CognitionMaster: An object-based image analysis framework

Diagnostic Pathology

Volumn 8, Issue 1, 2013, Pages

  Wienert, Stephan ^a,b   Heim, Daniel ^b   Kotani, Manato ^c,d   Lindequist, Björn ^e   Stenzinger, Albrecht ^f   Ishii, Masaru ^c,d   Hufnagl, Peter ^a,e   Beil, Michael ^g   Dietel, Manfred ^a   Denkert, Carsten ^a   Klauschen, Frederick ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b VMSCOPE GMBH   (Germany)

^c OSAKA UNIVERSITY   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^e Institut für Soziale Gesundheit Katholische Hochschule für Sozialwesen Berlin   (Germany)

^f UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^g UNIVERSITY OF ULM   (Germany)

Author keywords

Image analysis; Object based image analysis; Open source; Software

Indexed keywords

KI 67 ANTIGEN;

ALGORITHM; ARTICLE; BONE; BREAST TUMOR; CELL COMMUNICATION; CELL PROLIFERATION; CHEMISTRY; COMPUTER ASSISTED DIAGNOSIS; COMPUTER PROGRAM; FEMALE; HUMAN; IMMUNOHISTOCHEMISTRY; LABORATORY AUTOMATION; METHODOLOGY; MULTIPHOTON MICROSCOPY; OSTEOCLAST; PATHOLOGY; PREDICTIVE VALUE;

ALGORITHMS; AUTOMATION, LABORATORY; BONE AND BONES; BREAST NEOPLASMS; CELL COMMUNICATION; CELL PROLIFERATION; FEMALE; HUMANS; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IMMUNOHISTOCHEMISTRY; KI-67 ANTIGEN; MICROSCOPY, FLUORESCENCE, MULTIPHOTON; OSTEOCLASTS; PREDICTIVE VALUE OF TESTS; SOFTWARE;

MLCS; MLOWN;

EID: 84876312718     PISSN: None     EISSN: 17461596     Source Type: Journal    
DOI: 10.1186/1746-1596-8-34     Document Type: Article

References (29)

1. Graham J, Taylor CJ. Automated chromosome analysis using the magiscan image analyser. Anal Quant Cytol 1980, 2:237-242.
2. Salazar I, Cifuentes JM, Sánchez Quinteiro P, Garcia Caballero T. Structural, morphometric, and immunohistological study of the accessory olfactory bulb in the dog. Anat Rec 1994, 240:277-285. 10.1002/ar.1092400216, 7992895.
3. Portet S, Vassy J, Beil M, Millot G, Hebbache A, Rigaut JP, Schoëvaërt D. Quantitative analysis of cytokeratin network topology in the MCF7 cell line. Cytometry 1999, 35:203-213. 10.1002/(SICI)1097-0320(19990301)35:3<203::AID-CYTO3>3.0.CO;2-K, 10082301.
4. Brinkmann M, Lütkemeyer D, Gudermann F, Lehmann J. New technologies for automated cell counting based on optical image analysis; The Cellscreen'. Cytotechnology 2002, 38:119-127. 10.1023/A:1021118501866, 3449924, 19003093.
5. Gutiérrez R, Gómez F, Roa-Peña L, Romero E. A supervised visual model for finding regions of interest in basal cell carcinoma images. Diagn Pathol 2011, 6:26. 10.1186/1746-1596-6-26, 3079595, 21447178.
6. Grimm M, Krimmel M, Alexander D, Munz A, Kluba S, Keutel C, Hoffmann J, Polligkeit J, Reinert S, Hoefert S. Prognostic value of histamine H1 receptor expression in oral squamous cell carcinoma. Clin Oral Investig 2012, Epub ahead of print.
7. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Meth 2012, 9:671-675.
8. Jones TR, Kang I, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE. Cell profiler analyst: data exploration and analysis software for complex image-based screens. BMC Bioinforma 2008, 9:482.
9. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez J, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Meth 2012, 9:676-682.
10. de Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Le Montagner Y, Lagache T, Dufour A, Olivo-Marin J. Icy: an open bioimage informatics platform for extended reproducible research. Nat Meth 2012, 9:690-696.
11. OpenCV http://opencv.org.
12. Yoo TS, Ackerman MJ, Lorensen WE, Schroeder W, Chalana V, Aylward S, Metaxas D, Whitaker R. Engineering and algorithm design for an image processing Api: a technical report on ITK-the insight toolkit. Stud Health Technol Inform 2002, 85:586-592.
13. Kayser K, Görtler J, Borkenfeld S, Kayser G. How to measure diagnosis-associated information in virtual slides. Diagn Pathol 2011, 6(Suppl 1):S9. 10.1186/1746-1596-6-S1-S9, 3073227, 21489204.
14. Blaschke T, Strobl J. What's wrong with pixels? Some recent developments interfacing remote sensing and GIS. GIS-Zeitschrift für Geoinformationssysteme 2001, 06:12-17.
15. Hay GJ, Castilla G, Wulder MA, Ruiz JR. An automated object-based approach for the multiscale image segmentation of forest scenes. Int J Appl Earth Obs Geoinf 2005, 7:339-359.
16. Baatz M, Arini N, Schäpe A, Binnig G, Linssen B. Object-oriented image analysis for high content screening: detailed quantification of cells and sub cellular structures with the cellenger software. Cytometry A 2006, 69:652-658.
17. Bouzubar N, Walker KJ, Griffiths K, Ellis IO, Elston CW, Robertson JF, Blamey RW, Nicholson RI. Ki67 immunostaining in primary breast cancer: pathological and clinical associations. Br J Cancer 1989, 59:943-947. 10.1038/bjc.1989.200, 2246720, 2472168.
18. Gerdes J. Ki-67 and other proliferation markers useful for immunohistological diagnostic and prognostic evaluations in human malignancies. Semin Cancer Biol 1990, 1:199-206.
19. Ishii M, Egen JG, Klauschen F, Meier-Schellersheim M, Saeki Y, Vacher J, Proia RL, Germain RN. Sphingosine-1-phosphate mobilizes osteoclast precursors and regulates bone homeostasis. Nature 2010, 465:966.
20. Klauschen F, Ishii M, Qi H, Bajénoff M, Egen JG, Germain RN, Meier-Schellersheim M. Quantifying cellular interaction dynamics in 3D fluorescence microscopy data. Nat Protoc 2009, 4:1305-1311. 10.1038/nprot.2009.129, 3443679, 19696749.
21. #Develop http://www.icsharpcode.net/.
22. Tango http://tango.freedesktop.org/.
23. Doxygen http://doxygen.org.
24. Velić M, May D, Moresi L. A fast robust algorithm for computing discrete voronoi diagrams. J Math Model Algor 2009, 8:343-355.
25. Zerbe N, Hufnagl P, Schlüns K. Distributed computing in image analysis using open source frameworks and application to image sharpness assessment of histological whole slide images. Diagn Pathol 2011, 6:S16. 10.1186/1746-1596-6-S1-S16, 3073209, 21489186.
26. Romo D, Romero E, González F. Learning regions of interest from low level maps in virtual microscopy. Diagn Pathol 2011, 6:S22. 10.1186/1746-1596-6-S1-S22, 3073216, 21489193.
27. Kayser K, Görtler J, Borkenfeld S, Kayser G. Interactive and automated application of virtual microscopy. Diagn Pathol 2011, 6:S10. 10.1186/1746-1596-6-S1-S10, 3073203, 21489181.
28. Wienert S, Heim D, Saeger K, Stenzinger A, Beil M, Hufnagl P, Dietel M, Denkert C, Klauschen F. Detection and segmentation of cell nuclei in virtual microscopy images: a minimum-model approach. Sci Rep 2012, 2:503. 3394088, 22787560.
29. Ruifrok AC, Johnston DA. Quantification of histochemical staining by color deconvolution. Anal Quant Cytol Histol 2001, 23:291-299.