Automatic core segmentation and registration for fast tissue microarray de-arraying
作者： Hoai-Nam Nguyen , Charles Kervrann , Cyril Cauchois , Vincent Paveau
DOI: 10.1109/ISBI.2015.7164147
关键词:
摘要: Tissue core de-arraying is one of the most important steps in tissue microarray (TMA) image analysis. However, few solutions and mathematical frameworks are available. This paper presents a robust TMA method adapted for digital images from classical optical new fluorescent devices. The proposed algorithm composed three modules: (a) detection, (b) segmentation, (c) array indexing. detection cores performed by local adaptive thresholding isotropic wavelet transform coefficients. segmentation component uses parametric ellipse to delineate boundaries potential cores. Array indices each computed using thin-plate splines estimate deformation deposited grid. Our appropriate non-linear able quantify grids when compared existing algorithms.
sci-hub.se 参考文章(10)
Jean Duchon, Interpolation des fonctions de deux variables suivant le principe de la flexion des plaques minces Revue française d'automatique, informatique, recherche opérationnelle. Analyse numérique. ,vol. 10, pp. 5- 12 ,(1976) , 10.1051/M2AN/197610R300051
M. Holschneider, R. Kronland-Martinet, J. Morlet, Ph. Tchamitchian, A real-time algorithm for signal analysis with the help of the wavelet transform Wavelets. Time-Frequency Methods and Phase Space. pp. 286- 297 ,(1989) , 10.1007/978-3-642-97177-8_28
Antoine Basset, Jerome Boulanger, Patrick Bouthemy, Charles Kervrann, Jean Salamero, SLT-LoG: A vesicle segmentation method with automatic scale selection and local thresholding applied to TIRF microscopy international symposium on biomedical imaging. pp. 533- 536 ,(2014) , 10.1109/ISBI.2014.6867926
Rossana Dell’Anna, Francesca Demichelis, Mattia Barbareschi, Andrea Sboner, An automated procedure to properly handle digital images in large scale Tissue Microarray experiments Computer Methods and Programs in Biomedicine. ,vol. 79, pp. 197- 208 ,(2005) , 10.1016/J.CMPB.2005.04.004
Yinhai Wang, Kienan Savage, Claire Grills, Andrena McCavigan, Jacqueline A. James, Dean A. Fennell, Peter W. Hamilton, A TMA De-Arraying Method for High Throughput Biomarker Discovery in Tissue Research PLOS ONE. ,vol. 6, ,(2011) , 10.1371/JOURNAL.PONE.0026007
Juha Kononen, Lukas Bubendorf, Anne Kallionimeni, Maarit Bärlund, Peter Schraml, Stephen Leighton, Joachim Torhorst, Michael J Mihatsch, Guido Sauter, Olli-P. Kallionimeni, Tissue microarrays for high-throughput molecular profiling of tumor specimens Nature Medicine. ,vol. 4, pp. 844- 847 ,(1998) , 10.1038/NM0798-844
W. Chen, M. Reiss, D.J. Foran, A prototype for unsupervised analysis of tissue microarrays for cancer research and diagnostics international conference of the ieee engineering in medicine and biology society. ,vol. 8, pp. 89- 96 ,(2004) , 10.1109/TITB.2004.828891
Jean-Luc Starck, Jalal Fadili, Fionn Murtagh, The Undecimated Wavelet Decomposition and its Reconstruction IEEE Transactions on Image Processing. ,vol. 16, pp. 297- 309 ,(2007) , 10.1109/TIP.2006.887733
F.L. Bookstein, Principal warps: thin-plate splines and the decomposition of deformations IEEE Transactions on Pattern Analysis and Machine Intelligence. ,vol. 11, pp. 567- 585 ,(1989) , 10.1109/34.24792
P Thevenaz, R Delgado-Gonzalo, M Unser, The Ovuscule IEEE Transactions on Pattern Analysis and Machine Intelligence. ,vol. 33, pp. 382- 393 ,(2011) , 10.1109/TPAMI.2010.112