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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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Ferroptosis is controlled by the coordinated transcriptional regulation of glutathione and labile iron metabolism by the transcription factor BACH1

TL;DR: It is proposed that BACH1 controls the threshold of ferroPTosis induction and may represent a therapeutic target for alleviating ferroptosis-related diseases, including myocardial infarction.
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Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity

TL;DR: The importance of the indolic glucosinolate pathway in the growth restriction of P. indica and S. vermifera is demonstrated andIndole-phytoalexins and specifically indole-carboxylic acids derivatives are identified as potential key players in the maintenance of a mutualistic interaction with root endophytes.
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Functional and developmental identification of a molecular subtype of brain serotonergic neuron specialized to regulate breathing dynamics.

TL;DR: Findings show that serotonergic regulation of the respiratory chemoreflex is mediated by a specialized molecular subtype of 5HT neuron harboring unique physiological, biophysical, and hodological properties specified developmentally and demonstrate that the serotonergy system contains specialized modules contributing to its collective functional breadth.
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Ultra-selective looming detection from radial motion opponency

TL;DR: The discovery of an ultra-selective looming detecting neuron, lobula plate/lobula columnar, type II (LPLC2) in Drosophila is reported, and its selectivity is established by radial motion opponency.
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.
Journal ArticleDOI

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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