Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing

Nature Protocols

Volumn 6, Issue 12, 2011, Pages 1942-1952

  Winter, Mark ^a   Wait, Eric ^a   Roysam, Badrinath ^b   Goderie, Susan K ^c   Ali, Rania Ahmed Naguib ^c   Kokovay, Erzsebet ^c   Temple, Sally ^c   Cohen, Andrew R ^a  

^a University of Wisconsin   (United States)

^b UNIVERSITY OF HOUSTON   (United States)

^c Neural Stem Cell Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

ARTICLE; AUTOANALYSIS; CELL DIFFERENTIATION; CELL LINEAGE; CELL MIGRATION; CELL PROLIFERATION; CELL SHAPE; CELL SIZE; CELL TRACKING; CELLULAR DISTRIBUTION; COMPUTER PROGRAM; EXPERIMENTAL DESIGN; FLUORESCENCE IMAGING; IMAGE ANALYSIS; IMAGE DISPLAY; NEURAL STEM CELL; NONHUMAN; POPULATION DYNAMICS; PRIORITY JOURNAL; PROCESS DEVELOPMENT; QUANTITATIVE ANALYSIS; TIME LAPSE IMAGING; VALIDATION PROCESS; VERTEBRATE;

ALGORITHMS; ANIMALS; CELL CULTURE TECHNIQUES; CELL LINEAGE; CELL TRACKING; CELLS, CULTURED; EMBRYONIC STEM CELLS; MICE; MICROSCOPY, PHASE-CONTRAST; NEURAL STEM CELLS; SOFTWARE; TIME-LAPSE IMAGING;

VERTEBRATA;

EID: 84859016779     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2011.422     Document Type: Article

References (17)

1. Giebel, B. & Punzel, M. Lineage development of hematopoietic stem and progenitor cells. Biol. Chem. 389, 813-824 (2008).
2. Ogawa, M. Differentiation and proliferation of hematopoietic stem cells. Blood 81, 2844-2853 (1993). (Pubitemid 23162099)
3. Cohen, A.R., Gomes, F., Roysam, B. & Cayouette, M. Computational prediction of neural progenitor cell fates. Nat. Methods 7, 213-218 (2010).
4. Cohen, A.R., Bjornsson, C., Temple, S., Banker, G. & Roysam, B. Automatic summarization of changes in biological image sequences using algorithmic information theory. IEEE Trans. Pattern Anal. Mach. Intell. 31, 1386-1403 (2009).
5. Al-Kofahi, O. et al. Automated cell lineage tracing: a high-throughput method to analyze cell proliferative behavior developed using mouse neural stem cells. Cell Cycle 5, 327-335 (2006). (Pubitemid 43213505)
6. Gonzales, R., Woods, R. & Eddins, S. Digital Image Processing Using MATLAB (Gatesmark Publishing, 2009).
7. Papadimitriou, C.H. & Steiglitz, K. Combinatorial Optimization: Algorithms and Complexity (Dover Publications, 1998).
8. Koller, D. & Friedman, N. Probabilistic Graphical Models: Principles and Techniques (MIT Press, 2009).
9. Ravin, R. et al. Potency and fate specification in CNS stem cell populations in vitro. Cell Stem Cell 3, 670-680 (2008).
10. Murray, J.I., Bao, Z., Boyle, T.J. & Waterston, R.H. The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree. Nat. Protoc. 1, 1468-1476 (2006).
11. Shen, Q. et al. The timing of cortical neurogenesis is encoded within lineages of individual progenitor cells. Nat. Neurosci. 9, 743-751 (2006).
12. Gomes, F.L.A.F. et al. Reconstruction of rat retinal progenitor cell lineages in vitro reveals a surprising degree of stochasticity in cell fate decisions. Development 138, 227-235 (2011).
13. Eilken, H.M., Nishikawa, S.-I. & Schroeder, T. Continuous single-cell imaging of blood generation from haemogenic endothelium. Nature 457, 896-900 (2009).
14. Li, K. et al. Cell population tracking and lineage construction with spatiotemporal context. Med. Image Anal. 12, 546-566 (2008).
15. Chen, Y., Ladi, E., Herzmark, P., Robey, E. & Roysam, B. Automated 5-D analysis of cell migration and interaction in the thymic cortex from time-lapse sequences of 3-D multi-channel multi-photon images. J. Immunol. Methods 340, 65-80 (2009).
16. Qian, X. et al. Timing of CNS cell generation: a programmed sequence of neuron and glial cell production from isolated murine cortical stem cells. Neuron 28, 69-80 (2000).
17. Shen, Q. et al. Endothelial cells stimulate self-renewal and expand neurogenesis of neural stem cells. Science 304, 1338-1340 (2004). (Pubitemid 38697433)