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Illustration of attributes and descriptions of essential entities
in CCDB. Every microscopy product entity must be associated with
project, experiment, subject group, subject, animal, tissue,
processing description. This eight entities form the back born of the
CCDB schema.
| Table | 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 that the microscopy image tissue sample comes
from |
| 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 as well as a full text of the
procedure |
| Microscopy Product | Instrument, X
xize, 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 |
Detail 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 |
| Fixation | Fixative, Time of Fixation,
Temperature, Fixative Volume, Fixative Type | Detail
information about key experimental condition for the fixation
method of the microscopy sample |
| Embedding | Dehydration Agent,
Embedding Agent, Dehydration Time | Detail information
about key experimental condition for the embedding method of
the microscopy sample |
| Probe | Probe Type, Probe Name, Probe
Source, Probe Concentration, Probe Reference | Detail
information about probe |
| Protein | PDB_id, Name, Abbreviation,
Isoform | Detail 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 | Detail 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 product |
| 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 product |
| 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 how 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 that 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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