Recent advances in light and electron microscopy, along with new probes and labeling methods for cellular and molecular imaging, are driving a revolutionary expansion in biomedical research activities that involve exploration of complex biological systems. These new capabilities in instruments and methods are providing nearly seamless views across multiple scales of resolution of biological specimens. At the same time, researchers are increasingly generating extremely large and diverse datasets of enormous value, which are driving renewed demand for software and tools to facilitate aggregation, curation, refinement, and spatial and semantic assembly of these data. A key consumer of these data is the computational modeling and simulations community, which requires more accurate in-silico representations of supramolecular complexes and organelles in the context of complete cells and cells deployed in tissues to better model the impact of molecular changes found in diseases on the functioning of a cell. Building on prior success, we propose to continue to support, maintain, and extend the capabilities of the Cell Centered Database, which we have recently renamed the Cell Image Library (CIL). The CIL is a cell- centered community repository for storing, managing, and sharing multi-scale microscopy data encompassing cellular networks, cellular and subcellular microdomains, and their macromolecular components. The CIL is comprised of software for researchers to upload, organize, process, and share project data prior to publication. It also provides a searchable, public-facing website for users to disseminate their results and openly distribute their data for reuse by others. Our extended development plans include integration of computational workflows to facilitate generation of fully segmented, 3D structural models ready for meshing, discretization, and use in assembling more complete, realistic, and accurate models for simulations. We will also harden and extend our unique capabilities for supporting large data, in particular massive individual 3D datasets, to enable biomedical researchers to not only store, but to process and visualize their data at scale with tools that are easy to use and easily accessible.
This proposal requests funds to support continued maintenance and extension of the Cell Image Library (CIL) (formerly called the Cell Centered Database), a cell-centered community repository for storing, managing, and sharing multi-scale microscopy data encompassing cellular networks, cellular and subcellular microdomains, and their macromolecular components. The CIL is comprised of software for researchers to upload, organize, process, and share project data prior to publication, and a searchable, public-facing website for users to disseminate their results and freely distribute their data for reuse by others
| 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; 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 |
| 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 |
| Burette, Alain C; Lesperance, Thomas; Crum, John et al. (2012) Electron tomographic analysis of synaptic ultrastructure. J Comp Neurol 520:2697-711 |
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