Cytometry Development Workshop
Murphy Lab - Data
Images of T cells expressing different EGFP-tagged proteins collected by the Wülfing group as part of the following study.
K. T. Roybal, T. E. Buck, X. Ruan, B. H. Cho, D. J. Clark, R. Ambler, H. M. Tunbridge, J. Zhang, P. Verkade, C. Wülfing, and R. F. Murphy (2016) Computational spatiotemporal analysis identifies WAVE2 and Cofilin as joint regulators of costimulation-mediated T cell actin dynamics. Science Signaling 9:rs3. DOI: 10.1126/scisignal.aad4149
Images of clones expressing different EGFP-tagged proteins in the presence of various drugs, collected by automated microscopy as specified by an active learner.
A. W. Naik, J. D. Kangas, D. P. Sullivan, and R. F. Murphy (2016) Active Machine Learning-driven Experimentation to Determine Compound Effects on Protein Patterns. eLife 5:e10047 (DOI).
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), p. 518-521.
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.
2D 3T3 Randomly CD-Tagged Images
The 2D 3T3 Randomly CD-Tagged collections were 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 Set 1 collection is described in
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.A. Shariff, R.F. Murphy, and G. Rohde (2011) Automated Estimation of Microtubule Model Parameters from 3-D Live Cell Microscopy Images. Proceedings of the 2011 IEEE International Symposium on Biomedical Imaging (ISBI 2011), pp. 1330-1333.
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. Peng and R.F. Murphy (2011) Image-derived, Three-dimensional Generative Models of Cellular Organization. Cytometry Part A 79A:383-391.
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.
Last Updated: 19 Apr 2016
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