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
Designed proteins induce the formation of nanocage-containing extracellular vesicles
Jörg Votteler,Cassandra Ogohara,Sue Yi,Yang Hsia,Una Nattermann,David M. Belnap,Neil P. King,Wesley I. Sundquist +7 more
TL;DR: Results show how proteins can be programmed to direct the formation of hybrid biological materials that perform complex tasks, and establish EPNs as a class of designed, modular, genetically-encoded nanomaterials that can transfer molecules between cells.
Journal ArticleDOI
An intercrypt subpopulation of goblet cells is essential for colonic mucus barrier function.
Elisabeth E. L. Nyström,Beatriz Martínez-Abad,Liisa Arike,George M. H. Birchenough,Eric B. Nonnecke,Patricia A. Castillo,Frida Svensson,Charles L. Bevins,Gunnar C. Hansson,Malin Johansson +9 more
TL;DR: In this article, the intercrypt goblet cells (icGCs), located at the colonic luminal surface, produced mucus with properties that differed from the mucus secreted by crypt-residing goblets.
Journal ArticleDOI
Excessive tubulin polyglutamylation causes neurodegeneration and perturbs neuronal transport
Maria M. Magiera,Maria M. Magiera,Satish Bodakuntla,Satish Bodakuntla,Jakub Žiak,Jakub Žiak,Sabrina Lacomme,Patricia Marques Sousa,Patricia Marques Sousa,Sophie Leboucher,Sophie Leboucher,Torben J. Hausrat,Christophe Bosc,Christophe Bosc,Annie Andrieux,Annie Andrieux,Matthias Kneussel,Marc Landry,André Calas,Martin Balastik,Carsten Janke,Carsten Janke +21 more
TL;DR: It is demonstrated that excessive polyglutamylation induces neurodegeneration in a cell‐autonomous manner and can occur in many parts of the central nervous system, suggesting that impaired cargo transport plays an important role in the observed degenerative phenotypes.
Journal ArticleDOI
ALS-Linked Mutations Enlarge TDP-43-Enriched Neuronal RNA Granules in the Dendritic Arbor
Li Qun Liu-Yesucevitz,Amy Lin,Atsushi Ebata,Joon Y. Boon,Whitney Reid,Ya Fei Xu,Kendra Kobrin,George J. Murphy,Leonard Petrucelli,Benjamin Wolozin +9 more
TL;DR: It is reported that ALS-linked mutations in TDP-43 (A315T and Q343R) increase the size of neuronal T DP-43 granules in the dendritic arbor of rat hippocampal neurons and suggest a neuronally selective mechanism through which TDP -43 mutations might elicit neuronal dysfunction.
Journal ArticleDOI
Rare variants in FBN1 and FBN2 are associated with severe adolescent idiopathic scoliosis
Jillian G. Buchan,David M. Alvarado,Gabe Haller,Carlos Cruchaga,Matthew B. Harms,Tianxiao Zhang,Marcia C. Willing,Dorothy K. Grange,Alan C. Braverman,Nancy H. Miller,Jose A. Morcuende,Nelson L.S. Tang,Tsz Ping Lam,Bobby K. W. Ng,Jack C. Y. Cheng,Matthew B. Dobbs,Christina A. Gurnett +16 more
TL;DR: Clinical evaluations revealed that the majority of AIS cases with rare FBN1 variants do not meet diagnostic criteria for Marfan syndrome, though variants are associated with tall stature and upregulation of the transforming growth factor beta pathway.
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.