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Data Input/Output



Types of Data


The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from the microscope as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. This value was chosen because a given data set may only be taken once and therefore each microscopy product represents a unique dataset. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB.


Accessing Data


The goal of the CCDB project is to make unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Data in the CCDB can be accessed by performing a Search or by browsing through our Gallery. Data in the CCDB may be downloaded freely and reused for non-profit use within the terms of our usage agreement. Because of the large size of most datasets, we currently restrict downloading to 5 datasets at one time. We will gladly arrange for larger datasets to be sent via DVD or download by ftp. The CCDB makes available the original 2D micrographs, any reconstructions and segmentations derived from the data. Animations, representative images and quantitative analyses are also available for many datasets. At the time of download, the CCDB creates a file containing all of the descriptive data (i.e., metadata) that is stored with the dataset, e.g., specimen preparation details, imaging parameters. The metadata file also contains the owner of the data and any citation information. We ask that all users respect the intellectual property of their colleagues by including proper attribution information for all reuse of the data. Acknowledging the CCDB will also ensure that this resource can continue to provide access to data.


Contributing Data to Ccdb


The CCDB encourages contributions of data from the scientific community. Please contact Drs. Maryann Martone or Mark Ellisman for more information. The CCDB will provide accession numbers for those wishing to reference data in a manuscript at the time of submission and has a created a simple on-line form for data registration. Because each dataset receives a unique URL, the web link may also be used in publications and on websites to direct users to the CCDB. Data does not have to be published for inclusion into the CCDB.


Proper interpretation of imaging data requires a thorough understanding of the experimental and imaging conditions used to produce the specimen and image. Thus, all imaging data deposited in the CCDB must be accompanied by project, experimental, subject and protocol details. The CCDB allows the user to store detailed experimental protocols in the form of text files, but also contains fields for experimental parameters that are known to be important for interpreting structural and protein distribution data and would likely be the targets of specific queries. Examples of such details include information on specimen fixation, staining, immunolabeling and imaging conditions.


Data Management


The CCDB is developing "MyCCDB" for comprehensive management of 2D, 3D, and 4D light and electron microscopy data through a secure web portal. With an account to MyCCDB, users can manage their own data using the CCDB's powerful search and display capabilities and share it with their colleagues through a secure web interface. MyCCDB contains advanced features for organizing imaging data along with their experimental, imaging and analysis details. MyCCDB users may set up and manage groups to assign permissions for shared viewing, data entry and analysis. Users will also be able to track data downloads and access of any data they have contributed to the public CCDB. More advanced features will include interfaces for instruments and analysis tools so that data is automatically deposited to CCDB at time of acquisition and during subsequent processing. All data is kept private until it is released for publication to the public CCDB. For more information on using MyCCDB, please contact Dr. Maryann Martone.


OpenCCDB

With support from a National Institutes of Health community software grant, we have developed an open source version of CCDB for community use and development. OpenCCDB extends the capabilities of the Cell Centered Database by providing a set of robust core services and the facilities needed for CCDB data and software to be shared, modified, edited and documented by multiple users. OpenCCDB is built on an open source software platform and is freely available to the community, along with documentation, community tools, a secure portal, and services. OpenCCDB has a completely redesigned schema with better support for techniques such as serial tomography, specimen tracking, automated upload, and a more flexible design for the experimental and specimen preparation. We also offer a set of tools for visualizing, segmenting, and analyzing very large imaging data sets from the CCDB.

Visit OpenCCDB Now!


WIB


The CCDB has just released a new visualization and analysis tool, the Web Image Browser (WIB) for viewing and annotating high resolution microscopy images over the web. The WIB reads and manages tiled images in a manner similar to Google Maps or similar applications, allowing viewing of images of arbitrarily large size. Because it is specialized for microscopy images, WIB allows users to turn on and off different channels and adjust the contrast without the need to download the data. To see the WIB in action, click here. The WIB also allows users to annotate image features using the Neuroscience Information Framework terminologies. The WIB will be one of the core tools offered through the new Open CCDB, to be launched in June of 2010. In the meanwhile, visit the OpenCCDB beta web site.

 

Data Spotlight

June 14, 2013
Data Spotlight PictureThe CCDB just released 18 beautiful large scale brain mosaics detailing Pannexin expression in the rodent brain. This research aims to examine brain tissue at high resolution and, in combination with developing neuronformatics tools, to probe for binding partners and signalling partners to investigate the pannexin interactome . Data submissions for this project will consist of wide-scale high resolution confocal mosaic images of triple-labeled whole mouse brain sections. Pannexin 1 expression will be compared to that of pannexin 2 as well as the connexins. Other putative interaction partners of interest include the P2 purinergic receptors and components of the cytoskeleton. Original image data can be found under project P20002.

Publications:

*Multi-Channel Transfer Function with Dimensionality Reduction. Proc SPIE. 2010 Jan 18;7530:75300A. Kim HS, Schulze JP, Cone AC, Sosinsky GE, Martone ME. Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA. PMID: 20582228

*A comparative antibody analysis of pannexin1 expression in four rat brain regions reveals varying subcellular localizations. Front Pharmacol. 2013;4:6. Cone AC, Ambrosi C, Scemes E, Martone ME, Sosinsky GE. National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA. PMCID: PMC3565217



Recently Released Data

Data sets under curation

For a list of data sets currently under curation for release to the public CCDB, click here.

2D, 3D & 4D Data

The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography.


While many of the data sets are derived from the nervous system, the CCDB contains data from many systems. For each dataset, the CCDB makes available the raw data, reconstructions derived from the raw data and any segmentations and analyses performed on the data. Users may browse the data on-line or download it for re-use within the guidelines of our usage agreement. The CCDB also accepts contributions of data from the scientific community.

Knowledge Engineering

The CCDB is participating is several large scale informatics projects to develop and utilize ontologies and spatial reference systems for data mining and data federation. The CCDB is utilizing ontologies to link data across scales and modalities. Additional details may be found by visiting BIRN, the NIF and Senselab. CCDB will be releasing version 1.0 of an ontology for the subcellular anatomy of the nervous system.

Sao

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The first version of the SAO focuses on the subcellular anatomy of the nervous system, comprising neuronal and glial cells, their subcellular components, structural compartments and macromolecular constituents along with multicellular domains such as neuropil and the Node of Ranvier. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their approporiate subcellular domains. The SAO provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration. The SAO was built using Protègé 3.2 using OWL (web ontology language). A manuscript detailing the construction and rationale of the SAO is in preparation. To download the file, click here. The ontology may also be browsed on the web by clicking here.