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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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Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo.

TL;DR: This study provides the location and activity of Mitsui-7-induced enhancers and transcription start sites, providing a useful resource for targeted experiments elucidating the biological effects of nanomaterials and the identification of biomarkers for early detection of MWCNT-induced inflammation.
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Morphologic and Genomic Analyses of New Isolates Reveal a Second Lineage of Cedratviruses.

TL;DR: Biological and genomic analyses showed viruses with different particle sizes, genome lengths, and architecture, revealing the existence of a second lineage of this new group of giant viruses.
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Triploid Atlantic salmon Salmo salar have a higher dietary phosphorus requirement for bone mineralization during early development.

TL;DR: There was a ploidy × diet interaction on vertebral deformities, with triploids having higher prevalence's of fish with ≥1 deformed vertebra in all dietary groups except continuous NP.
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Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly.

TL;DR: This work comprehensively investigates proteins involved in the assembly of the 1,2-propanediol utilization bacterial microcompartment from Salmonella enterica serovar Typhimurium LT2, and provides insight into the assembly mechanism of these bacterial organelles and will aid downstream engineering efforts.
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Dramatic evolution of body length due to postembryonic changes in cell size in a newly discovered close relative of Caenorhabditis elegans

TL;DR: A description of the broad developmental patterns of a newly discovered species, C. sp.
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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