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
Tissue clearing of both hard and soft tissue organs with the PEGASOS method.
Dian Jing,Dian Jing,Shiwen Zhang,Shiwen Zhang,Wenjing Luo,Xiaofei Gao,Yi Men,Chi Ma,Xiaohua Liu,Yating Yi,Yating Yi,Abhijit Bugde,Bo O. Zhou,Zhihe Zhao,Quan Yuan,Jian Q. Feng,Liang Gao,Woo Ping Ge,Hu Zhao +18 more
TL;DR: A polyethylene glycol-associated solvent system (PEGASOS), which rendered nearly all types of tissues transparent and preserved endogenous fluorescence, and revealed the distribution pattern of neural network in 3-D within the marrow space of long bone suggests that the PEGASos method is a useful tool for general biomedical research.
Journal ArticleDOI
CodY Regulates Thiol Peroxidase Expression as Part of the Pneumococcal Defense Mechanism against H2O2 Stress.
Barak Hajaj,Hasan Yesilkaya,Sulman Shafeeq,Xiangyun Zhi,Rachel Benisty,Shiran Tchalah,Oscar P. Kuipers,Nurith Porat +7 more
TL;DR: It is hypothesized that H2O2 activates a transcription factor which in turn up-regulates tpxD expression, which triggers a conformational change in CodY, resulting in enhanced binding to DNA and a schematic model illustrating the contribution of TpxD and CodY to pneumococcal global transcriptional response to H2 O2 is proposed.
Journal ArticleDOI
A Triple Helix-Loop-Helix/Basic Helix-Loop-Helix Cascade Controls Cell Elongation Downstream of Multiple Hormonal and Environmental Signaling Pathways in Arabidopsis
TL;DR: It is shown that IBH1 interacts with and inhibits a DNA binding basic helix-loop-helix (bHLH) protein, HBI1, in Arabidopsis thaliana, and the results indicate that PREs activate the DNA binding bHLH factor H BI1 by sequestering its inhibitor IBH 1.
Journal ArticleDOI
Compensatory metabolic networks in pancreatic cancers upon perturbation of glutamine metabolism
Douglas E. Biancur,Joao A. Paulo,Beata Małachowska,Beata Małachowska,Maria Quiles Del Rey,Cristovão M. Sousa,Xiaoxu Wang,Albert S. W. Sohn,Gerald C. Chu,Steven P. Gygi,J. Wade Harper,Wojciech Fendler,Wojciech Fendler,Joseph D. Mancias,Alec C. Kimmelman +14 more
TL;DR: It is shown that despite marked early effects on in vitro proliferation caused by GLS inhibition, pancreatic cancer cells have adaptive metabolic networks that sustain proliferation in vitro and in vivo.
Journal ArticleDOI
Neural progenitor cells regulate microglia functions and activity
Kira I. Mosher,Robert H. Andres,Robert H. Andres,Takeshi Fukuhara,Takeshi Fukuhara,Gregor Bieri,Maiko Hasegawa-Moriyama,Maiko Hasegawa-Moriyama,Yingbo He,Raphael Guzman,Raphael Guzman,Tony Wyss-Coray,Tony Wyss-Coray +12 more
TL;DR: This paper found that neural progenitor cells (NPCs) have a secretory protein profile distinct from other brain cells and modulate microglial activation, proliferation and phagocytosis.
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.