DOI: 10.1007/978-3-319-28549-8_8. Segmenting and Tracking Multiple Dividing Targets Using ilastik

Segmenting and Tracking Multiple Dividing Targets Using ilastik

10.1007/978-3-319-28549-8_8

Crossref book-chapter

Springer International Publishing

Advances in Anatomy, Embryology and Cell Biology (297)

Bibliography

Haubold, C., Schiegg, M., Kreshuk, A., Berg, S., Koethe, U., & Hamprecht, F. A. (2016). Segmenting and Tracking Multiple Dividing Targets Using ilastik. Focus on Bio-Image Informatics, 199â229.

Authors 6

Carsten Haubold (first)
Martin Schiegg (additional)
Anna Kreshuk (additional)
Stuart Berg (additional)
Ullrich Koethe (additional)
Fred A. Hamprecht (additional)

References 22 Referenced 45

Andriluka M, Roth S, Schiele B (2008) People-tracking-by-detection and people-detection-by-tracking. In: IEEE conference on computer vision and pattern recognition (CVPR). http://www.mis.tu-darmstadt.de/node/382 (10.1109/CVPR.2008.4587583)
Benfold B, Reid I (2011) Stable multi-target tracking in real-time surveillance video. In: IEEE conference on computer vision and pattern recognition (CVPR). IEEE, New York, pp 3457–3464 / IEEE conference on computer vision and pattern recognition (CVPR) by B Benfold (2011)
Berthold MR, Cebron N, Dill F, Gabriel TR, Kötter T, Meinl T, Ohl P, Sieb C, Thiel K, Wiswedel B (2007) KNIME: the Konstanz information miner. In: Data analysis, machine learning and applications. Studies in classification, data analysis, and knowledge organization (GfKL 2007). Springer, Heidelberg (10.1007/978-3-540-78246-9_38)
Bise R, Yin Z, Kanade T (2011) Reliable Cell Tracking by Global Data Association. In: IEEE international symposium on biomedical imaging (ISBI), pp 1004–1010 (10.1109/ISBI.2011.5872571)
Breiman L (2001) Random forests. Mach Learn 45(1):5–32 (10.1023/A:1010933404324) / Mach Learn by L Breiman (2001)
Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, et al (2006) Cellprofiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7(10):R100 (10.1186/gb-2006-7-10-r100) / Genome Biol by AE Carpenter (2006)
Chenouard N, Bloch I, Olivo-Marin JC (2013) Multiple hypothesis tracking for cluttered biological image sequences. IEEE Trans Pattern Anal Mach Intell 35(11):2736–3750 (10.1109/TPAMI.2013.97) / IEEE Trans Pattern Anal Mach Intell by N Chenouard (2013)
Cordelières FP, Petit V, Kumasaka M, Debeir O, Letort V, Gallagher SJ, Larue L (2013) Automated cell tracking and analysis in phase-contrast videos (iTrack4u): development of java software based on combined mean-shift processes. PLoS One 8(11):e81266 (10.1371/journal.pone.0081266) / PLoS One by FP Cordelières (2013)
De Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Le Montagner Y, et al (2012) Icy: an open bioimage informatics platform for extended reproducible research. Nat Methods 9(7):690–696 (10.1038/nmeth.2075) / Nat Methods by F Chaumont De (2012)
Jaqaman K, Loerke D, Mettlen M, Kuwata H, Grinstein S, Schmid SL, Danuser G (2008) Robust single-particle tracking in live-cell time-lapse sequences. Nat Methods 5(8):695–702 (10.1038/nmeth.1237) / Nat Methods by K Jaqaman (2008)
Krzic U, Gunther S, Saunders TE, Streichan SJ, Hufnagel L (2012) Multiview light-sheet microscope for rapid in toto imaging. Nat Methods 9(7):730–733 (10.1038/nmeth.2064) / Nat Methods by U Krzic (2012)
Kuhn HW (1955) The Hungarian method for the assignment problem. Nav Res Logist Q 2(1–2):83–97 (10.1002/nav.3800020109) / Nav Res Logist Q by HW Kuhn (1955)
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)
Magnusson KE, Jaldén J (2012) A batch algorithm using iterative application of the Viterbi algorithm to track cells and construct cell lineages. In: International symposium on biomedical imaging (ISBI). IEEE, New York, pp 382–385 / International symposium on biomedical imaging (ISBI) by KE Magnusson (2012)
Maška M, Ulman V, Svoboda D, Matula P, Matula P, Ederra C, Urbiola A, España T, Venkatesan S, Balak DM, et al (2014) A benchmark for comparison of cell tracking algorithms. Bioinformatics 30(11):1609–1617 (10.1093/bioinformatics/btu080) / Bioinformatics by M Maška (2014)
Nick Perry JS Jean-Yves Tinevez (2012) Fiji trackmate. http://fiji.sc/TrackMate
Padfield D, Rittscher J, Roysam B (2011) Coupled minimum-cost flow cell tracking for high-throughput quantitative analysis. Med Image Anal 15(4):650–668 (10.1016/j.media.2010.07.006) / Med Image Anal by D Padfield (2011)
Pirsiavash H, Ramanan D, Fowlkes CC (2011) Globally-optimal greedy algorithms for tracking a variable number of objects. In: IEEE conference on computer vision and pattern recognition (CVPR). IEEE, New York, pp 1201–1208 / IEEE conference on computer vision and pattern recognition (CVPR) by H Pirsiavash (2011)
Schiegg M, Hanslovsky P, Kausler BX, Hufnagel L, Hamprecht FA (2013) Conservation tracking. In: IEEE international conference on computer vision (ICCV). IEEE, New York, pp 2928–2935 / IEEE international conference on computer vision (ICCV) by M Schiegg (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)
Sommer C, Straehle C, Kothe U, Hamprecht FA (2011) Ilastik: Interactive learning and segmentation toolkit. In: IEEE international symposium on biomedical imaging: from nano to macro (ISBI). IEEE, New York, pp 230–233 / IEEE international symposium on biomedical imaging: from nano to macro (ISBI) by C Sommer (2011)
Zhang L, Li Y, Nevatia R (2008) Global data association for multi-object tracking using network flows. In: IEEE conference on computer vision and pattern recognition, (CVPR). IEEE, New York, pp 1–8 / IEEE conference on computer vision and pattern recognition, (CVPR) by L Zhang (2008)

Dates

Type	When
Created	9 years, 3 months ago (May 21, 2016, 6:39 p.m.)
Deposited	5 years, 11 months ago (Sept. 8, 2019, 5:34 a.m.)
Indexed	3 months ago (May 16, 2025, 12:27 p.m.)
Issued	9 years, 7 months ago (Jan. 1, 2016)
Published	9 years, 7 months ago (Jan. 1, 2016)
Published Online	9 years, 3 months ago (May 21, 2016)
Published Print	9 years, 7 months ago (Jan. 1, 2016)

Funders 0

None

BibTeX

@inbook{Haubold_2016, title={Segmenting and Tracking Multiple Dividing Targets Using ilastik}, ISBN={9783319285498}, ISSN={2192-7065}, url={http://dx.doi.org/10.1007/978-3-319-28549-8_8}, DOI={10.1007/978-3-319-28549-8_8}, booktitle={Focus on Bio-Image Informatics}, publisher={Springer International Publishing}, author={Haubold, Carsten and Schiegg, Martin and Kreshuk, Anna and Berg, Stuart and Koethe, Ullrich and Hamprecht, Fred A.}, year={2016}, pages={199–229} }

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