Literature DB >> 22743772

Fiji: an open-source platform for biological-image analysis.

Johannes Schindelin1, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, Jean-Yves Tinevez, Daniel James White, Volker Hartenstein, Kevin Eliceiri, Pavel Tomancak, Albert Cardona.   

Abstract

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

Entities:  

Mesh：

Year:  2012        PMID： 22743772      PMCID： PMC3855844          DOI： 10.1038/nmeth.2019

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  30 in total

1.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

Review 2.  Automated image analysis for high-content screening and analysis.

Authors:  Aabid Shariff; Joshua Kangas; Luis Pedro Coelho; Shannon Quinn; Robert F Murphy
Journal:  J Biomol Screen       Date:  2010-05-20

3.  Geometrical consistent 3D tracing of neuronal processes in ssTEM data.

Authors:  Verena Kaynig; Thomas J Fuchs; Joachim M Buhmann
Journal:  Med Image Comput Comput Assist Interv       Date:  2010

4.  The chemical basis of morphogenesis. 1953.

Authors:  A M Turing
Journal:  Bull Math Biol       Date:  1990       Impact factor: 1.758

5.  Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes.

Authors:  Mark H Longair; Dean A Baker; J Douglas Armstrong
Journal:  Bioinformatics       Date:  2011-07-04       Impact factor: 6.937

6.  A whole-genome assembly of Drosophila.

Authors:  E W Myers; G G Sutton; A L Delcher; I M Dew; D P Fasulo; M J Flanigan; S A Kravitz; C M Mobarry; K H Reinert; K A Remington; E L Anson; R A Bolanos; H H Chou; C M Jordan; A L Halpern; S Lonardi; E M Beasley; R C Brandon; L Chen; P J Dunn; Z Lai; Y Liang; D R Nusskern; M Zhan; Q Zhang; X Zheng; G M Rubin; M D Adams; J C Venter
Journal:  Science       Date:  2000-03-24       Impact factor: 47.728

7.  An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy.

Authors:  Albert Cardona; Stephan Saalfeld; Stephan Preibisch; Benjamin Schmid; Anchi Cheng; Jim Pulokas; Pavel Tomancak; Volker Hartenstein
Journal:  PLoS Biol       Date:  2010-10-05       Impact factor: 8.029

8.  Automated cell lineage tracing in Caenorhabditis elegans.

Authors:  Zhirong Bao; John I Murray; Thomas Boyle; Siew Loon Ooi; Matthew J Sandel; Robert H Waterston
Journal:  Proc Natl Acad Sci U S A       Date:  2006-02-13       Impact factor: 11.205

9.  Network anatomy and in vivo physiology of visual cortical neurons.

Authors:  Davi D Bock; Wei-Chung Allen Lee; Aaron M Kerlin; Mark L Andermann; Greg Hood; Arthur W Wetzel; Sergey Yurgenson; Edward R Soucy; Hyon Suk Kim; R Clay Reid
Journal:  Nature       Date:  2011-03-10       Impact factor: 49.962

10.  BrainAligner: 3D registration atlases of Drosophila brains.

Authors:  Hanchuan Peng; Phuong Chung; Fuhui Long; Lei Qu; Arnim Jenett; Andrew M Seeds; Eugene W Myers; Julie H Simpson
Journal:  Nat Methods       Date:  2011-05-01       Impact factor: 28.547
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  2000 in total

1.  Perivascular Adventitial Fibroblast Specialization Accompanies T Cell Retention in the Inflamed Human Dermis.

Authors:  Alexander M S Barron; Julio C Mantero; Jonathan D Ho; Banafsheh Nazari; Katharine L Horback; Jag Bhawan; Robert Lafyatis; Christina Lam; Jeffrey L Browning
Journal:  J Immunol       Date:  2018-12-03       Impact factor: 5.422

2.  Toward 19F magnetic resonance thermometry: spin-lattice and spin-spin-relaxation times and temperature dependence of fluorinated drugs at 9.4 T.

Authors:  Christian Prinz; Paula Ramos Delgado; Thomas Wilhelm Eigentler; Ludger Starke; Thoralf Niendorf; Sonia Waiczies
Journal:  MAGMA       Date:  2018-12-04       Impact factor: 2.310

3.  The mitochondrial alternative oxidase from Chlamydomonas reinhardtii enables survival in high light.

Authors:  Yuval Kaye; Weichao Huang; Sophie Clowez; Shai Saroussi; Adam Idoine; Emanuel Sanz-Luque; Arthur R Grossman
Journal:  J Biol Chem       Date:  2018-12-03       Impact factor: 5.157

4.  α-Parvin and β-parvin in the rat uterus during decidualisation and uterine receptivity.

Authors:  Leigh Nicholson; Romanthi Madawala; Laura Lindsay; Christopher R Murphy
Journal:  Histochem Cell Biol       Date:  2018-12-05       Impact factor: 4.304

5.  The Chick Caudolateral Epiblast Acts as a Permissive Niche for Generating Neuromesodermal Progenitor Behaviours.

Authors:  Peter Baillie-Johnson; Octavian Voiculescu; Penny Hayward; Benjamin Steventon
Journal:  Cells Tissues Organs       Date:  2018-12-05       Impact factor: 2.481

6.  The Caenorhabditis elegans SMOC-1 Protein Acts Cell Nonautonomously To Promote Bone Morphogenetic Protein Signaling.

Authors:  Melisa S DeGroot; Herong Shi; Alice Eastman; Alexandra N McKillop; Jun Liu
Journal:  Genetics       Date:  2018-12-05       Impact factor: 4.562

7.  Fungal ligands released by innate immune effectors promote inflammasome activation during Aspergillus fumigatus infection.

Authors:  Benoit Briard; Rajendra Karki; R K Subbarao Malireddi; Anannya Bhattacharya; David E Place; Jayadev Mavuluri; Jennifer L Peters; Peter Vogel; Masahiro Yamamoto; Thirumala-Devi Kanneganti
Journal:  Nat Microbiol       Date:  2018-12-03       Impact factor: 17.745

8.  Coupling of Human Rhodopsin to a Yeast Signaling Pathway Enables Characterization of Mutations Associated with Retinal Disease.

Authors:  Benjamin M Scott; Steven K Chen; Nihar Bhattacharyya; Abdiwahab Y Moalim; Sergey V Plotnikov; Elise Heon; Sergio G Peisajovich; Belinda S W Chang
Journal:  Genetics       Date:  2018-12-04       Impact factor: 4.562

9.  Improved Multiplex Immunohistochemistry for Immune Microenvironment Evaluation of Mouse Formalin-Fixed, Paraffin-Embedded Tissues.

Authors:  Noah Sorrelle; Debolina Ganguly; Adrian T A Dominguez; Yuqing Zhang; Huocong Huang; Lekh N Dahal; Natalie Burton; Arturas Ziemys; Rolf A Brekken
Journal:  J Immunol       Date:  2018-12-03       Impact factor: 5.422

10.  Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting.

Authors:  Maria-Jesus Olarte; Siyoung Kim; Morris E Sharp; Jessica M J Swanson; Robert V Farese; Tobias C Walther
Journal:  Dev Cell       Date:  2020-07-29       Impact factor: 12.270
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