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Data and File Management
Each data record in the CCDB consists of the following:
  • a complete description of the experimental and imaging details, including general project and experiment information. Details about the subjects, including animal and tissue data, processing methods, microscopy technique, reconstruction, and segmentation are provided.
  • text files, such as protocols.
  • image and segmentation files, including raw image data, reconstruction volume data, and segmented object data, as well as file names along with their descriptions and annotations.
  • quantitative measurements derived from an image or reconstruction.

Data files are stored on the BIRN data grid (link) and may be downloaded for personal use within the usage guidelines. Many data sets are downloaded as a tar file containing multiple images and ancillary files required to view or interpret the data. The CCDB makes available a set of tools for viewing and manipulating the most common data formats stored in the CCDB.

The CCDB manages data using an object-relational framework that integrates Oracle 9i and the BIRN data grid. The image and analysis files are stored on the grid, and the descriptive data and measurements are stored in Oracle 9i. An illustration of the file management system is presented in the figure in the right sidebar.

Depositing Data
To contribute data, researchers must first submit an application. Contact Dr. Maryann Martone for more information.
data management figure

File Management
System Diagram
     
 
Entities
The eight essential entities described in the following table form the basis of the CCDB, as each entity recorded in the database is associated with these essential components. The attributes and descriptions of all CCDB entities are listed in the following table. A detailed schema depicting the relationships among these entities is presented here. 		 
     
 
Essential Entities
Entity Fields Description
Project Name, Description, Leader, Funding Agency, Project Starting Date, Project Ending Date, Collaborators, Publications General information about the project
Experiment Experiment Title, Experiment Purpose, Experiment Date, Experimenter General information about experiment, such as the researcher name, title, and date
Subject Group Subject Group Name, Group By Method, Treatment Method Information about how the subjects of experiment are grouped
Subject Species, Scientific Name, Strain, Transgenic_id Subject information about subject from which the microscopy image tissue sample is derived
Animal Age Class, Age, Sex, Weight Age, weight Information about each animal
Tissue Anatomic Location, Tissue Product Storage, Microtome, Thickness, Orientation Information about how and where the tissue was obtained, treated, and stored
Processing Tissue group_type, Protocol Information about the protocol used to prepare the slides and a full text of the procedure
Microscopy Product Instrument, X Size, Y Size, X Resolution, Y Resolution, Creation Date, PURL, Product Type, Microscope Type, Image Base Name, Session Name, Gridbox_count, Grid Info, Slide_info, Plane Count Detailed information about the microscopy instrument and image sets including the size of the image, image naming, image count, storage, etc. for a set of microscopy images
Additional Entities
Entity Fields Description
Fixation Fixative, Time of Fixation, Temperature, Fixative Volume, Fixative Type Detailed information about key experimental condition for the fixation method of the microscopy sample
Embedding Dehydration Agent, Embedding Agent, Dehydration Time Detailed information about key experimental condition for the embedding method of the microscopy sample
Probe Probe Type, Probe Name, Probe Source, Probe Concentration, Probe Reference Detailed information about probe
Protein PDB_id, Name, Abbreviation, Isoform Detailed information about the protein, the PDB_id is the entry to link to PDB Database
Antibody Clonality, Antigen Source, Purification Method, Raised in Animal, Antibody Type, Source, Reference Detailed information about the antibody sources
Probe Detection Type, Chromgen, Notes Information about the method of detection by using the probe
Stain Stain Name, Stain Description Information about stain agent and procedure for the staining
Transmitted Image Light Source, Transmitted Type Information about transmitted light images
Fluorescent Image Fluorophorcolors, Filter Information about Fluorescent images
Confocal Image Layer Type Information about stain agent and procedure for the staining
Epifluorescent Image Light Source Information about stain agent and procedure for the staining
Electron Microscopy Image Magnification, EM Parameter File, Spot size, Apperturesetting, Recording Medium, Embedding Medium, Accelerating Information about the Electron Microscopy experiment including the name of the parameter files. These parameters are common to all the electron microscopy image products
Light Microscopy Image Cover Slip Thickness, Lens, Lens Magnification, Numbericalaperture, Immersion Medium, Mounting Medium, Refractive Index Information about the light microscopy experiment. These parameters are common to all the light microscopy image products
Double Tilt Image X Dimension Maximum, X Dimension Minimum, X Dimension Tilt Increment, Y Dimension Range Max, Y Dimension Range min, Y Dimension Tilt Increment, Technique Description Information about how the size range of the double tilt image, and the tilt angle in x and y dimensions for each image that useful for the reconstruction
Mosaic Image Position in X Dimension, Position in Y Dimension, Technique Description Information about the mosaic position of the mosaic image and technique
Stereopairs Image Stereo Angles, Stereo Description Information about how the stereo pair images are obtained
Time Series Image Frame Count, Frame Interval, Stimulation Interval, Stimulation Start, Stimulation Strength, Time Series Type, Time Series Description Information about how time intervals are chosen for the time series image
Survey Image Survey Type Description Information about images only for survey
Through Focus Image Through Focus PSF File Name, Through Focus Description Information about the through focus images
Serial Section Image Serialsection_zresolution, Cutting Planes, Serialsection_description Information about serial images
Single tilt Image Range_min Range_max, Tilt Increment, Single tilt Description Information about the tilt angles and range for the single tilt images
Optical Section Image OpticalsectionPSF File Name,Opticalsection_zresolution, Cutting plane, Opticalsection Description Information about the parameter files and other related technique to obtain the optical section images
Image2d Magnification, Current Intensity, Image Parameter Filename, Defocus, Electron Dose, Exposure Time, Tilt Angle, Z Position, X, Y Position, Image Date, Image Filename, Image File Format, Image Description Information about one specific image, such as image producing date, image format, etc.
Reconstruction Recon_type, Recon_program, Recon_algorithm, Recon_desc, Volumename, Basename_orgfile, Volumedimension, Voxelscale, Recon_date, Correlatedvolumename, Imagemapfile, Deconvoprogram, Deconvoalgorithm, Deconvoiterators, Missingangles_count, Missingangles, Alignmentmethod, Alignmentprogram, Fiducialmarkfile, Cropping Coordinate Information about the parameters, algorithm, and software that is used in the reconstruction
Segmentation Seg person Name, Object name, Object type, Object Description, Segmentedobject2dimage, Seg_desc, Analyze_desc, Seg_algorithm, Seg_filename, Ismanual, Seg_filename, Volume, Surface Area, Length, Number of Object, Diameter, Labeling Intensity, Labeling Rank, Threshhold Information about the object measurement attributes after segmentation and procedure to obtain the segmented images
 
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