DOI: 10.1007/978-3-319-28549-8_7. KNIME for Open-Source Bioimage Analysis: A Tutorial

KNIME for Open-Source Bioimage Analysis: A Tutorial

10.1007/978-3-319-28549-8_7

Crossref book-chapter

Springer International Publishing

Advances in Anatomy, Embryology and Cell Biology (297)

Bibliography

Dietz, C., & Berthold, M. R. (2016). KNIME for Open-Source Bioimage Analysis: A Tutorial. Focus on Bio-Image Informatics, 179â197.

Authors 2

Christian Dietz (first)
Michael R. Berthold (additional)

References 20 Referenced 63

Aligeti M, Behrens RT, Pocock GM, Schindelin J, Dietz C, Eliceiri KW, Swanson CM, Malim MH, Ahlquist P, Sherer NM (2014) Cooperativity among rev-associated nuclear export signals regulates HIV-1 gene expression and is a determinant of virus species tropism. J Virol 88(24):14,207–14,221. doi: 10.1128/JVI.01897-14 . http://jvi.asm.org/content/88/24/14207.full.pdf+html (10.1128/JVI.01897-14)
Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, MacDonald D, Moore WJ, Neves C, Patterson A et al (2012) Omero: flexible, model-driven data management for experimental biology. Nat Methods 9(3):245–253 (10.1038/nmeth.1896) / Nat Methods by C Allan (2012)
Berthold MR, Cebron N, Dill F, Gabriel TR, Kötter T, Meinl T, Ohl P, Sieb C, Thiel K, Wiswedel B (2008) KNIME: the Konstanz information miner. Springer, Berlin / KNIME: the Konstanz information miner by MR Berthold (2008)
Breiman L (2001) Random forests. Mach Learn 45(1):5–32 (10.1023/A:1010933404324) / Mach Learn by L Breiman (2001)
Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath B, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B et al (2012) Biological imaging software tools. Nat Methods 9(7):697–710 (10.1038/nmeth.2084) / Nat Methods by KW Eliceiri (2012)
Gunkel M, Flottmann B, Heilemann M, Reymann J, Erfle H (2014) Integrated and correlative high-throughput and super-resolution microscopy. Histochem Cell Biol 141(6):597–603. doi: 10.1007/s00418-014-1209-y . http://dx.doi.org/10.1007/s00418-014-1209-y (10.1007/s00418-014-1209-y)
Haralick RM, Shanmugam K, Dinstein IH (1973) Textural features for image classification. IEEE Trans Syst Man Cybern (6):610–621 (10.1109/TSMC.1973.4309314) / IEEE Trans Syst Man Cybern by RM Haralick (1973)
Kamentsky L, Jones TR, Fraser A, Bray MA, Logan DJ, Madden KL, Ljosa V, Rueden C, Eliceiri KW, Carpenter AE (2011) Improved structure, function and compatibility for cellprofiler: modular high-throughput image analysis software. Bioinformatics 27(8):1179–1180 (10.1093/bioinformatics/btr095) / Bioinformatics by L Kamentsky (2011)
Khotanzad A, Hong YH (1990) Invariant image recognition by zernike moments. IEEE Trans Pattern Anal Mach Intell 12(5):489–497 (10.1109/34.55109) / IEEE Trans Pattern Anal Mach Intell by A Khotanzad (1990)
Linkert M, Rueden CT, Allan C, Burel JM, Moore W, Patterson A, Loranger B, Moore J, Neves C, MacDonald D et al (2010) Metadata matters: access to image data in the real world. J Cell Biol 189(5):777–782 (10.1083/jcb.201004104) / J Cell Biol by M Linkert (2010)
Ljosa V, Sokolnicki KL, Carpenter AE (2012) Annotated high-throughput microscopy image sets for validation. Nat Methods 9(7):637 (10.1038/nmeth.2083) / Nat Methods by V Ljosa (2012)
Lodermeyer V et al (2013) 90k, an interferon-stimulated gene product, reduces the infectivity of HIV-1. Retrovirology 10(1):11 (10.1186/1742-4690-10-111) / Retrovirology by V Lodermeyer (2013)
Otsu N (1975) A threshold selection method from gray-level histograms. Automatica 11(285–296):23–27 / Automatica by N Otsu (1975)
Pietzsch T, Preibisch S, Tomančák P, Saalfeld S (2012) Imglib2 - generic image processing in java. Bioinformatics 28(22):3009–3011 (10.1093/bioinformatics/bts543) / Bioinformatics by T Pietzsch (2012)
Royer LA et al (2015) ClearVolume: open-source live 3D visualization for light-sheet microscopy. Nat Methods 12(6):480–481 (10.1038/nmeth.3372) / Nat Methods by LA Royer (2015)
Saha AK, Kappes F, Mundade A, Deutzmann A, Rosmarin DM, Legendre M, Chatain N, Al-Obaidi Z, Adams BS, Ploegh HL, Ferrando-May E, Mor-Vaknin N, Markovitz DM (2013) Intercellular trafficking of the nuclear oncoprotein dek. Proc Natl Acad Sci 110(17):6847–6852. doi: 10.1073/pnas.1220751110 (10.1073/pnas.1220751110) / Proc Natl Acad Sci by AK Saha (2013)
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B et al (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9(7):676–682 (10.1038/nmeth.2019) / Nat Methods by J Schindelin (2012)
Schölkopf B, Alexander JS (2002) Learning with kernels: support vector machines, regularization, optimization, and beyond. MIT, Cambridge / Learning with kernels: support vector machines, regularization, optimization, and beyond by B Schölkopf (2002)
Strauch M, Luedke A, Muench D, Laudes T, Galizia CG, Martinelli E, Lavra L, Paolesse R, Ulivieri A, Catini A, Capuano R, Di Natale C (2014) More than apples and oranges: detecting cancer with a fruit fly’s antenna (10.1038/srep03576)
Tamura H, Mori S, Yamawaki T (1978) Textural features corresponding to visual perception. IEEE Trans Syst Man Cybern 8(6):460–473 (10.1109/TSMC.1978.4309999) / IEEE Trans Syst Man Cybern by H Tamura (1978)

Dates

Type	When
Created	9 years, 3 months ago (May 21, 2016, 2:39 p.m.)
Deposited	5 years, 11 months ago (Sept. 8, 2019, 1:34 a.m.)
Indexed	1 week, 1 day ago (Aug. 24, 2025, 6:58 p.m.)
Issued	9 years, 8 months ago (Jan. 1, 2016)
Published	9 years, 8 months ago (Jan. 1, 2016)
Published Online	9 years, 3 months ago (May 21, 2016)
Published Print	9 years, 8 months ago (Jan. 1, 2016)

Funders 0

None

BibTeX

@inbook{Dietz_2016, title={KNIME for Open-Source Bioimage Analysis: A Tutorial}, ISBN={9783319285498}, ISSN={2192-7065}, url={http://dx.doi.org/10.1007/978-3-319-28549-8_7}, DOI={10.1007/978-3-319-28549-8_7}, booktitle={Focus on Bio-Image Informatics}, publisher={Springer International Publishing}, author={Dietz, Christian and Berthold, Michael R.}, year={2016}, pages={179–197} }

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