KNIME for open-source bioimage analysis: A tutorial

Advances in Anatomy Embryology and Cell Biology

Volumn 219, Issue , 2016, Pages 179-197

  Dietz, Christian ^a   Berthold, Michael R ^a  

^a UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; COMPUTER PROGRAM; DEVICES; FLUORESCENCE MICROSCOPY; HUMAN; IMAGE PROCESSING; PROCEDURES; STATISTICS AND NUMERICAL DATA; WORKFLOW;

ALGORITHMS; ANIMALS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, FLUORESCENCE; SOFTWARE; WORKFLOW;

EID: 84976347324     PISSN: 03015556     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-319-28549-8_7     Document Type: Article

References (20)

1. 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
2. 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
3. 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
4. Breiman L (2001) Random forests. Mach Learn 45(1):5–32
5. 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. NatMethods 9(7):697–710
6. 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
7. Haralick RM, Shanmugam K, Dinstein IH (1973) Textural features for image classification. IEEE Trans Syst Man Cybern (6):610–621
8. 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
9. Khotanzad A, Hong YH (1990) Invariant image recognition by zernike moments. IEEE Trans Pattern Anal Mach Intell 12(5):489–497
10. 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
11. Ljosa V, Sokolnicki KL, Carpenter AE (2012) Annotated high-throughput microscopy image sets for validation. Nat Methods 9(7):637
12. Lodermeyer V et al (2013) 90k, an interferon-stimulated gene product, reduces the infectivity of HIV-1. Retrovirology 10(1):11
13. Otsu N (1975) A threshold selection method from gray-level histograms. Automatica 11(285–296):23–27
14. Pietzsch T, Preibisch S, Tomanˇcák P, Saalfeld S (2012) Imglib2-generic image processing in java. Bioinformatics 28(22):3009–3011
15. Royer LA et al (2015) ClearVolume: open-source live 3D visualization for light-sheet microscopy. Nat Methods 12(6):480–481
16. 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
17. 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
18. Schölkopf B, Alexander JS (2002) Learning with kernels: support vector machines, regularization, optimization, and beyond. MIT, Cambridge
19. 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
20. Tamura H, Mori S, Yamawaki T (1978) Textural features corresponding to visual perception. IEEE Trans Syst Man Cybern 8(6):460–473