L.P. Coelho, A. Shariff and R. F. Murphy (2009). Nuclear segmentation in microsope cell images: A hand-segmented dataset and comparison of algorithms. Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging (ISBI 2009), in press.

T. Zhao and R.F. Murphy (2007). Automated learning of generative models for subcellular location: Building blocks for systems biology. Cytometry 71A:978-990.

S.-C. Chen, T. Zhao, G. J. Gordon, and R. F. Murphy (2007). Automated Image Analysis of Protein Localization in Budding Yeast. Bioinformatics 23:i66-i71.

The 2D 3T3 "Set1" collection was created by generating randomly CD-tagged cell clones in collaboration with Dr. Peter Berget and Jonathan Jarvik and then imaging them by automated microscopy. The collection is described in:

E. Garcia Osuna, J. Hua, N.W. Bateman, T. Zhao, P.B. Berget and R.F. Murphy (2007). Large-Scale Automated Analysis of Protein Subcellular Location Patterns in Randomly-Tagged 3T3 Cells. Annals Biomed. Eng. 35:1081-1087.

The 3D 3T3 collection was collected in collaboration with Dr. Jonathan Jarvik and Peter Berget and consists of fluorescence microscope images of cell lines expressing GFP-tagged proteins. The cell lines were obtained by CD-tagging to produce internal GFP-fusions in random proteins. The images were collected using spinning disk confocal microscopy and only images of GFP fluorescence were collected. The collection is described in:

X. Chen, M. Velliste, S. Weinstein, J.W. Jarvik and R.F. Murphy (2003). Location proteomics - Building subcellular location trees from high resolution 3D fluorescence microscope images of randomly-tagged proteins. Proc. SPIE 4962: 298-306.

The 3D HeLa-UCE collection was created by Dr. Jack Rohrer's group and consists of fluorescence microscope images of cells expressing GFP-tagged constructs of the mannose-6-phosphate uncovering enzyme (UCE). The images were collected using laser-scanning confocal microscopy following the same protocol as the 3D HeLa collection. The collection is described in:

P. Nair, B.E. Schaub, K. Huang, X. Chen, R.F. Murphy, J.M. Griffith, H.J. Geuze, and J. Rohrer (2005). Characterization of the TGN Exit Signal of the human Mannose 6-Phosphate Uncovering Enzyme. J. Cell Sci. 118:2949-2956.

The 3D HeLa collection consists of fluorescence microscope for the same probes as in the 2D HeLa collection (except that Propidium iodide was used in place of DAPI). The images were collected using laser-scanning confocal microscopy. Parallel images of total DNA and total protein are included. The collection is described in:

M. Velliste and R.F. Murphy (2002). Automated Determination of Protein Subcellular Locations from 3D Fluorescence Microscope Images. Proceedings of the 2002 IEEE International Symposium on Biomedical Imaging (ISBI 2002), pp. 867-870.

T. Zhao, S. Soto, and R.F. Murphy (2006). Improved Comparison of Protein Subcellular Location Patterns. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging (ISBI 2006), pp. 562-565.

Fluorescence microscope images of HeLa cells using ten different labels (DAPI, anti-ER, anti-giantin, anti-gpp130, anti-lamp2, anti-mitochondria, anti-nucleolin, phalloidin, anti-transferrin receptor, anti-tubulin).

These images have been referenced in the following publications:

R. F. Murphy, M. V. Boland and M. Velliste (2000). Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images. Proc Int Conf Intell Syst Mol Biol (ISMB 2000) 8: 251-259. [PDF Reprint with high res images (3.8 MB)] [PDF Reprint with compressed images (176 K)]

M. V. Boland and R. F. Murphy (2001). A Neural Network Classifier Capable of Recognizing the Patterns of all Major Subcellular Structures in Fluorescence Microscope Images of HeLa Cells. Bioinformatics 17:1213-1223. [PDF Reprint] [Screen PDF]

E.J.S. Roques and R.F. Murphy (2002). Objective evaluation of differences in protein subcellular distribution. Traffic 3: 61-65. [PDF Reprint]

Fluorescence microscope images of CHO cells using five different labels (anti-giantin, Hoechst 33258 (DNA), anti-lamp2, anti-nop4, anti-tubulin).

These images were used in our image classification and typical image selection projects, and have been referenced in the following publications:

M. V. Boland, M. K. Markey and R. F. Murphy (1998) Automated Recognition of Patterns Characteristic of Subcellular Structures in Fluorescence Microscopy Images. Cytometry 33: 366-375. [PDF reprint]

M. K. Markey, M. V. Boland and R. F. Murphy (1999). Towards Objective Selection of Representative Microscope Images. Biophys. J. 76:2230-2237. [PDF Reprint]

Last Updated: 22 Jun 2009

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