Literature DB >> 27207367

KNIME for Open-Source Bioimage Analysis: A Tutorial.

Christian Dietz1, Michael R Berthold2.   

Abstract

The open analytics platform KNIME is a modular environment that enables easy visual assembly and interactive execution of workflows. KNIME is already widely used in various areas of research, for instance in cheminformatics or classical data analysis. In this tutorial the KNIME Image Processing Extension is introduced, which adds the capabilities to process and analyse huge amounts of images. In combination with other KNIME extensions, KNIME Image Processing opens up new possibilities for inter-domain analysis of image data in an understandable and reproducible way.

Mesh:

Year:  2016        PMID: 27207367     DOI: 10.1007/978-3-319-28549-8_7

Source DB:  PubMed          Journal:  Adv Anat Embryol Cell Biol        ISSN: 0301-5556            Impact factor:   1.231


  21 in total

1.  Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility.

Authors:  Diana A Stavreva; David A Garcia; Gregory Fettweis; Prabhakar R Gudla; George F Zaki; Vikas Soni; Andrew McGowan; Geneva Williams; Anh Huynh; Murali Palangat; R Louis Schiltz; Thomas A Johnson; Diego M Presman; Matthew L Ferguson; Gianluca Pegoraro; Arpita Upadhyaya; Gordon L Hager
Journal:  Mol Cell       Date:  2019-08-14       Impact factor: 17.970

2.  Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates.

Authors:  Michael H Hauer; Andrew Seeber; Vijender Singh; Raphael Thierry; Ragna Sack; Assaf Amitai; Mariya Kryzhanovska; Jan Eglinger; David Holcman; Tom Owen-Hughes; Susan M Gasser
Journal:  Nat Struct Mol Biol       Date:  2017-01-09       Impact factor: 15.369

3.  Epigenetic Regulation of DNA Repair Pathway Choice by MacroH2A1 Splice Variants Ensures Genome Stability.

Authors:  Robin Sebastian; Eri K Hosogane; Eric G Sun; Andy D Tran; William C Reinhold; Sandra Burkett; David M Sturgill; Prabhakar R Gudla; Yves Pommier; Mirit I Aladjem; Philipp Oberdoerffer
Journal:  Mol Cell       Date:  2020-07-09       Impact factor: 17.970

4.  SpotLearn: Convolutional Neural Network for Detection of Fluorescence In Situ Hybridization (FISH) Signals in High-Throughput Imaging Approaches.

Authors:  Prabhakar R Gudla; Koh Nakayama; Gianluca Pegoraro; Tom Misteli
Journal:  Cold Spring Harb Symp Quant Biol       Date:  2017-11-28

5.  Locomotor speed control circuits in the caudal brainstem.

Authors:  Paolo Capelli; Chiara Pivetta; Maria Soledad Esposito; Silvia Arber
Journal:  Nature       Date:  2017-10-23       Impact factor: 49.962

6.  MYC amplifies gene expression through global changes in transcription factor dynamics.

Authors:  Simona Patange; David A Ball; Yihan Wan; Tatiana S Karpova; Michelle Girvan; David Levens; Daniel R Larson
Journal:  Cell Rep       Date:  2022-01-25       Impact factor: 9.423

7.  Integrated Cells and Collagen Fibers Spatial Image Analysis.

Authors:  Georgii Vasiukov; Tatiana Novitskaya; Maria-Fernanda Senosain; Alex Camai; Anna Menshikh; Pierre Massion; Andries Zijlstra; Sergey Novitskiy
Journal:  Front Bioinform       Date:  2021-11-08

8.  Recent trends of green human resource management: Text mining and network analysis.

Authors:  Chetan Sharma; Sumit Sakhuja; Shivinder Nijjer
Journal:  Environ Sci Pollut Res Int       Date:  2022-07-05       Impact factor: 5.190

9.  ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis.

Authors:  Ellen T A Dobson; Beth Cimini; Anna H Klemm; Carolina Wählby; Anne E Carpenter; Kevin W Eliceiri
Journal:  Curr Protoc       Date:  2021-05

10.  Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection.

Authors:  Yihan Wan; Dimitrios G Anastasakis; Joseph Rodriguez; Murali Palangat; Prabhakar Gudla; George Zaki; Mayank Tandon; Gianluca Pegoraro; Carson C Chow; Markus Hafner; Daniel R Larson
Journal:  Cell       Date:  2021-05-11       Impact factor: 66.850

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