Automated Identification and Localization of Hematopoietic Stem Cells in 3D Intravital Microscopy Data

Stem Cell Reports

Volumn 5, Issue 1, 2015, Pages 139-153

  Khorshed, Reema A ^a   Hawkins, Edwin D ^a   Duarte, Delfim ^a   Scott, Mark K ^a,b   Akinduro, Olufolake A ^a   Rashidi, Narges M ^a,c   Spitaler, Martin ^a,d   Lo Celso, Cristina ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; AUTOMATION; BONE MARROW; CELL AGGREGATION; CELL DEATH; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DECISION TREE; HEMATOPOIETIC STEM CELL; IMAGE ANALYSIS; MACHINE LEARNING; MICROSCOPY; MOUSE; NONHUMAN; OSTEOBLAST; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING; HUMAN; IMAGE PROCESSING; INTRAVITAL MICROSCOPY; STEM CELL NICHE; ULTRASTRUCTURE;

BONE MARROW; HEMATOPOIETIC STEM CELLS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; INTRAVITAL MICROSCOPY; STEM CELL NICHE;

EID: 84937523490     PISSN: 22136711     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.stemcr.2015.05.017     Document Type: Article

References (35)

1. Agarwal, C., and Sharma, A. (2011). Image understanding using decision tree based machine learning. Proceedings of the 2011 International Conference on Information Technology and Multimedia (ICIM), 1-8.
2. O. Aydemir, and T. Kayikcioglu Decision tree structure based classification of EEG signals recorded during two dimensional cursor movement imagery J. Neurosci. Methods 229 2014 68 75
3. M. Baatz, and A. Schäpe Multiresolution segmentation-an optimization approach for high quality multi-scale image segmentation J. Strobl, T. Blaschke, G. Griesebner, Angew. Geogr. Info. verarbeitung 2000 Wichmann-Verlag Heidelberg 12 23
4. L.M. Calvi, G.B. Adams, K.W. Weibrecht, J.M. Weber, D.P. Olson, M.C. Knight, R.P. Martin, E. Schipani, P. Divieti, F.R. Bringhurst, and et al. Osteoblastic cells regulate the haematopoietic stem cell niche Nature 425 2003 841 846
5. G. Chung, and L.A. Vese Image segmentation using a multilayer level-set approach Comput. Vis. Sci. 12 2009 267 285
6. H.E. Fleming, V. Janzen, C. Lo Celso, J. Guo, K.M. Leahy, H.M. Kronenberg, and D.T. Scadden Wnt signaling in the niche enforces hematopoietic stem cell quiescence and is necessary to preserve self-renewal in vivo Cell Stem Cell 2 2008 274 283
7. D.A. Hume Applications of myeloid-specific promoters in transgenic mice support in vivo imaging and functional genomics but do not support the concept of distinct macrophage and dendritic cell lineages or roles in immunity J. Leukoc. Biol. 89 2011 525 538
8. Z. Kalajzic, P. Liu, I. Kalajzic, Z. Du, A. Braut, M. Mina, E. Canalis, and D.W. Rowe Directing the expression of a green fluorescent protein transgene in differentiated osteoblasts: comparison between rat type I collagen and rat osteocalcin promoters Bone 31 2002 654 660
9. A. Köhler, V. Schmithorst, M.D. Filippi, M.A. Ryan, D. Daria, M. Gunzer, and H. Geiger Altered cellular dynamics and endosteal location of aged early hematopoietic progenitor cells revealed by time-lapse intravital imaging in long bones Blood 114 2009 290 298
10. M.F. Krummel, and I. Macara Maintenance and modulation of T cell polarity Nat. Immunol. 7 2006 1143 1149
11. Y. Kunisaki, I. Bruns, C. Scheiermann, J. Ahmed, S. Pinho, D. Zhang, T. Mizoguchi, Q. Wei, D. Lucas, K. Ito, and et al. Arteriolar niches maintain haematopoietic stem cell quiescence Nature 502 2013 637 643
12. S.W. Lane, Y.J. Wang, C. Lo Celso, C. Ragu, L. Bullinger, S.M. Sykes, F. Ferraro, S. Shterental, C.P. Lin, D.G. Gilliland, and et al. Differential niche and Wnt requirements during acute myeloid leukemia progression Blood 118 2011 2849 2856
13. C. Lo Celso, H.E. Fleming, J.W. Wu, C.X. Zhao, S. Miake-Lye, J. Fujisaki, D. Côté, D.W. Rowe, C.P. Lin, and D.T. Scadden Live-animal tracking of individual haematopoietic stem/progenitor cells in their niche Nature 457 2009 92 96
14. C. Lo Celso, C.P. Lin, and D.T. Scadden In vivo imaging of transplanted hematopoietic stem and progenitor cells in mouse calvarium bone marrow Nat. Protoc. 6 2011 1 14
15. X. Lou, M. Kang, P. Xenopoulos, S. Muñoz-Descalzo, and A.K. Hadjantonakis A rapid and efficient 2D/3D nuclear segmentation method for analysis of early mouse embryo and stem cell image data Stem Cell Reports 2 2014 382 397
16. G. Mallinis, N. Koutsias, M. Tsakiri-Strati, and M. Karteris Object-based classification using Quickbird imagery for delineating forest vegetation polygons in a Mediterranean test site ISPRS J. Photogramm. Remote Sens. 63 2008 237 250
17. S. Méndez-Ferrer, T.V. Michurina, F. Ferraro, A.R. Mazloom, B.D. Macarthur, S.A. Lira, D.T. Scadden, A. Ma'ayan, G.N. Enikolopov, and P.S. Frenette Mesenchymal and haematopoietic stem cells form a unique bone marrow niche Nature 466 2010 829 834
18. B.S. Moon A Gaussian smoothing algorithm to generate trend curves Korean J. Comput. Appl. Math. 8 2001 507 518
19. S.J. Morrison, and D.T. Scadden The bone marrow niche for haematopoietic stem cells Nature 505 2014 327 334
20. M.D. Muzumdar, B. Tasic, K. Miyamichi, L. Li, and L. Luo A global double-fluorescent Cre reporter mouse Genesis 45 2007 593 605
21. K. Nandy, J. Kim, D.P. McCullough, M. McAuliffe, K.J. Meaburn, T.P. Yamaguchi, P.R. Gudla, and S.J. Lockett Segmentation and quantitative analysis of individual cells in developmental tissues Methods Mol. Biol. 1092 2014 235 253
22. N. Otsu A threshold selection method from gray-level histograms IEEE Trans. Syst. Man Cybern. 9 1979 62 66
23. S. Pop, A.C. Dufour, J.F. Le Garrec, C.V. Ragni, C. Cimper, S.M. Meilhac, and J.C. Olivo-Marin Extracting 3D cell parameters from dense tissue environments: application to the development of the mouse heart Bioinformatics 29 2013 772 779
24. F. Progatzky, M.J. Dallman, and C. Lo Celso From seeing to believing: labelling strategies for in vivo cell-tracking experiments Interface Focus 3 2013 20130001
25. N.M. Rashidi, M.K. Scott, N. Scherf, A. Krinner, J.S. Kalchschmidt, K. Gounaris, M.E. Selkirk, I. Roeder, and C. Lo Celso In vivo time-lapse imaging shows diverse niche engagement by quiescent and naturally activated hematopoietic stem cells Blood 124 2014 79 83
26. L. Ritsma, S.I. Ellenbroek, A. Zomer, H.J. Snippert, F.J. de Sauvage, B.D. Simons, H. Clevers, and J. van Rheenen Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging Nature 507 2014 362 365
27. P. Rompolas, E.R. Deschene, G. Zito, D.G. Gonzalez, I. Saotome, A.M. Haberman, and V. Greco Live imaging of stem cell and progeny behaviour in physiological hair-follicle regeneration Nature 487 2012 496 499
28. Saikumar, T., Nagarani, M., Yojana, K., and Shashidhar, B. (2012). Image segmentation of an adaptive threshold algorithm using watershed transform and fuzzy c-means clustering on level set method. Proceedings of the 2012 International Conference on Advances in Engineering, Science and Management (ICAESM), 33-38.
29. Sales, E., Gomez, W., and Pereira, W.C.A. (2011). Evaluation performance of local adaptive binarization algorithms for trabecular bone on simulated μCT. Proceedings of the 2011 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), 3084-3087.
30. A. Sanchez-Aguilera, Y.J. Lee, C. Lo Celso, F. Ferraro, K. Brumme, S. Mondal, C. Kim, A. Dorrance, H.R. Luo, D.T. Scadden, and D.A. Williams Guanine nucleotide exchange factor Vav1 regulates perivascular homing and bone marrow retention of hematopoietic stem and progenitor cells Proc. Natl. Acad. Sci. USA 108 2011 9607 9612
31. D.T. Scadden Nice neighborhood: emerging concepts of the stem cell niche Cell 157 2014 41 50
32. J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, and et al. Fiji: an open-source platform for biological-image analysis Nat. Methods 9 2012 676 682
33. M.K. Scott, O. Akinduro, and C. Lo Celso In vivo 4-dimensional tracking of hematopoietic stem and progenitor cells in adult mouse calvarial bone marrow J. Vis. Exp. 91 2014 e51683
34. Ye, Q.-Z. (1988). The signed Euclidean distance transform and its applications. Proceedings of the 9th International Conference on Pattern Recognition, 495-499.
35. Yeo, S.Y., Xie, X., Sazonov, I., and Nithiarasu, P. (2011). Level set segmentation with robust image gradient energy and statistical shape prior. Proceedings of the 2011 18th IEEE International Conference on Image Processing (ICIP), 3397-3400.