Abstract:
:CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research. CellProfiler's infrastructure is greatly improved, and we provide a protocol for cloud-based, large-scale image processing. New plugins enable running pretrained deep learning models on images. Designed by and for biologists, CellProfiler equips researchers with powerful computational tools via a well-documented user interface, empowering biologists in all fields to create quantitative, reproducible image analysis workflows.
journal_name
PLoS Bioljournal_title
PLoS biologyauthors
McQuin C,Goodman A,Chernyshev V,Kamentsky L,Cimini BA,Karhohs KW,Doan M,Ding L,Rafelski SM,Thirstrup D,Wiegraebe W,Singh S,Becker T,Caicedo JC,Carpenter AEdoi
10.1371/journal.pbio.2005970subject
Has Abstractpub_date
2018-07-03 00:00:00pages
e2005970issue
7eissn
1544-9173issn
1545-7885pii
pbio.2005970journal_volume
16pub_type
杂志文章相关文献
PLOS BIOLOGY文献大全abstract::The intrinsic flexibility of proteins allows them to undergo large conformational fluctuations in solution or upon interaction with other molecules. Proteins also commonly assemble into complexes with diverse quaternary structure arrangements. Here we investigate how the flexibility of individual protein chains influe...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1001870
更新日期:2014-05-27 00:00:00
abstract::In neurons polarized trafficking of vesicle-bound membrane proteins gives rise to the distinct molecular composition and functional properties of axons and dendrites. Despite their central role in shaping neuronal form and function, surprisingly little is known about the molecular processes that mediate polarized targ...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1001021
更新日期:2011-03-01 00:00:00
abstract::The recent United States measles epidemic has sparked another contentious national discussion about childhood vaccination. A growing number of parents are expressing concerns about the safety of vaccines, often fueled by misinformation from the internet, books, and other nonmedical sources. Many of these concerned par...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1002227
更新日期:2015-08-07 00:00:00
abstract::The Hedgehog signaling is a determinant pathway for tumor progression. However, while inhibition of the Hedgehog canonical pathway-Patched-Smoothened-Gli-has proved efficient in human tumors with activating mutations in this pathway, recent clinical data have failed to show any benefit in other cancers, even though So...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1001623
更新日期:2013-01-01 00:00:00
abstract::Cell differentiation is remarkably stable but can be reversed by somatic cell nuclear transfer, cell fusion, and iPS. Nuclear transfer to amphibian oocytes provides a special opportunity to test transcriptional reprogramming without cell division. We show here that, after nuclear transfer to amphibian oocytes, mitotic...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1001914
更新日期:2014-07-29 00:00:00
abstract::Antibiotic combination therapies are important for the efficient treatment of many types of infections, including those caused by antibiotic-resistant pathogens. Combination treatment strategies are typically used under the assumption that synergies are conserved across species and strains, even though recent results ...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.3000856
更新日期:2020-09-17 00:00:00
abstract::Many genes are regulated as an innate part of the eukaryotic cell cycle, and a complex transcriptional network helps enable the cyclic behavior of dividing cells. This transcriptional network has been studied in Saccharomyces cerevisiae (budding yeast) and elsewhere. To provide more perspective on these regulatory mec...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.0030225
更新日期:2005-07-01 00:00:00
abstract::Translation termination at premature termination codons (PTCs) triggers degradation of the aberrant mRNA, but the mechanism by which a termination event is defined as premature is still unclear. Here we show that the physical distance between the termination codon and the poly(A)-binding protein PABPC1 is a crucial de...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.0060092
更新日期:2008-04-29 00:00:00
abstract::Cancer research has become a global enterprise, and the number of researchers, as well as the cost for their activities, has skyrocketed. The budget for the National Cancer Institute of the United States National Institutes of Health alone was US$5.2 billion in 2015. Since most of the research is funded by public mone...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.2000314
更新日期:2016-09-29 00:00:00
abstract::Hox transcription factors control a number of developmental processes with the help of the PBC class proteins. In vitro analyses have established that the formation of Hox/PBC complexes relies on a short conserved Hox protein motif called the hexapeptide (HX). This paradigm is at the basis of the vast majority of expe...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1001351
更新日期:2012-01-01 00:00:00
abstract::The steroid hormone progesterone (P4) mediates many physiological processes through either nuclear receptors that modulate gene expression or membrane P4 receptors (mPRs) that mediate nongenomic signaling. mPR signaling remains poorly understood. Here we show that the topology of mPRβ is similar to adiponectin recepto...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.3000901
更新日期:2020-11-02 00:00:00
abstract::Mimivirus is the largest known virus whose genome and physical size are comparable to some small bacteria, blurring the boundary between a virus and a cell. Structural studies of Mimivirus have been difficult because of its size and long surface fibers. Here we report the use of enzymatic digestions to remove the surf...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1000092
更新日期:2009-04-28 00:00:00
abstract::Morphological development of fungi and their combined production of secondary metabolites are both acting in defence and protection. These processes are mainly coordinated by velvet regulators, which contain a yet functionally and structurally uncharacterized velvet domain. Here we demonstrate that the velvet domain o...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1001750
更新日期:2013-12-01 00:00:00
abstract::How should funding agencies enable researchers to explore high-risk but potentially high-reward science? One model that appears to work is the NSF-funded synthesis center, an incubator for community-led, innovative science. ...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1001468
更新日期:2013-01-01 00:00:00
abstract::During pregnancy, the ETS transcription factor ELF5 establishes the milk-secreting alveolar cell lineage by driving a cell fate decision of the mammary luminal progenitor cell. In breast cancer, ELF5 is a key transcriptional determinant of tumor subtype and has been implicated in the development of insensitivity to an...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1002330
更新日期:2015-12-30 00:00:00
abstract::Amyloid-β (Aβ) accumulation in the brain is a hallmark of Alzheimer's disease (AD) pathology. However, the molecular mechanism controlling microglial Aβ phagocytosis is poorly understood. Here we found that the E3 ubiquitin ligase Pellino 1 (Peli1) is induced in the microglia of AD-like five familial AD (5×FAD) mice, ...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.3000837
更新日期:2020-10-05 00:00:00
abstract::Many species are experiencing sustained environmental change mainly due to human activities. The unusual rate and extent of anthropogenic alterations of the environment may exceed the capacity of developmental, genetic, and demographic mechanisms that populations have evolved to deal with environmental change. To begi...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1000357
更新日期:2010-04-27 00:00:00
abstract::Adult humans possess a sophisticated repertoire of mathematical faculties. Many of these capacities are rooted in symbolic language and are therefore unlikely to be shared with nonhuman animals. However, a subset of these skills is shared with other animals, and this set is considered a cognitive vestige of our common...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.0050328
更新日期:2007-12-01 00:00:00
abstract::Over the past 3 decades, in a series of studies on some of the most extensively studied toxic chemicals and pollutants, scientists have found that the amount of toxic chemical linked with the development of a disease or death-which is central to determining "safe" or "hazardous" levels-is proportionately greater at th...
journal_title:PLoS biology
pub_type: 社论
doi:10.1371/journal.pbio.2003066
更新日期:2017-12-19 00:00:00
abstract::[This corrects the article DOI: 10.1371/journal.pbio.1002454.]. ...
journal_title:PLoS biology
pub_type: 杂志文章,已发布勘误
doi:10.1371/journal.pbio.1002624
更新日期:2018-03-14 00:00:00
abstract::Cell motility is essential for protozoan and metazoan organisms and typically relies on the dynamic turnover of actin filaments. In metazoans, monomeric actin polymerises into usually long and stable filaments, while some protozoans form only short and highly dynamic actin filaments. These different dynamics are partl...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.2005345
更新日期:2018-07-16 00:00:00
abstract::Sensory loss induces cross-modal plasticity, often resulting in altered performance in remaining sensory modalities. Whereas much is known about the macroscopic mechanisms underlying cross-modal plasticity, only scant information exists about its cellular and molecular underpinnings. We found that Caenorhabditis elega...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1002348
更新日期:2016-01-08 00:00:00
abstract::The cerebellum has been proposed to be a crucial component in the state estimation process that combines information from motor efferent and sensory afferent signals to produce a representation of the current state of the motor system. Such a state estimate of the moving human arm would be expected to be used when the...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.0050316
更新日期:2007-11-01 00:00:00
abstract::[This corrects the article DOI: 10.1371/journal.pbio.2001951.]. ...
journal_title:PLoS biology
pub_type: 已发布勘误
doi:10.1371/journal.pbio.1002603
更新日期:2017-05-01 00:00:00
abstract::The most consistent result in more than two decades of experimental evolution is that the fitness of populations adapting to a constant environment does not increase indefinitely, but reaches a plateau. Using experimental evolution with bacteriophage, we show here that the converse is also true. In populations small e...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.0050094
更新日期:2007-04-01 00:00:00
abstract::In mammalian oocytes, three actin binding proteins, Formin 2 (Fmn2), Spire, and profilin, synergistically organize a dynamic cytoplasmic actin meshwork that mediates translocation of the spindle toward the cortex and is required for successful fertilization. Here we characterize Fmn2 and elucidate the molecular mechan...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.1001795
更新日期:2014-02-25 00:00:00
abstract::Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines." Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding o...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.2003691
更新日期:2017-12-28 00:00:00
abstract::In fungi, mating between partners depends on the molecular recognition of two peptidyl mating pheromones by their respective receptors. The fission yeast Schizosaccharomyces pombe (Sp) has two mating types, Plus (P) and Minus (M). The mating pheromones P-factor and M-factor, secreted by P and M cells, are recognized b...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.3000101
更新日期:2019-01-22 00:00:00
abstract::Over the past decade, the high-dose refuge (HDR) strategy, aimed at delaying the evolution of pest resistance to Bacillus thuringiensis (Bt) toxins produced by transgenic crops, became mandatory in the United States and is being discussed for Europe. However, precopulatory dispersal and the mating rate between residen...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.0040181
更新日期:2006-06-01 00:00:00
abstract::One of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. So far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. Here, we use an unsupervised, systematic approach for associating genes a...
journal_title:PLoS biology
pub_type: 杂志文章
doi:10.1371/journal.pbio.0030134
更新日期:2005-05-01 00:00:00