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Quality Classification of Microscopic Imagery with Weakly Supervised Learning

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Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 7588))

Abstract

In this post-genomic era, microscopic imaging is playing a crucial role in biomedical research and important information is to be discovered by quantitatively mining the resulting massive imagery databases. To this end, an important prerequisite is robust, high quality imagery databases. This is because defect images will jeopardize downstream tasks such as feature extraction and statistical analysis, yielding misleading results or even false conclusions. This paper presents a weakly supervised learning framework to tackle this problem. Our framework resembles a cascade of classifiers with feature and similarity measure designed for both global and local defects. We evaluated the framework on a database of images and obtained a 96.9% F-score for the important normal class. Click-and-play open source software is provided.

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References

  1. Bray, M.A., Fraser, A.N., Hasaka, T.P., et al.: Workflow and Metrics for Image Quality Control in Large-Scale High-Content Screens. J. Biomol. Screening (2011)

    Google Scholar 

  2. Breunig, M.M., Kriegel, H.P., Ng, R.T.J., et al.: LOF: identifying density-based local outliers. ACM Sigmod Record 29(2), 93–104 (2000)

    Article  Google Scholar 

  3. Chandola, V., Banerjee, A., Kumar, V.: Outlier detection: A survey. ACM Comput. Surv. (2007)

    Google Scholar 

  4. Echeverri, C.J., Perrimon, N.: High-throughput RNAi screening in cultured cells: a user’s guide. Nat. Rev. Genet. 7(5), 373–384 (2006)

    Article  Google Scholar 

  5. Goode, A., Sukthankar, R., Mummert, L., et al.: Distributed online anomaly detection in high-content screening. In: ISBI (2008)

    Google Scholar 

  6. Hastie, T., Tibshirani, R., Friedman, J.: The Elements of Statistical Learning. Springer Series in Statistics. Springer New York Inc., New York (2001)

    MATH  Google Scholar 

  7. Hero, A.O.: Geometric entropy minimization (GEM) for anomaly detection and localization. In: NIPS (2006)

    Google Scholar 

  8. Kaynig, V., Fischer, B., Buhmann, J.M.: Probabilistic image registration and anomaly detection by nonlinear warping. In: CVPR (2008)

    Google Scholar 

  9. Knox, E.M., Ng, R.T.: Algorithms for mining distance-based outliers in large datasets. In: VLDB (1998)

    Google Scholar 

  10. Lazarevic, A., Kumar, V.: Feature bagging for outlier detection. In: KDD (2005)

    Google Scholar 

  11. Liu, F.T., Ting, K.M., Zhou, Z.H.: Isolation Forest. In: ICDM (2008)

    Google Scholar 

  12. Liu, R., Li, Z., Jia, J.: Image partial blur detection and classification. In: CVPR (2008)

    Google Scholar 

  13. MAQC Consortium The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol. 24(9), 1151–1161 (2006)

    Google Scholar 

  14. Pele, O., Werman, M.: Fast and robust earth mover’s distances. In: ICCV (2009)

    Google Scholar 

  15. Pepperkok, R., Ellenberg, J.: High-throughput fluorescence microscopy for systems biology. Nat. Rev. Mol. Cell Bio. 7(9), 690–696 (2006)

    Article  Google Scholar 

  16. Reymann, J., Beil, N., Beneke, J., et al.: Next-generation 9216-microwell cell arrays for high-content screening microscopy. Bio.Techniques 47(4), 877 (2009)

    Google Scholar 

  17. Rubner, Y., Tomasi, C., Guibas, L.J.: A Metric for Distributions with Applications to Image Databases. In: ICCV (1998)

    Google Scholar 

  18. Schoelkopf, B., Platt, J.C., Shawe-Taylor, J., et al.: Estimating the support of a high-dimensional distribution. Neural. Comput. 13(7), 1443–1471 (2001)

    Article  MATH  Google Scholar 

  19. Schoelkopf, B., Smola, A.J.: Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond. The MIT Press, Cambridge (2002)

    Google Scholar 

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© 2012 Springer-Verlag Berlin Heidelberg

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Lou, X., Fiaschi, L., Koethe, U., Hamprecht, F.A. (2012). Quality Classification of Microscopic Imagery with Weakly Supervised Learning. In: Wang, F., Shen, D., Yan, P., Suzuki, K. (eds) Machine Learning in Medical Imaging. MLMI 2012. Lecture Notes in Computer Science, vol 7588. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35428-1_22

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  • DOI: https://doi.org/10.1007/978-3-642-35428-1_22

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-35427-4

  • Online ISBN: 978-3-642-35428-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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