Robust image registration of biological microscopic images

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Wang, Ching Wei ^a,b   Ka, Shuk Man ^b,c   Chen, Ann ^b,c  

^a NATIONAL TAIWAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Taiwan)

^b NATIONAL DEFENSE MEDICAL CENTER   (Taiwan)

^c TRI SERVICE GENERAL HOSPITAL   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANATOMY AND HISTOLOGY; ANIMAL; BRAIN; C57BL MOUSE; DEVICES; DROSOPHILA MELANOGASTER; IMAGE PROCESSING; MICROSCOPY; MOUSE; PROCEDURES; STAINING; THREE DIMENSIONAL IMAGING;

ALGORITHMS; ANIMALS; BRAIN; DROSOPHILA MELANOGASTER; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MICE; MICE, INBRED C57BL; MICROSCOPY; STAINING AND LABELING;

EID: 84906061895     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep06050     Document Type: Article

References (33)

1. Mosconi, L. Brain glucose metabolism in the early and specific diagnosis of Alzheimer's disease. FDG-PET studies in MCI and AD. Eur. J. Nucl. Med. Mol. Imaging. 32, 486-510 (2005). (Pubitemid 40591181)
2. Maintz, J. B. A. & Viergever, M. A. A survey of medical image registration. Med. Image Anal. 2, 1-36 (1998). (Pubitemid 128500719)
3. Cachier, P. Recalage non rigide d'images medicales volumiques - contribution aux approches iconiques et geometriques. Ph.D. Thesis, Ecole Centrale des Arts et Manufactures (2002).
4. Hill, D., Batchelor, P., Holden, M. & Hawkes, D. Medical image registration. Phy. in Med. and Biol. 3, R1-45 (2001).
5. Makela, T. et al. Areview of cardiac image registration methods. IEEE Trans. Med. Imag. 21, 1011-21 (2002).
6. Oliveira, F. P. & Tavares, J. M. Medical image registration: a review. Comput. Methods Biomech. Biomed. Engin. 17, 79-93 (2014).
7. Zitova, B. & Flusser, J. Image registration methods: a survey. Imag. Vis. Comput. 21, 977-1000 (2003).
8. Tan, Y., Hua, J. & Dong, M. 3D reconstruction from 2D images with hierarchical continuous simplices. Visual Comput. 23, 905-914 (2007). (Pubitemid 350092408)
9. Peng, H. et al. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat. Biotechnology 28, 348-53 (2010).
10. Pitiot, A. & Guimond, A. Geometrical regularization of displacement fields for histological image registration. Med. Image Anal. 12, 16-25 (2008). (Pubitemid 351189162)
11. Fiala, J. C. Reconstruct: a free editor for serial section microscopy. J. Microscopy 218, 52-61 (2005). (Pubitemid 40524168)
12. Cardona, A. et al. An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy. PLoS Biology 8, e1000502 (2010).
13. Cardona, A. et al. TrakEM2 Software for Neural Circuit Reconstruction. PLoS ONE 7, e38011 (2012).
14. Saalfeld, S., Cardona, A., Hartenstein, V. & Tomancak, P. As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets. Bioinfo. 26, i57-i63 (2010).
15. Saalfeld, S., Fetter, R., Cardona, A. & Tomancak, P. Elastic volume reconstruction from series of ultra-thin microscopy sections. Nat. Methods 9, 717-720 (2012).
16. Chakravarty, M. et al. The creation of a brain atlas for image guided neurosurgery using serial histological data. Neuro Image 30, 359-376 (2006).
17. Dauguet, J. et al. Three-dimensional reconstruction of stained histological slices and 3D non-linear registration with in-vivo MRI for whole baboon brain. Kidney Int. 164, 191-204 (2007). (Pubitemid 46935978)
18. Peng, H. et al. Brain Aligner: 3D registration atlases of Drosophila brains. Nat. Methods 8, 493-498 (2011).
19. Alic, L. et al. Facilitating tumor functional assessment by spatially relating 3D tumor histology and in vivo MRI image registration approach. PLoS One 6, e22835 (2011).
20. Sorzano, C., Thevenaz, P. & Unser, M. Elastic Registration of Biological Images using Vector-Spline Regularization. IEEE Trans. Biomed. Engin. 52, 652-663 (2005). (Pubitemid 40477175)
21. Arganda-Carreras, I. et al. Consistent and Elastic Registration of Histological Sections using Vector-Spline Regularization. LNCS, Comput. Vis. Approaches to Med. Imag. Anal. 4241, 85-95 (2006). (Pubitemid 44703398)
22. Bay, H., Ess, A., Tutelaars, T. & Gool, L. Speeded Up Robust Features (SURF). Comput. Vis. Imag. Understand. 110, 346-359 (2008).
23. Kroon, D. OpenSURF (including Image Warp). http://www.mathworks.com/ matlabcentral/fileexchange/28300-opensurf-including-image-warp (2010) Date of access:01/08/2012.
24. Saalfeld, S. CLAHE (Contrast Limited Adaptive Histogram Equalization). http://rsbweb.nih.gov/ij/plugins/clahe/index.html (2009) Date of access:1/8/2012.
25. Wang, C. & Chen, H. Improved Image Alignment Method in application to X-ray Images and Biological Images. Bioinfo. 29, 1879-1887 (2013).
26. D'Amico, G. The commonest glomerulonephritis in the world IgA nephropathy. Q. J. Med. 65, 709-727 (1987). (Pubitemid 18047151)
27. Chao, T. K. et al. The endogenous immune response modulates the course of IgAimmune complex-mediated nephropathy. Kidney Int. 70, 283-297 (2006).
28. SPSS Inc. SPSS for Windows, Rel.17.0.1. 2008. Chicago: SPSS Inc.
29. Rasband, W. S. Image J. U.S. National Institutes of Health, http://imagej.nih.gov/ij/ (1997-2012) Date of access:1/8/2012.
30. Wang, C. & Yu, C. Automated morphological classification of lung cancer subtypes using H&E tissue images. Mach. Vis. Appl. 24, 1383-1391 (2013).
31. Berger, C., Koeijer, J., Glas, W. & Madhuizen, H. Color Separation in Forensic Image Processing. J. Forensic Sciences 51, 100-102 (2006).
32. Ruifrok, A. C. & Johnston, D. A. Quantification of histochemical staining by color deconvolution. Anal. Quant. Cytol. Histol. 23, 291-299 (2001). (Pubitemid 32762920)
33. Wang, C. Fast automatic quantitative cell replication with fluorescent live cell imaging. BMC Bioinfo. 13, 1-10 (2012).