Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images

Bioinformatics

Volumn 30, Issue 17, 2014, Pages

  Frasconi, Paolo ^a   Silvestri, Ludovico ^b   Soda, Paolo ^c   Cortini, Roberto ^a   Pavone, Francesco S ^b   Iannello, Giulio ^c  

^a UNIVERSITY OF FLORENCE   (Italy)

^b UNIVERSITY OF FLORENCE   (Italy)

^c UNIVERSITY CAMPUS BIO MEDICO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; BRAIN; CONFOCAL MICROSCOPY; CYTOLOGY; MOUSE; NERVE CELL; PROCEDURES; THREE DIMENSIONAL IMAGING;

ALGORITHMS; ANIMALS; BRAIN; IMAGING, THREE-DIMENSIONAL; MICE; MICROSCOPY, CONFOCAL; NEURONS;

EID: 84906322330     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu469     Document Type: Conference Paper

References (44)

1. Becker, K. et al. (2012) Chemical clearing and dehydration of GFP expressing mouse brains. PLoS One, 7, e33916.
2. Bentley, J.L. (1975) Multidimensional binary search trees used for associative searching. Commun. ACM, 18, 509-517.
3. Biamonte, F. et al. (2009) Interactions between neuroactive steroids and reelin haploinsufficiency in Purkinje cell survival. Neurobiol. Dis., 36, 103-115.
4. Bohland, J.W. et al. (2009) A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Comput. Biol., 5, e1000334.
5. Bria, A. and Iannello, G. (2012) Terastitcher-A tool for fast automatic 3d-stitching of teravoxel-sized microscopy images. BMC Bioinformatics, 13, 316.
6. Briggman, K.L. and Bock, D.D. (2011) Volume electron microscopy for neuronal circuit reconstruction. Curr. Opin. Neurobiol., 22, 154-161.
7. Briggman, K.L. et al. (2011) Wiring specificity in the direction-selectivity circuit of the retina. Nature, 471, 183-188.
8. Buggenthin, F. et al. (2013) An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy. BMC Bioinformatics, 14, 297.
9. Caruana, R. (1997) Multitask learning. Mach. Learn., 28, 41-75.
10. Chung, K. et al. (2013) Structural and molecular interrogation of intact biological systems. Nature, 497, 332-337.
11. Cleveland, W.S. (1979) Robust locally weighted regression and smoothing scatterplots. J. Am. Stat. Assoc., 74, 829-836.
12. Comaniciu, D. and Meer, P. (2002) Mean shift: a robust approach toward feature space analysis. IEEET Pattern Anal., 24, 603-619.
13. Dodt, H.-U. et al. (2007) Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods, 4, 331-336.
14. Forero, M.G. et al. (2010) Deadeasy Mito-Glia: Automatic counting of mitotic cells and glial cells in Drosophila. PLoS One, 5, e10557.
15. Gong, H. et al. (2013) Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution. NeuroImage, 74, 87-98.
16. Goodfellow, I.J. et al. (2013) Pylearn2: a machine learning research library arXiv preprint arXiv:1308.4214.
17. Helmstaedter, M. et al. (2011) High-Accuracy neurite reconstruction for highthroughput neuroanatomy. Nat. Neurosci., 14, 1081-1088.
18. Hinton, G.E. et al. (2006) A fast learning algorithm for deep belief nets. Neural Comput., 18, 1527-1554.
19. Jain, V. et al. (2007) Supervised learning of image restoration with convolutional networks. In: Proceedings of the 11th International Conference on Computer Vision (ICCV). IEEE Piscataway, pp. 1-8.
20. Kapur, J. et al. (1985) A new method for gray-level picture thresholding using the entropy of the histogram. Comput. Vis., Graph. Image Process, 29, 273-285.
21. Kasthuri, N. and Lichtman, J.W. (2007) The rise of the projectome. Nat. Methods, 4, 307-308.
22. Keller, P.J. and Dodt, H.-U. (2012) Light sheet microscopy of living or cleared specimens. Curr. Opin. Neurobiol., 22, 138-143.
23. Kleinfeld, D. et al. (2011) Large-scale automated histology in the pursuit of connectomes. J. Neurosci., 31, 16125-16138.
24. Knott, G. et al. (2008) Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling. J. Neurosci., 28, 2959-2964.
25. LaTorre, A. et al. (2013) 3D segmentations of neuronal nuclei from confocal microscope image stacks. Front. Neuroanat., 7, 49.
26. Li, A. et al. (2010) Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain. Science, 330, 1404-1408.
27. Lichtman, J.W. and Denk, W. (2011) The big and the small: challenges of imaging the brains circuits. Science, 334, 618-623.
28. Mayerich, D. et al. (2008) Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain. J. Microsc., 231, 134-143.
29. Navlakha, S. et al. (2013) Unsupervised segmentation of noisy electron microscopy images using salient watersheds and region merging. BMC Bioinformatics, 14, 294.
30. Oh, S.W. et al. (2014) A mesoscale connectome of the mouse brain. Nature, 508, 207-214.
31. Osten, P. and Margrie, T.W. (2013) Mapping brain circuitry with a light microscope. Nat. Methods, 10, 515-523.
32. Pedregosa, F. et al. (2011) Scikit-learn: machine learning in python. J. Mach. Learn. Res., 12, 2825-2830.
33. Peng, H. et al. (2010) V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat. Biotechnol., 28, 348-353.
34. Peng, H. et al. (2014) Extensible visualization and analysis for multidimensional images using Vaa3D. Nat. Protoc., 9, 193-208.
35. Quan, T. et al. (2013) NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model. Sci. Rep., 3, 1414.
36. Ragan, T. et al. (2012) Serial two-photon tomography for automated ex vivo mouse brain imaging. Nat. Methods, 9, 255-258.
37. Sahoo, P.K. et al. (1988) A survey of thresholding techniques. Comput. Vis., Graph Image Process, 41, 233-260.
38. Schmitz, C. and Hof, P. (2005) Design-based stereology in neuroscience. Neuroscience, 130, 813-831.
39. Silvestri, L. et al. (2012) Confocal light sheet microscopy: micron-scale neuroanatomy of the entire mouse brain. Opt. Express, 20, 20582-20598.
40. Sporns, O. et al. (2005) The human connectome: a structural description of the human brain. PLoS Comput. Biol., 1, e42.
41. Tenenbaum, J.B. et al. (2000) A global geometric framework for nonlinear dimensionality reduction. Science, 290, 2319-2323.
42. Tomomura, M. et al. (2001) Purification of Purkinje cells by fluorescence-Activated cell sorting from transgenic mice that express green fluorescent protein. Eur. J. Neurosci., 14, 57-63.
43. Woodruff-Pak, D. (2006) Stereological estimation of Purkinje neuron number in C57BL/6 mice and its relation to associative learning. Neuroscience, 141, 233-243.
44. Zhou, K. et al. (2004) Iso-charts: stretch-driven mesh parameterization using spectral analysis. In: Proceedings of the Eurographics/ACM SIGGRAPH symposium on Geometry processing. ACM, New York, pp. 45-54