10-10 00:00:00

  • The COG database: an updated version includes eukaryotes.

    abstract:BACKGROUND:The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appea...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Tatusov RL,Fedorova ND,Jackson JD,Jacobs AR,Kiryutin B,Koonin EV,Krylov DM,Mazumder R,Mekhedov SL,Nikolskaya AN,Rao BS,Smirnov S,Sverdlov AV,Vasudevan S,Wolf YI,Yin JJ,Natale DA

    更新日期:2003-09-11 00:00:00

  • FANTOM: Functional and taxonomic analysis of metagenomes.

    abstract:BACKGROUND:Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context. RESULTS:He...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Sanli K,Karlsson FH,Nookaew I,Nielsen J

    更新日期:2013-02-01 00:00:00

  • Critique of the pairwise method for estimating qPCR amplification efficiency: beware of correlated data!

    abstract:BACKGROUND:A recently proposed method for estimating qPCR amplification efficiency E analyzes fluorescence intensity ratios from pairs of points deemed to lie in the exponential growth region on the amplification curves for all reactions in a dilution series. This method suffers from a serious problem: The resulting ra...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Tellinghuisen J

    更新日期:2020-07-08 00:00:00

  • Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks.

    abstract:BACKGROUND:Protein function prediction is an important problem in the post-genomic era. Recent advances in experimental biology have enabled the production of vast amounts of protein-protein interaction (PPI) data. Thus, using PPI data to functionally annotate proteins has been extensively studied. However, most existi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Xiong W,Liu H,Guan J,Zhou S

    更新日期:2013-01-01 00:00:00

  • Novel computational analysis of protein binding array data identifies direct targets of Nkx2.2 in the pancreas.

    abstract:BACKGROUND:The creation of a complete genome-wide map of transcription factor binding sites is essential for understanding gene regulatory networks in vivo. However, current prediction methods generally rely on statistical models that imperfectly model transcription factor binding. Generation of new prediction methods ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Hill JT,Anderson KR,Mastracci TL,Kaestner KH,Sussel L

    更新日期:2011-02-25 00:00:00

  • SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets.

    abstract:BACKGROUND:Given a set of t n-length DNA sequences, q satisfying 0 < q ≤ 1, and l and d satisfying 0 ≤ d < l < n, the quorum planted motif search (qPMS) finds l-length strings that occur in at least qt input sequences with up to d mismatches and is mainly used to locate transcription factor binding sites in DNA sequenc...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Yu Q,Wei D,Huo H

    更新日期:2018-06-18 00:00:00

  • Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model.

    abstract:BACKGROUND:Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on c...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: He X,Sarma MS,Ling X,Chee B,Zhai C,Schatz B

    更新日期:2010-05-20 00:00:00

  • A randomized approach to speed up the analysis of large-scale read-count data in the application of CNV detection.

    abstract:BACKGROUND:The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data. Typically, the genome is divided into tiling windows and windowed read-count data is generated for the entire geno...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Wang W,Sun W,Wang W,Szatkiewicz J

    更新日期:2018-03-01 00:00:00

  • A multiobjective approach to the genetic code adaptability problem.

    abstract:BACKGROUND:The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×10(84) possible genetic codes. The main question related to the organization of the genetic code is why ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: de Oliveira LL,de Oliveira PS,Tinós R

    更新日期:2015-02-19 00:00:00

  • Incorporating biological information in sparse principal component analysis with application to genomic data.

    abstract:BACKGROUND:Sparse principal component analysis (PCA) is a popular tool for dimensionality reduction, pattern recognition, and visualization of high dimensional data. It has been recognized that complex biological mechanisms occur through concerted relationships of multiple genes working in networks that are often repre...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Li Z,Safo SE,Long Q

    更新日期:2017-07-11 00:00:00

  • Primary orthologs from local sequence context.

    abstract:BACKGROUND:The evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don't code for proteins, yielding a need to infer evolutionary history of sequences irrespective of what kind of functional element they may encode. Thus, sequence-, as opposed to ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Gao K,Miller J

    更新日期:2020-02-06 00:00:00

  • Multi-omic analysis of signalling factors in inflammatory comorbidities.

    abstract:BACKGROUND:Inflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a long series of pathologic events that started years before. The systemic characteristics and relate...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Xiao H,Bartoszek K,Lio' P

    更新日期:2018-11-30 00:00:00

  • Identification of properties important to protein aggregation using feature selection.

    abstract:BACKGROUND:Protein aggregation is a significant problem in the biopharmaceutical industry (protein drug stability) and is associated medically with over 40 human diseases. Although a number of computational models have been developed for predicting aggregation propensity and identifying aggregation-prone regions in pro...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Fang Y,Gao S,Tai D,Middaugh CR,Fang J

    更新日期:2013-10-28 00:00:00

  • Exploring matrix factorization techniques for significant genes identification of Alzheimer's disease microarray gene expression data.

    abstract:BACKGROUND:The wide use of high-throughput DNA microarray technology provide an increasingly detailed view of human transcriptome from hundreds to thousands of genes. Although biomedical researchers typically design microarray experiments to explore specific biological contexts, the relationships between genes are hard...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Kong W,Mou X,Hu X

    更新日期:2011-01-01 00:00:00

  • Predicting Bevirimat resistance of HIV-1 from genotype.

    abstract:BACKGROUND:Maturation inhibitors are a new class of antiretroviral drugs. Bevirimat (BVM) was the first substance in this class of inhibitors entering clinical trials. While the inhibitory function of BVM is well established, the molecular mechanisms of action and resistance are not well understood. It is known that mu...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Heider D,Verheyen J,Hoffmann D

    更新日期:2010-01-20 00:00:00

  • RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks.

    abstract:BACKGROUND:In recent years, protein-protein interaction (PPI) networks have been well recognized as important resources to elucidate various biological processes and cellular mechanisms. In this paper, we address the problem of predicting protein complexes from a PPI network. This problem has two difficulties. One is r...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Maruyama O,Kuwahara Y

    更新日期:2017-12-06 00:00:00

  • Robust joint score tests in the application of DNA methylation data analysis.

    abstract:BACKGROUND:Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Li X,Fu Y,Wang X,Qiu W

    更新日期:2018-05-18 00:00:00

  • Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples.

    abstract:BACKGROUND:While researchers have utilized versions of the Affymetrix human GeneChip for the assessment of expression patterns in non human primate (NHP) samples, there has been no comprehensive sequence analysis study undertaken to demonstrate that the probe sequences designed to detect human transcripts are reliably ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Wang Z,Lewis MG,Nau ME,Arnold A,Vahey MT

    更新日期:2004-10-26 00:00:00

  • Coverage statistics for sequence census methods.

    abstract:BACKGROUND:We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce a coding of the shape of the coverage depth function as a tree and explain how thi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Evans SN,Hower V,Pachter L

    更新日期:2010-08-18 00:00:00

  • SPdb--a signal peptide database.

    abstract:BACKGROUND:The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further proc...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Choo KH,Tan TW,Ranganathan S

    更新日期:2005-10-13 00:00:00

  • Detection of biological switches using the method of Gröebner bases.

    abstract:BACKGROUND:Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular information to the nucleus where important biological functions are executed. RESULTS:In this wor...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Arkun Y

    更新日期:2019-11-28 00:00:00

  • BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways.

    abstract:BACKGROUND:Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcriptome data with pathway based interpretation. Over the years, the amount of omics data has become hu...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Kim I,Choi S,Kim S

    更新日期:2018-02-19 00:00:00

  • A multiple-alignment based primer design algorithm for genetically highly variable DNA targets.

    abstract:BACKGROUND:Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to populatio...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Brodin J,Krishnamoorthy M,Athreya G,Fischer W,Hraber P,Gleasner C,Green L,Korber B,Leitner T

    更新日期:2013-08-21 00:00:00

  • dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data.

    abstract:BACKGROUND:PCR clonal artefacts originating from NGS library preparation can affect both genomic as well as RNA-Seq applications when protocols are pushed to their limits. In RNA-Seq however the artifactual reads are not easy to tell apart from normal read duplication due to natural over-sequencing of highly expressed ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章


    authors: Sayols S,Scherzinger D,Klein H

    更新日期:2016-10-21 00:00:00