Histopathology
(New page: This page describes the algorithm and the use of the program for nucleus and whole cell segmentation and nucleus/cellular scale biomarker quantification. The algorithms have been implement...) |
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This page describes the algorithm and the use of the program for nucleus and whole cell segmentation and nucleus/cellular scale biomarker quantification. The algorithms have been implemented in c++ and IDL and instructions to use the program are also included. | This page describes the algorithm and the use of the program for nucleus and whole cell segmentation and nucleus/cellular scale biomarker quantification. The algorithms have been implemented in c++ and IDL and instructions to use the program are also included. | ||
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| + | ==Background and motivation== | ||
| + | Detecting molecules of interest and quantifying them plays an increasingly important role in modern medical diagnosis and treatment planning[1]. Currently, most systems are visually based qualitative descriptors which suffer from the consequent limitations. There are other algorithms that quantify biomarkers on a pixel-by-pixel basis or a regional basis[2-5]. Segmenting the cells and nuclei allows us to classify the different cell types based on antigens that mark specific cell. This enables us to quantify the biomarker of interest in the relevant cell type. This is a more biologically relevant measure and can be more useful in medical diagnosis. | ||
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| + | ==References== | ||
| + | 1. Hammerschmied CG, Walter B, Hartmann A. [Renal cell carcinoma 2008 : Histopathology, molecular genetics and new therapeutic options.]. Pathologe 2008;29(5):354-63.<br /> | ||
| + | 2. Camp RL, Chung GG, Rimm DL. Automated subcellular localization and quantification of protein expression in tissue microarrays. Nat Med 2002;8(11):1323-7.<br /> | ||
| + | 3. Mulrane L, Rexhepaj E, Penney S, Callanan JJ, Gallagher WM. Automated image analysis in histopathology: a valuable tool in medical diagnostics. Expert Rev Mol Diagn 2008;8(6):707-25.<br /> | ||
| + | 4. Taylor CR, Levenson RM. Quantification of immunohistochemistry--issues concerning methods, utility and semiquantitative assessment II. Histopathology 2006;49(4):411-24.<br /> | ||
| + | 5. Tamai S. [Expert systems and automatic diagnostic systems in histopathology--a review]. Rinsho Byori 1999;47(2):126-31.<br /> | ||
Revision as of 19:23, 8 May 2009
This page describes the algorithm and the use of the program for nucleus and whole cell segmentation and nucleus/cellular scale biomarker quantification. The algorithms have been implemented in c++ and IDL and instructions to use the program are also included.
Background and motivation
Detecting molecules of interest and quantifying them plays an increasingly important role in modern medical diagnosis and treatment planning[1]. Currently, most systems are visually based qualitative descriptors which suffer from the consequent limitations. There are other algorithms that quantify biomarkers on a pixel-by-pixel basis or a regional basis[2-5]. Segmenting the cells and nuclei allows us to classify the different cell types based on antigens that mark specific cell. This enables us to quantify the biomarker of interest in the relevant cell type. This is a more biologically relevant measure and can be more useful in medical diagnosis.
References
1. Hammerschmied CG, Walter B, Hartmann A. [Renal cell carcinoma 2008 : Histopathology, molecular genetics and new therapeutic options.]. Pathologe 2008;29(5):354-63.
2. Camp RL, Chung GG, Rimm DL. Automated subcellular localization and quantification of protein expression in tissue microarrays. Nat Med 2002;8(11):1323-7.
3. Mulrane L, Rexhepaj E, Penney S, Callanan JJ, Gallagher WM. Automated image analysis in histopathology: a valuable tool in medical diagnostics. Expert Rev Mol Diagn 2008;8(6):707-25.
4. Taylor CR, Levenson RM. Quantification of immunohistochemistry--issues concerning methods, utility and semiquantitative assessment II. Histopathology 2006;49(4):411-24.
5. Tamai S. [Expert systems and automatic diagnostic systems in histopathology--a review]. Rinsho Byori 1999;47(2):126-31.
