About the CCDB

Enter the CCDB

Visualization & Analysis Tools

Status/Updates

User Agreement
& Disclaimer

Project Team Members

Related Links

Developer Docs

Help

Feedback

Depositing Data into the CCDB File Management System

1. A complete scientific description (meta data) of the experimental and imaging details,

2. Image files (binary data) and parameter files.

3. Image file information (e.g. file name, file size, file type).

4. Image file annotation (e.g. symbol, definition).

5. Quantitative information derived from an image or reconstruction.

The above data is distributed between Oracle 9i and the SRB.

As the CCDB is developed, more and more data will be automatically uploaded to the CCDB without the need for manual entry. In the meanwhile, entering data into the CCDB will take a little time. However, users will gain the benefit of having a complete, searchable record for a particular data set, which can be retrieved from anywhere via the SRB. The extra time spent preparing data for entry into the CCDB will be well worth the effort.

The CCDB Image file management system is shown in Fig. 1. An ER (entity-relationship) diagram of the CCDB is shown in Figure 2.

Fig 1: Overview of information management system for the CCDB. Image and analysis files are stored in the SRB while descriptive data and measurements are stored in Oracle 9i.

Figure 2: ER diagram of CCDB in oracle 9i

I: Scientific Description Information

1. Project: name, description, leader, funding agency, project starting data, project ending data, collaborators, publications etc.

2. Experiment: experiment title, experiment purpose, experiment date, experimenter, etc.

3. Subject Group: subject group name, group by and treatment information.

4. Subject: species, scientificname, strain, transgenic id

5. Animal: ageclass, age, sex, weight

6. Tissue: anatomic location, tissueprodstorage, microtome, thickness, orientation

7. Processing:
   • tissue group type, protocol

     Many of the experimental and tissue processing details for a data set are included as specific fields in the CCDB. The fields were chosen not to provide a complete description of the particular protocol used for a specimen, but to provide for the ability to query key details, e.g., antibody or fixative. Users are encouraged to provide a plain text file of the detailed protocol used to prepare the sample and store it in the CCDB.

   • fixation: fixative, time of fixation, temperature, fixative volume, fixative type

   • embedding: dehydration agent, embedding agent, dehydration time

   • protein localization:
     1. probe: probe type, probe name, probe source, probe concentration, probe reference

     2. protein: name, abbreviation, isoform

     3. antibody: clonality, antigen source animal, purification method, raise in animal, antibody type, source, reference

     4. probe detection: type, chromgen, notes

   • stain: stain name, stain description

8. Microscopic technique:
   • Instrument, x size, y size, x resolution, y resolution, create date. PURL, product type, microscope type, image base name, session name, gridbox_count, grid info, slide info, plane count

   • Lmproduct:
     1. Transmittedimages: light source, transmitted type

     2. Fluorescentmsimages: fluorophorcolors, filter
        • Confocalimages: laser type

        • Multiphotomiages: laser type

        • Epifluorescentmsimages: light source

   • Emproduct: magnification, EM parameter file, spot size, apperturesetting, recording medium, embedding medium, accelerating voltage, energy filter type, energy filter slit, energy filter dispersion

   • Doubletiltimage: x dimension range max, x dimension range min, x dimension tilt increment, y dimension range max, y dimension range min, y dimension tilt increment, technique description

   • Mosaic: position in x dimension, position in y dimension, technique description

   • Stereopairs: stereo angles, stereo description

   • Timeseries: frame count, frame interval, stimulation interval, stimulation start, stimulation strength, time series type, time series description

   • Survey: survey type description

   • Throughfocus: through focus PSF file name, through focus description

   • Serialsection: serialsection_zresolution, cutting planes, serialsection_description

   • Singletilt: singletilt description, range_min range_max, tilt increment

   • Optical section series: opticalsectionPSF file name, opticalsection_zresolution, cutting plane, opticalsection description

9. Anatomical detail: system, tissue, organ, region, subregion, celltype, structure, atlas map location, atlas, atlas coordinate system

10. Region of interest: elements, objectname, regionarea, average intensity, intensity variation, rank region description and region type

11. 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

12. 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, croppingcoordinate1, croppingcoordinate2.

13. Segmentation: segperson name, object name, object type, object description, Segmentedobject2dimage, seg_desc, analyze_desc, seg_algorithm, ismanual, seg_filename, ismanual, seg_filename, volume, surface area, length, number of object, diameter, labeling intensity, labeling rank, threshold.

II: Text Files

III: Image and Segmentation Files:

Figure 3: Image File structure and naming convention for files stored in SRB

IV: Preparing data for entry into the CCDB

1. Tar Files
   • Raw image data: A single tar file should be prepared with the raw image data, e.g., the entire tilt series along with the fiducial mark file and any origin settings. Both the unaligned images and the cropped, aligned images may be included. If the cropping coordinates are stored in the CCDB, it is not necessary to store the cropped files. The user should be able to recreate the reconstruction from the raw data using the information provided by the CCDB and the image data provided. The file should be named: basename_img.tar.
     The filename is stored in the image_filename field of the image2d_objtab

   • Volume data: A single tar file should be prepared with all 3D volume data. For Analyze files, the tar file should include the .img and .hdr files. The tar file may also include any volumes derived from the original which are deemed useful, e.g., filtered volumes. If additional segmentation was performed on the volume, the volume file that was segmented should be included and identified. The file should be named: basename_vol.tar. The filename is stored in the volumename field of the reconstruction3d_objtab

   • Segmented data: A single tar file should be prepared of all segmented data. For Synu data prepared from Xvoxtrace files, this file should include the Xvoxtrace trace file, all synu objects created from this file and the Viewdata file. The file should be named: basename_seg.tar. The filename is stored in the seg_filename field of the segmentedobject_objtab

2. Representative images

   In order to provide visualization of the content of a data set on the web, the CCDB offers low resolution 2D images for browsing, without the need for downloading data. At this time, users have to provide these types of images along with the full resolution 3D data. Thumbnails for each image will be created by the database administrator. The CCDB has adopted standard sizes and naming conventions for these images. For each reconstruction stored in the CCDB, the user should prepare the following:

   • Raw Image Thumbnail: A 2D image representing the raw imaging data used to create the reconstruction, e.g., a single tilt image. The maximum dimension should be 512 and the format should be jpeg. The image should be named: basename_img.jpg.

   • Reconstruction Thumbnail: A 2D image representing the 3D volume. This image may be a single slice through a volume or a projection through the volume, whichever is deemed by the user to be more informative. The maximum dimension of this image should be 512 and the format should be jpeg. A brief description of the image which will be displayed when the image is selected should also be prepared. The image should be named: basename_vol.jpg. The description of the image is stored in reconimage_desc of the reconstructionimages_objtab. The filename is stored in recon_filename of the reconstructionimages_objtab

   • Segmented Object Thumbnail: A 2D image representing the segmented image. This image may be annotated, i.e., have labels placed on it identifying objects segmented from the reconstruction. The maximum dimension of this image should be 512 and the format should be jpeg. A brief description of the image which will be displayed when the image is selected should also be prepared. The image should be named: basename_seg.jpg. The description of the image is stored in seg_desc of the reconstructionimages_objtab. The filename is stored in seg_filename of the reconstructionimages_objtab

3. Animation or Movie Files
   Animation or movie files may also be stored for each reconstruction for viewing on the web. These types of files are useful for viewing and evaluating 3D volume or segmentation data and may include the following:
   • Reconstruction Animation: A movie loop of the volume data. This loop may display the reconstructed object rotating along a single axis or may display the individual slices of the volume. Again, the user should provide whatever would be most useful to someone trying to evaluate the data prior to downloading it. A brief description should also be prepared. The movie loop should be prepared in mpeg format and should be no larger than 10 megabytes. The movie file should be named basename_vol.mpg.
     The description of the image is stored in animation_desc of the animation_objtab. The filename is stored in animation_filename of the animation_objtab

   • Segmented Object Animation A movie loop through the slices of the aligned and cropped imaging data used to create the reconstruction. The movie should be in mpeg format and no larger than 10 megabytes. The movie should be named: basename_img.mpg. The description of the image is stored in animation_desc of the animation_objtab. The filename is stored in animation_filename of the animation_objtab.

   Users may also choose to make available other 2D images and movie loops relating to the raw data, volume or segmented data, but they are not required. If such images are created, they should adhere to the size requirements and naming conventions described above.

V: Image File Information

The following fields are included in the CCDB for image data:

1. Reconstruction Images: rotationmatix, recon_filename, reconimage_desc

2. Animation and Movies: animation_filename, animation_fileformat, animation_desc

3. ImageMap file: volumename, basename_orgfile, correlatedvolumename, imagemapfile, fiducialmarkfile

4. Segmented Object: seg_filename, segmentedobject2dimage

5. 2D Images: image_filename, image_fileformat, image_date

VI: Image File Annotation

Annotation: annotation symbol, annotation description

VII: Image Quantitative Measurement Information

For neuronal tree structures created with Neurolucida, the CCDB has parsers for the Neuron Summary, Dendrite, Axon, Spine and Cell Body tables output by NeuroExplorer.