This proposal outlines plans for continued development and maintenance of the OpenCCDB software suite, a set of tools for web-based management, visualization and annotation of large multidimensional light and electron microscopic imaging data sets. Modern analytical and molecularly-based biomedical investigations increasingly draw upon multiscale and multimodal cell-centered imaging to gain insight into spatially constrained interactions of molecular machinery of cells and tissues. The OpenCCDB was developed under the auspices of the Cell Centered Database (CCDB0 project, an on-line repository and platform for sharing microscopic imaging data of cells and tissues. The CCDB project was predicated on developing solutions for federating access to very large 3D imaging data sets, produced by diverse instrumentations and maintained across diverse technological platforms. The CCDB model is built on flexible and expandable data stores that can be fielded globally but accessed through CCDB's central metadata system and linked through data federations like the Neuroscience Information Framework (http://neuinfo.org). During the last funding period, the American Society for Cell Biology launched its own data repository, with support from ARRA funding. The Cell: An Image Library currently contains >37,000 exemplary imaging data sets from light and electron microscopy, all available through an elegant cell-centered user interface. To provide a more unified and sustainable resource for research and education, the ASCB Council and Executive Committee voted in 2011 to partner their effort with the group at UCSD, combining their curatorial and interface design expertise and accomplishments with UCSD's database and software development expertise and accomplishments. In so doing, ASCB transitioned control of the development and future sustainability of their user portal environment, """"""""The Cell:An Image Library"""""""" to the CCDB team at UCSD. Immediately, this new alliance applied CCDB's open source software framework, OpenCCDB, to the task of extending the functionality of The Cell: An Image Library system, adding new capability to upload and explore massive datasets, facilitate data sharing, and completely federate its underlying database with the CCDB. The resultant integrated environment offers the scientific community a more comprehensive solution to propel cell-centric biomedical research and education than that offered previously. In this proposal, we outline aims to develop and deploy additional personalized data management and annotation tools within the context of The Cell: An Image Library, by combining the power and tools of a social networking site with specialized tools for web-based management, sharing, annotation and federation of very large microscopic imaging data sets.
This renewal application outlines plans to harden and further develop the code base of the Open CCDB software platform in support of the new joint cell-centered microscopy resource established through the merging of the Cell Image Library and the Cell Centered Database.
| Ilouz, Ronit; Lev-Ram, Varda; Bushong, Eric A et al. (2017) Isoform-specific subcellular localization and function of protein kinase A identified by mosaic imaging of mouse brain. Elife 6: |
| Mills, Elizabeth A; Davis, Chung-ha O; Bushong, Eric A et al. (2015) Astrocytes phagocytose focal dystrophies from shortening myelin segments in the optic nerve of Xenopus laevis at metamorphosis. Proc Natl Acad Sci U S A 112:10509-14 |
| Davis, Chung-ha O; Kim, Keun-Young; Bushong, Eric A et al. (2014) Transcellular degradation of axonal mitochondria. Proc Natl Acad Sci U S A 111:9633-8 |
| Jones, Cory; Sayedhosseini, Mojtaba; Ellisman, Mark et al. (2013) Neuron Segmentation in Electron Microscopy Images Using Partial Differential Equations. Proc IEEE Int Symp Biomed Imaging 2013:1457-1460 |
| Orloff, David N; Iwasa, Janet H; Martone, Maryann E et al. (2013) The cell: an image library-CCDB: a curated repository of microscopy data. Nucleic Acids Res 41:D1241-50 |
| Lu, Wei; Bushong, Eric A; Shih, Tiffany P et al. (2013) The cell-autonomous role of excitatory synaptic transmission in the regulation of neuronal structure and function. Neuron 78:433-9 |
| Jones, Cory; Liu, Ting; Ellisman, Mark et al. (2013) Semi-Automatic Neuron Segmentation in Electron Microscopy Images Via Sparse Labeling. Proc IEEE Int Symp Biomed Imaging 2013:1304-1307 |
| Seyedhosseini, Mojtaba; Ellisman, Mark H; Tasdizen, Tolga (2013) SEGMENTATION OF MITOCHONDRIA IN ELECTRON MICROSCOPY IMAGES USING ALGEBRAIC CURVES. Proc IEEE Int Symp Biomed Imaging 2013:860-863 |
| Cone, Angela C; Ambrosi, Cinzia; Scemes, Eliana et al. (2013) A comparative antibody analysis of pannexin1 expression in four rat brain regions reveals varying subcellular localizations. Front Pharmacol 4:6 |
| Burette, Alain C; Lesperance, Thomas; Crum, John et al. (2012) Electron tomographic analysis of synaptic ultrastructure. J Comp Neurol 520:2697-711 |
Showing the most recent 10 out of 12 publications
