Visualization of image data from cells to organisms

Walter, Thomas; Shattuck, David W.; Baldock, Richard; Bastin, Mark E.; Carpenter, Anne E.; Duce, Suzanne L.; Ellenberg, Jan; Fraser, Adam; Hamilton, Nicholas A.; Pieper, Steve; Ragan, Mark A.; Schneider, Jürgen; Tomančák, Pavel; Hériché, Jean‐Karim

doi:10.1038/nmeth.1431

Cited by 242 publications

(217 citation statements)

References 88 publications

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“…Furthermore, computational analysis of time-lapse imaging data is still challenging. It requires sophisticated, automated data-processing procedures including cell segmentation, foci identification and single-particle tracking, which often need to be tailored to the specific experimental system [70].…”

Section: Limitations Of Live-cell Imagingmentioning

confidence: 99%

Dynamics of the DNA damage response: insights from live-cell imaging

Karanam¹,

Loewer²,

Lahav³

2013

Briefings in Functional Genomics

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All organisms have to safeguard the integrity of their genome to prevent malfunctioning and oncogenic transformation. Sophisticated DNA damage response mechanisms have evolved to detect and repair genomic lesions. With the emergence of live-cell microscopy of individual cells, we now begin to appreciate the complex spatiotemporal kinetics of the DNA damage response and can address the causes and consequences of the heterogeneity in the responses of genetically identical cells. Here, we highlight key discoveries where live-cell imaging has provided unprecedented insights into how cells respond to DNA double-strand breaks and discuss the main challenges and promises in using this technique.

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Section: Limitations Of Live-cell Imagingmentioning

confidence: 99%

Dynamics of the DNA damage response: insights from live-cell imaging

Karanam¹,

Loewer²,

Lahav³

2013

Briefings in Functional Genomics

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“…Theoretically, each isoform in a given regulatory network could be tagged with a fluorescent or other detectable reporter such that its localization pattern can be analyzed. Recent advances in high-throughput microscopy (Walter et al 2010) should allow systematic analysis of isoform-specific localization. Additionally, regulated exons could overlap with posttranslational modification sites in protein isoforms.…”

Section: Determining the Role Of Tissue-specific Isoformsmentioning

confidence: 99%

Networking in a global world: Establishing functional connections between neural splicing regulators and their target transcripts

Calarco¹,

Zhen²,

Blencowe³

2011

RNA

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Recent genome-wide analyses have indicated that almost all primary transcripts from multi-exon human genes undergo alternative pre-mRNA splicing (AS). Given the prevalence of AS and its importance in expanding proteomic complexity, a major challenge that lies ahead is to determine the functional specificity of isoforms in a cellular context. A significant fraction of alternatively spliced transcripts are regulated in a tissue-or cell-type-specific manner, suggesting that these mRNA variants likely function in the generation of cellular diversity. Complementary to these observations, several tissue-specific splicing factors have been identified, and a number of methodological advances have enabled the identification of large repertoires of target transcripts regulated by these proteins. An emerging theme is that tissue-specific splicing factors regulate coherent sets of splice variants in genes known to function in related biological pathways. This review focuses on the recent progress in our understanding of neural-specific splicing factors and their regulatory networks and outlines existing and emerging strategies for uncovering important biological roles for the isoforms that comprise these networks.

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“…Exposed to data overflow, neuroimaging researchers, however, could benefit from innovative tools and methods enabling the query, analysis and cross-linking of complex, heterogeneous and large scale data resources (Walter et al, 2010). As other scientific communities, the neuroimaging community is well aware of the important role of information technology for the advancement of its scientific goals, with the design of many data management systems and processing workflow tools, enabling data sharing and replicability of analyses.…”

Section: Heterogeneous Data To Be Managed In Neuroimaging Fieldmentioning

confidence: 99%

PLM as a strategy for the management of heterogeneous information in bio-medical imaging field

Eynard

Joliot

Boutinaud

et al. 2017

IJITM

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Abstract:The amount of heterogeneous information that researchers in bio-medical imaging (BMI) field have to manage has grown significantly, and their costs remain high. Large-scale sharing and reusing of this information has become unavoidable. Some data management systems have been developed in neuroimaging field, however they miss to integrate the data provenance all along the research works, from study specifications to scientific publication. The manufacturing industry was confronted to similar issues twenty years ago and designed product lifecycle management (PLM) systems to properly share and manage product information all along its lifecycle and among project teams. Therefore, PLM systems are proposed to be a relevant strategy to manage BMI research studies information. The generic, flexible and PLM-oriented data model called BMI-lifecycle management (BMI-LM) is described, as well as a neuroimaging classification which brings flexibility to the information management system. A test implementation into a PLM system is presented, and the feedback from the GIN researchers is discussed.Keywords: bio-medical imaging; BMI; product lifecycle management; PLM; information management; heterogeneous information; data model.Reference to this paper should be made as follows: Allanic, M., Hervé, P-Y., Durupt, A., Joliot, M., Boutinaud, P. and Eynard, B. (2017) 'PLM as a strategy for the management of heterogeneous information in bio-medical imaging field', Int.

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Visualization of image data from cells to organisms

Cited by 242 publications

References 88 publications

Dynamics of the DNA damage response: insights from live-cell imaging

Dynamics of the DNA damage response: insights from live-cell imaging

Networking in a global world: Establishing functional connections between neural splicing regulators and their target transcripts

PLM as a strategy for the management of heterogeneous information in bio-medical imaging field

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