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
Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development.
Mazène Hochane,Patrick R. van den Berg,Xueying Fan,Noémie M. L. P. Bérenger-Currias,Esmée Adegeest,Monika Bialecka,Maaike Nieveen,Maarten Menschaart,Susana M. Chuva de Sousa Lopes,Susana M. Chuva de Sousa Lopes,Stefan Semrau +10 more
TL;DR: A single-cell transcriptomics study of the human fetal kidney is presented, identifying 22 cell types and a host of marker genes and exploring the heterogeneity of the nephrogenic niche, localized podocyte precursors, and confirmed disease-associated marker genes.
Journal ArticleDOI
Biocompatible hydrogels of chitosan-alkali lignin for potential wound healing applications
Kartik Ravishankar,Manigandan Venkatesan,Raj Preeth Desingh,Aparna Mahalingam,Balaji Sadhasivam,Rajalakshmi Subramaniyam,Raghavachari Dhamodharan +6 more
TL;DR: The chitosan-alkali lignin gelation system was further capable of removing ferric ions from contaminated water by way of complexation and coagulation and in presence of the hydrogel, NIH 3T3 mouse fibroblast cells showed good cell migration characteristics suggesting that the gel might be suitable for wound healing application.
Journal ArticleDOI
How tough is Brittle Bone? Investigating Osteogenesis Imperfecta in Mouse Bone
Alessandra Carriero,Alessandra Carriero,Alessandra Carriero,Elizabeth A. Zimmermann,Elizabeth A. Zimmermann,Adriana Paluszny,Simon Y. Tang,Hrishikesh Bale,Hrishikesh Bale,Björn Busse,Björn Busse,Tamara Alliston,Galateia J. Kazakia,Robert O. Ritchie,Robert O. Ritchie,Sandra J. Shefelbine +15 more
TL;DR: Findings from the heterozygous oim bone suggest that increasing the quantity of healthy collagen in these bones helps to recover toughness at the multiple length scales, and demonstrates how modifications at the bone molecular level have ramifications at larger length scales affecting the overall mechanical integrity of the bone.
Journal ArticleDOI
Progress and Opportunities in the Characterization of Cellulose - An Important Regulator of Cell Wall Growth and Mechanics.
TL;DR: Benefits and limitations of different analytical techniques for characterizing cellulose structure and its interaction with other wall polymers are highlighted and emerging opportunities for future developments of structural characterization tools and multi-modal analyses are delineated.
Journal ArticleDOI
Macroalgal blooms alter community structure and primary productivity in marine ecosystems.
Devin A. Lyons,Christos Arvanitidis,Andrew J. Blight,Eva Chatzinikolaou,Tamar Guy-Haim,Jonne Kotta,Helen Orav-Kotta,Ana M. Queirós,Gil Rilov,Paul J. Somerfield,Tasman P. Crowe +10 more
TL;DR: The results suggest that, in addition to their direct social and economic costs, macroalgal blooms have ecological effects that may alter their capacity to deliver important ecosystem services.
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.