Automatic detection of labeling patterns in microscopic sections

advertisement
6. References
Abramoff, MD, Magalhaes, PJ, Ram, SJ 2004, ‘Image Processing with ImageJ’,
Biophotonics International, vol. 11, no. 7, pp. 36-42.
Biomedical Informatics Research Network (BIRN) 2007, Brain Morphometry BIRN –
Workflows, University of California, San Diego, USA. Available from:
http://www.nbirn.net/research/morphometry/workflows.shtm [28 January 2009]
Bloomberg, DS 2008, Color quantization using modified median cut, Leptonica report.
Available from: http://www.leptonica.com/papers/mediancut.pdf [2 December
2008]
Brey, EM, Lalani, Z, Johnston, C, Wong, M, McIntire, LV, Duke, PJ, Patrick Jr., CW
2003, ‘Automated Selection of DAB-labeled Tissue for Immunohistochemical
Quantification’, The Journal of Histochemistry & Cytochemistry, vol. 51, no. 5,
pp. 575-584.
Burger, W & Burge, MJ 2008, Digital Image Processing – An algorithmic introduction
using Java, Springer, New York, USA. ISBN: 978-1-84628-379-6
Carnegie Mellon University Software Engineering Institute 2009, Software Product
Line Acquisition: A Companion to a Framework for Software Product Line
Practice Version 3.0, Pittsburgh, Pennsylvania, USA. Available from:
http://www.sei.cmu.edu/productlines/companion/softwareSI.htm [9 January 2009]
Carpenter, AE, Jones, TR, Lamprecht, MR, Clarke, C, Kang, IH, Friman, O, Guertin,
DA, Chang, JH, Lindquist, RA, Moffat, J , Golland, P, Sabatini, DM 2006,
‘CellProfiler: image analysis software for identifying and quantifying cell
phenotypes’, Genome Biology, vol. 7, no. 10, R100
Fuller, LU & Fuller, R 2007, PhotoShop CS3 Bible, Wiley Publishing Inc., Indianapolis,
USA. ISBN: 978-0-470-11541-1
1
Kennel, G 2006, Color and Mastering for Digital Cinema: A Digital Cinema Industry
Handbook. Focal Press, Burlington, MA, USA. ISBN: 9780240808741
Heimer, L & Robards, MJ 1981, Neuroanatomical tract tracing methods, Plenum Press,
New York, USA. ISBN 0-306-40593-8
Heimer, L & Zaborszky, L 1989, Neuroanatomical tract-tracing methods 2. – Recent
progress, Plenum Press, New York, USA. ISBN 0-306-43165-3
Hjornevik, T, Leergaard, TB, Darine, D, Moldestad, O, Dale, AM, Willoch, F, Bjaalie,
JG 2007, ‘Three-dimensional atlas system for mouse and rat brain imaging data’,
Frontiers in Neuroinformatics, vol. 1, art. 4, pp. 1-11.
ISO 10526:1999/CIE S005/E-1998, CIE Standard Illuminants for Colorimetry.
Available from: http://www.cie.co.at/publ/abst/s005.html [9 December 2008]
Jeans, A, Esiri, M 2008, ‘Brain histology’, Practical neurology, vol. 8, no. 5, pp. 303310.
Kjode, JO, Darine, D, Leergaard, TB, Bjaalie, JG 2008, Database application for
management of microscopic images. Poster presented at Neuroinformatics 2008
Conference, Stockholm, Sweden
Land, PW & Simons, DJ 1985, ‘Cytochrome oxidase staining in the rat SmI barrel
cortex’, J Comp Neurol., vol. 238, no. 2, pp. 225-35.
Landini, G 2008, Colour Deconvolution. Available from:
http://www.dentistry.bham.ac.uk/landinig/software/cdeconv/cdeconv.html
[12 December 2008]
Lillehaug, S, Øyan, D, Leergaard, TB & Bjaalie, JG 2002, ‘Comparison of semiautomatic and automatic data acquisition methods for studying three-dimensional
distributions of large neuronal populations and axonal plexuses’, Network
Comput. Neural Syst., vol. 13, pp. 343-356.
Meijering, E, Jacob, M, Sarria, JCF, Steiner, P, Hirling, H & Unser, M 2004, ‘Design
and Validation of a Tool for Neurite Tracing and Analysis in Fluorescence
Microscopy Images’, Cytometry, vol. 58A, no. 2, pp. 167-176.
2
National Institutes of Health (NIH) 2009a, ImageJ Software Documentation. Available
from: http://rsb.info.nih.gov/ij/docs/index.html [12 January 2009]
National Institutes of Health (NIH) 2009b, NIH Listserv ImageJ Interest Group Mailing
List Archives. Available from: https://list.nih.gov/archives/imagej.html [21
January 2009]
Neural Systems and Graphics Computing Laboratory (NeSys) 2009a, Rodent Brain
Navigator, Centre for Molecular Biology and Neuroscience, University of Oslo,
Norway. Available from: http://ocelot.uio.no/navigate [23 January 2009]
Neural Systems and Graphics Computing Laboratory (NeSys) 2009b, The Rodent Brain
WorkBench, Centre for Molecular Biology and Neuroscience, University of Oslo,
Norway. Available from: http://www.rbwb.org [23 January 2009]
Ruifrok, AC 1997, ‘Quantification of immunohistochemical staining by color
translation and automated thresholding’, Analytical and Quantitative Cytology
and Histology, vol. 19, no. 2, pp. 107-113.
Ruifrok, AC & Johnston, DA 2001, ‘Quantification of histological staining by color
deconvolution’, Analytical and Quantitative Cytology and Histology, vol. 23, no.
4, pp. 291-299.
Sharma, A 2003, Understanding Color Management, Delmar Cengage Learning, USA.
ISBN: 9781401814476
Smith, AR 1978, ‘Color gamut transform pairs’, ACM SIGGRAPH Computer Graphics,
vol. 12, no. 3, pp. 12-19.
Sun Microsystems 2002, Designing Enterprise Applications with the J2EE Platform,
Second Edition. Available from:
http://java.sun.com/blueprints/guidelines/designing_enterprise_applications_2e/
[29 January 2009]
Tiwari, A & Sekhar, AKT 2007, ‘Workflow based framework for life science
informatics’, Computational Biology and Chemistry, vol. 31, pp. 305-319.
3
van Dongen, YC, Leergaard, TB, Kjode, JO, Bjaalie, JG 2007, Towards a digital atlas
system for tracing axonal connectivity in the entire rat brain. Abstract for Nordic
Neuroinformatics Workshop 2007, Life Science Center, Espoo, Finland
World Wide Web Consortium (W3C) 2008, CSS Color Module Level 3, W3C Working
Draft 21 July 2008. Available from: http://www.w3.org/TR/css3-color/#hsl-color
[30 January 2009]
Wouterlood, FG, Vinkenoog, M, Oever, MVD 2002, 'Tracing tools to resolve neural
circuits', Network: Computation in Neural Systems, vol. 13, no. 3, pp. 327-342.
X-Rite
Inc.
2009,
How
Munsell
Color
Works.
Available
from:
http://www.xrite.com/product_overview.aspx?ID=1062 [30 January 2009]
Zaborszky, L, Wouterlood, FG & Lanciego, JL 2006, Neuroanatomical tract tracing 3 –
Molecules, Neurons, and Systems, Springer, New York, USA. ISBN-10: 0-38728941-0, ISBN-13: 978-0387-28941-0
4
Download