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 High-throughput cellular imaging and microfluidic technologies are enabling phenotypic measurements on single-cell and population-wide scales. The extraction of information from such imaging data is necessary for establishing the relationships between the behavior of molecular networks in cells and quantitative phenotypic features under a variety of conditions. We are developing image processing and analysis methods to detect and count objects (including subcellular and multicellular structures), statistically describe their shape (both in two and three dimensions), and track localization of objects over time (such as a protein within a cell or the interactions of two cells). In conjunction with the Informatics Core we are developing software tools for effective management of such large data sets from high-throughput equipment and the ability to rapidly customize analysis pipelines, annotate the results, and analyze the data in an integrated fashion with other systems measurements.
Publications:
J. Selinummi, A. Niemistö, R. Saleem, G. W. Carter, J. Aitchison, O. Yli-Harja, I. Shmulevich, and J. Boyle, "A Case Study on 3-D Reconstruction and Shape Description of Peroxisomes in Yeast, " IEEE International Conference on Signal Processing and Communication (ICSPC07), Dubai, United Arab Emirates (UAE), November 24-27, 2007.
A. Niemistö, T. Korpelainen, R. Saleem, O. Yli-Harja, J. Aitchison, I. Shmulevich, "A K-Means Segmentation Method for Finding 2-D Object Areas Based on 3-D Image Stacks Obtained by Confocal Microscopy," 29th International Conference of the IEEE Engineering in Medicine and Biology Society, Lyon, France, August 23-26, 2007.
A. Niemistö, J. Selinummi, R. Saleem, I. Shmulevich, J. Aitchison, O. Yli-Harja, "Extraction of the number of peroxisomes in yeast cells by automated image analysis," The 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, New York, New York, August 30 - September 3, 2006.
A. Niemistö, V. Dunmire, O. Yli-Harja, W. Zhang, I. Shmulevich, "Robust quantification of in vitro angiogenesis through image analysis," IEEE Transactions on Medical Imaging, Vol. 24, No. 4, pp. 549-553, 2005.
A. Niemistö, I. Shmulevich, O. Yli-Harja, L. Chirieac, S. R. Hamilton, “Automated Quantification of Lymph Node Size and Number in Surgical Specimens of Stage II Colorectal Cancer,” 27th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Shanghai, China, September 1-4, 2005, pp. 6313 - 6316.
A. Niemistö, L. Hu, O. Yli-Harja, W. Zhang, I. Shmulevich, "Quantification of in vitro cell invasion through image analysis," in Proceedings of the 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS'04), San Francisco, California, USA, Sep. 1-5, 2004, pp. 1703-1706.
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