Software tools, data structures, and interfaces for microscope imaging

Cold Spring Harbor Protocols

Volumn 7, Issue 1, 2012, Pages 50-61

  Stuurman, Nico ^a   Swedlow, Jason R ^a  

^a Simons Center for Quantitative Biology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CAMERA; COLOR; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTRAST ENHANCEMENT; DATA ANALYSIS SOFTWARE; DIGITAL IMAGING; IMAGE ANALYSIS; IMAGE DISPLAY; IMAGE PROCESSING; INFORMATION PROCESSING; MACHINE LEARNING; MICROSCOPY; PHOTON; PHOTOSENSITIVITY; QUANTITATIVE ANALYSIS; REVIEW; THREE DIMENSIONAL IMAGING; METHODOLOGY;

IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY; SOFTWARE;

EID: 84255189972     PISSN: 19403402     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.top067504     Document Type: Review

References (23)

1. Axelrod D, Koppel DE, Schlessinger J, Elson E, Webb WW. 1976. Mobility measurement by analysis of fluorescence photobleaching recovery kinetics. Biophys J 16: 1055-1069.
2. Bettencourt-Dias M, Giet R, Sinka R, Mazumdar A, Loc WG, Balloux F, Zafiropoulos PJ, Yamaguchi S, Winter S, Carthew RW, et al. 2004. Genome-wide survey of protein kinases required for cell cycle progression. Nature 432: 980-987.
3. Boland MV, Murphy RF. 2001. A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinformatics 17: 1213-1223.
4. Braga J, Desterro JM, Carmo-Fonseca M. 2004. Intracellular macromolecular mobility measured by fluorescence recovery after photobleaching with confocal laser scanning microscopes. Mol Biol Cell 15: 4749-4760.
5. Danuser G, Waterman-Storer CM. 2006. Quantitative fluorescent speckle microscopy of cytoskeleton dynamics. Annu Rev Biophys Biomol Struct 35: 361-387.
6. Goldberg IG, Allan C, Burel J-M, Creager D, Falconi A, Hochheiser HS, Johnston J, Mellen J, Sorger PK, Swedlow JR. 2005. The Open Microscopy Environment (OME) Data Model and XML file: Open tools for informatics and quantitative analysis in biological imaging. Genome Biol 6: R47.
7. Goshima G, Wollman R, Goodwin SS, Zhang N, Scholey JM, Vale RD, Stuurman N. 2007. Genes required for mitotic spindle assembly in Drosophila S2 cells. Science 316: 417-421.
8. Jaqaman K, Loerke D, Mettlen M, Kuwata H, Grinstein S, Schmid SL, Danuser G. 2008. Robust single-particle tracking in live-cell time-lapse sequences. Nat Methods 5: 695-702.
9. Lippincott-Schwartz J, Snapp E, Kenworthy A. 2001. Studying protein dynamics in living cells. Nat Rev Mol Cell Biol 2: 444-456.
10. Neumann B, Held M, Liebel U, Erfle H, Rogers P, Pepperkok R, Ellenberg J. 2006. High-throughput RNAi screening by time-lapse imaging of live human cells. Nat Methods 3: 385-390.
11. Orlov N, Shamir L, Macura T, Johnston J, Eckley DM, Goldberg IG. 2008. WND-CHARM: Multi-purpose image classification using compound image transforms. Pattern Recogn Lett 29: 1684-1693.
12. Platani M, Goldberg I, Lamond AI, Swedlow JR. 2002.Cajal body dynamics and association with chromatin are ATP-dependent. Nat Cell Biol 4: 502-508.
13. Rabut G, Ellenberg J. 2004. Automatic real-time three-dimensional cell tracking by fluorescence microscopy. J Microsc 216: 131-137.
14. Rabut G, Doye V, Ellenberg J. 2004. Mapping the dynamic organization of the nuclear pore complex inside single living cells. Nat Cell Biol 6: 1114-1121.
15. Ramadan N, Flockhart I, Booker M, Perrimon N, Mathey-Prevot B. 2007. Design and implementation of high-throughput RNAi screens in cultured Drosophila cells. Nat Protoc 2: 2245-2264.
16. Rossner M, Yamada KM. 2004. What's in a picture? The temptation of image manipulation. J Cell Biol 166: 11-15.
17. Russ JC. 2007. The image processing handbook CRC, Boca Raton, FL.
18. Sprague BL, McNally JG. 2005. FRAP analysis of binding: Proper and fitting. Trends Cell Biol 15: 84-91.
19. Swedlow JR, Sedat JW, Agard DA. 1997. Deconvolution in optical microscopy. In Deconvolution of images and spectra (ed. Jansson PA), 284-309. Academic Press, New York.
20. Swedlow JR, Goldberg IG, Eliceiri KW. 2009. Bioimage informatics for experimental biology. Annu Rev Biophys 38: 327-346.
21. Wallace W, Schaefer LH, Swedlow JR. 2001. A workingperson's guide to deconvolution in light microscopy. BioTechniques 31: 1076-1097.
22. Wouters FS, Verveer PJ, Bastiaens PI. 2001. Imaging biochemistry inside cells. Trends Cell Biol 11: 203-211.
23. Zhou J, Peng H. 2007. Automatic recognition and annotation of gene expression patterns of fly embryos. Bioinformatics 23: 589-596.