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.read more
Citations
More filters
Journal ArticleDOI
Sewage sludge application as a vehicle for microplastics in eastern Spanish agricultural soils
TL;DR: Qualification of microplastic pollution in agricultural fields through the application of sewage sludge is largely unknown, and soils' plastic loads increased by 280 light density microplastics kg-1 and 430 heavy densitymicroplasticskg-1 with each successive application of Sewage sludge, indicating that wastewater sludge application results in accumulation of micro Plastics in agricultural soils.
Journal ArticleDOI
Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells
Johan H. van Heerden,Johan H. van Heerden,Johan H. van Heerden,Meike T. Wortel,Meike T. Wortel,Meike T. Wortel,Frank J. Bruggeman,Frank J. Bruggeman,Joseph J. Heijnen,Yves J. M. Bollen,Robert Planqué,Josephus Hulshof,Tom O'Toole,S. Aljoscha Wahl,Bas Teusink,Bas Teusink,Bas Teusink +16 more
TL;DR: How cell fate can be determined by glycolytic dynamics combined with cell heterogeneity purely at the metabolic level is revealed, extending fundamental knowledge of this central pathway that is dysfunctional in diseases such as diabetes and cancer.
Journal ArticleDOI
Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium
Sandrine Brugiroux,Markus Beutler,Carina Pfann,Debora Garzetti,Hans-Joachim Ruscheweyh,Diana Ring,Manuel Diehl,Simone Herp,Yvonne Lötscher,Saib Hussain,Boyke Bunk,Rüdiger Pukall,Daniel H. Huson,Philipp C. Münch,Alice C. McHardy,Kathy D. McCoy,Andrew J. Macpherson,Alexander Loy,Thomas Clavel,David Berry,Bärbel Stecher +20 more
TL;DR: A collection of murine bacterial strains and a modular design approach are used to create a minimal bacterial community that provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium and established a highly versatile experimental system that showed efficacy in an enteric infection model.
Journal ArticleDOI
Cell to whole-plant phenotyping: the best is yet to come.
TL;DR: Overall, attention is focused on spatial and temporal resolution because these are crucial aspects of imaging procedures in plant phenotyping systems.
Journal ArticleDOI
Lattice distortion in a strong and ductile refractory high-entropy alloy
Chanho Lee,Gian Song,Michael C. Gao,Rui Feng,Peiyong Chen,Jamieson Brechtl,Yan Chen,Ke An,Wei Guo,Jonathan D. Poplawsky,Song Li,A.T. Samaei,Wei Chen,Alice Hu,Hahn Choo,Peter K. Liaw +15 more
TL;DR: In this paper, a NbTaTiV refractory HEA with a single body-centered-cubic (BCC) structure using an integrated experimental and theoretical approach was developed.
References
More filters
Journal ArticleDOI
Fiji: an open-source platform for biological-image analysis
Johannes Schindelin,Ignacio Arganda-Carreras,Erwin Frise,Verena Kaynig,Mark Longair,Tobias Pietzsch,Stephan Preibisch,Curtis Rueden,Stephan Saalfeld,Benjamin Schmid,Jean-Yves Tinevez,Daniel J. White,Volker Hartenstein,Kevin W. Eliceiri,Pavel Tomancak,Albert Cardona +15 more
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.
Journal ArticleDOI
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
Anne E. Carpenter,Thouis R. Jones,Michael R. Lamprecht,Colin Clarke,In Han Kang,Ola Friman,David A. Guertin,Joo Han Chang,Robert A. Lindquist,Jason Moffat,Polina Golland,David M. Sabatini +11 more
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.
Journal ArticleDOI
Computer control of microscopes using µManager.
Arthur D. Edelstein,Nenad Amodaj,Karl Hoover,Ronald D. Vale,Ronald D. Vale,Nico Stuurman,Nico Stuurman +6 more
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.
Journal ArticleDOI
Icy: an open bioimage informatics platform for extended reproducible research
Fabrice de Chaumont,Stephane Dallongeville,Nicolas Chenouard,Nicolas Hervé,Sorin Pop,Thomas Provoost,Vannary Meas-Yedid,Praveen Pankajakshan,Timothee Lecomte,Yoann Le Montagner,Thibault Lagache,Alexandre Dufour,Jean-Christophe Olivo-Marin +12 more
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.