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
Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish
Y. Albert Pan,Tom Freundlich,Tamily A. Weissman,David Schoppik,X. Cindy Wang,Steven Zimmerman,Brian Ciruna,Joshua R. Sanes,Jeff W. Lichtman,Alexander F. Schier +9 more
TL;DR: The Zebrabow tool set presented here provides a resource for next-generation color-based anatomical and lineage analyses in zebrafish and provides evidence that embryonic corneal epithelial clones are replaced by large, wedge-shaped clones formed by centripetal expansion of cells from the peripheral cornea.
Journal ArticleDOI
ImageJ for the Next Generation of Scientific Image Data
Curtis Rueden,Kevin W. Eliceiri +1 more
TL;DR: These efforts towards interoperability and extensibility in the ImageJ consortium are presented, actively developing key software libraries like ImgLib and ImageJ Ops that are utilized to analyze and visualize biological image data, to the developmental benefit of not only of the applications but the libraries themselves.
Journal ArticleDOI
Artemisinins Target GABAA Receptor Signaling and Impair α Cell Identity
Jin Li,Tamara Casteels,Thomas Frogne,Camilla Ingvorsen,Christian Honoré,Monica Courtney,Kilian Huber,Nicole Schmitner,Robin A. Kimmel,Roman A. Romanov,Roman A. Romanov,Caterina Sturtzel,Charles-Hugues Lardeau,Johanna Klughammer,Matthias Farlik,Sara Sdelci,Andhira Vieira,Fabio Avolio,François Briand,Igor Baburin,Peter Májek,Florian M. Pauler,Thomas Penz,Alexey Stukalov,Manuela Gridling,Katja Parapatics,Charlotte Barbieux,Ekaterine Berishvili,Ekaterine Berishvili,Andreas Spittler,Jacques Colinge,Keiryn L. Bennett,Steffen Hering,Thierry Sulpice,Christoph Bock,Christoph Bock,Christoph Bock,Martin Distel,Tibor Harkany,Tibor Harkany,Dirk Meyer,Giulio Superti-Furga,Giulio Superti-Furga,Patrick Collombat,Jacob Hecksher-Sørensen,Stefan Kubicek +45 more
TL;DR: It is shown that the protein gephyrin is the mammalian target of these antimalarial drugs and that the mechanism of action of these molecules depends on the enhancement of GABAA receptor signaling.
Journal ArticleDOI
Programmable biofilm-based materials from engineered curli nanofibres
Peter Q. Nguyen,Peter Q. Nguyen,Zsofia Botyanszki,Zsofia Botyanszki,Pei Kun Richie Tay,Pei Kun Richie Tay,Neel Joshi,Neel Joshi +7 more
TL;DR: Biofilm-Integrated Nanofiber Display is a versatile nanobiotechnological platform for developing robust materials with programmable functions, demonstrating the potential of utilizing biofilms as large-scale designable biomaterials.
Journal ArticleDOI
Bacterial cell wall biogenesis is mediated by SEDS and PBP polymerase families functioning semi-autonomously.
Hongbaek Cho,Carl N. Wivagg,Mrinal Kapoor,Zachary T. Barry,Patricia D. A. Rohs,Hyunsuk Suh,Jarrod A. Marto,Ethan C. Garner,Thomas G. Bernhardt +8 more
TL;DR: It is found that aPBP activity is not necessary for glycan polymerization by the cell elongation machinery, as is commonly believed, and the results indicate that cell wall synthesis is mediated by two distinct polymerase systems, shape, elongation, division, sporulation (SEDS)-family proteins working within the cytoskeletal machines and aP BP enzymes functioning outside these complexes.
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.