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NIH Image to ImageJ: 25 years of image analysis

TLDR
The origins, challenges and solutions of NIH Image and ImageJ software are discussed, and how their history can serve to advise and inform other software projects.
Abstract
For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.

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Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center

TL;DR: It is shown that the activity of chloramphenicol and linezolid critically depends on the nature of specific amino acids of the nascent chain carried by the ribosome and by the identity of the residue entering the A site, which indicates that the nascent protein modulates the properties of the Ribosomal catalytic center and affects binding of its ligands.
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Tryptophan-2,3-dioxygenase (TDO) inhibition ameliorates neurodegeneration by modulation of kynurenine pathway metabolites

TL;DR: It is found that increased levels of KYNA relative to 3-HK are likely central to the protection conferred by TDO inhibition in a fruit fly model of Huntington’s disease and that TRP treatment strongly reduces neurodegeneration by shifting KP flux toward KYNA synthesis.
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Sun Navigation Requires Compass Neurons in Drosophila

TL;DR: Using a flight simulator, it is found that Drosophila adopt arbitrary headings with respect to a simulated sun, thus performing menotaxis, and individuals remember their heading preference between successive flights-even over several hours.
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Visually induced initiation of Drosophila innate courtship-like following pursuit is mediated by central excitatory state

TL;DR: It is reported that moving light spots can induce courtship-like following pursuit in tethered wild-type male flies provided the fly is primed by optogenetic stimulation of specific dsx-expressing neuronal clusters in the lateral protocerebrum (LPR).
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The NAD + -mediated self-inhibition mechanism of pro-neurodegenerative SARM1

TL;DR: The cryo-EM structures of full-length Sarm1 proteins at 2.6- to 3.0-Å resolution have suggested the novel NAD+-mediated self-inhibition of this central pro-neurodegenerative protein.
References
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Journal ArticleDOI

Fiji: an open-source platform for biological-image analysis

TL;DR: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis that facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.
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CellProfiler: image analysis software for identifying and quantifying cell phenotypes

TL;DR: The first free, open-source system designed for flexible, high-throughput cell image analysis, CellProfiler is described, which can address a variety of biological questions quantitatively.
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ImageJ for microscopy

TL;DR: The near-comprehensive range of import filters that allow easy access to image and meta-data, a broad suite processing and analysis routine, and enthusiastic support from a friendly mailing list are invaluable for all microscopy labs and facilities-not just those on a budget.
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Computer control of microscopes using µManager.

TL;DR: This unit provides step‐by‐step protocols describing how to get started working with µManager, as well as some starting points for advanced use of the software.
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Icy: an open bioimage informatics platform for extended reproducible research

TL;DR: Icy is a collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless development of sophisticated imaging workflows.
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