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Fluorescence Microscopy Annotation Schema

Version 1.2, May 28, 2003

Note: Each table always contains a field named after the table so that individual entries in the table may be easily identified (ex. laboratory_id for table laboratory). This field contains a unique number for each record to link to that record from another table. Text fields are specified to contain a maximum of 4000 characters.

DBUser

This table contains any information about the access user/password of the database.

Username

Name of the database user. Text field

Password

Password of the database user. Text field.

Laboratory

This table contains any information about the laboratory conducting the experiment including contact information.

Laboratory_id

Name

Name of the laboratory conducting the experiment. This is usually the last name of the principal investigator. Text field

Address

Mailing address of laboratory conducting the experiment. Text field.

Email_address

Email address of laboratory conducting the experiment. Text field.

Phone_number

Phone number of laboratory conducting the experiment. Text field

Researcher This table contains information about the specific researcher conducting the experiment including contact information.

Researcher_id

Laboratory_id

ID referencing linked record from Laboratory containing the details about the lab of the researcher.

Name

Name of researcher conducting the experiment. Text field.

Email_address

Email address of researcher conducting the experiment. Text field.

Phone_number

Phone number of researcher conducting the experiment. Text field

Experiment

This table contains general information about the experiment such as title and date started.

Experiment_id

Researcher_id

ID referencing linked record from Researcher containing details about the researcher conducting this experiment.

Title

Title of the experiment. Text field.

Date

Starting date of experiment. Date field.

Slide This table simply holds several links to other tables. One record is created for each individual slide.

Slide_id

Cell_type_id

ID referencing linked record from Cell_Type containing data about the type of cell used for this slide.

Experiment_id

ID referencing linked record from Experiment containing information about the experiment in general including title and starting date.

Protocol_id

ID referencing linked record from Protocol containing information about the protocol used.

Sample_label_id

ID referencing linked record from Sample_Label containing information about the sample label used.

Protocol This table contains specific information about the protocol used to prepare the slides including a full text write up of the procedure.

Protocol_id

Title

Title of protocol. Text field.

Author

Name of author of the protocol. Text field.

Reference

URL referencing protocol. Hyperlink.

Fixation

Type of fixation used. Possible types include "None" or "Paraformaldahyde". This will be a restricted text field.

Permeabilization

Type of permeabilization used. Possible types include "None", "Saponin", or "Triton". This will be a restricted text field.

Substrate

Type of substrate used. Possible types include "Glass" or "Collagen-coated glass". This will be a restricted text field.

Temperature

Temperature at which protocol was carried out in Celsius. Float number field.

Protocol_text

Detailed procedure describing entire protocol used for this experiment. The procedure will be stored as a memo which will allow up to 64K characters (copy of document referred to by the "reference" field). CLOB field.

Cell_Type This table contains the name of the type of cell used in the slides.
Cell_type_id

Name

Common name for cells used on this slide. Possible entries include "HeLa" and "CHO". Text field.

ATCC_Number

The ATCC number designated for this cell type (e.g., CCL-2 for HeLa cells). The name field will be the primary way in which users identify the cell type. This field is simply for reference should more information be needed about the cell type, and to insure that although there may be two different cell types with the same common name, they can be differentiated between. Text field.

MESH_Heading

The MeSH term for the cell line (e.g., "Hela cells"). Text field.

MESH_Tree_Number

The location in the MeSH hiearchy for the cell line (e.g., A11.251.210.770.460 for HeLa Cells). Text field.

Organism

Name of organism (species) from which the cells were derived. Text field.

Sample_Label This table contains a description dye(s) used to label the cells of this slide.
Sample_label_id

Name

Written description of a specific combination of dyes used to label the cells on this slide. It is important to note that a slide of cells may be labeled with more than one combination of dyes. Text field.

Label_JUNC This table stores the "position" of a label relative to other labels in one particular combination of dyes.

Sample_label_id

Label_id

ID referencing linked record from Label containing details about the label used such as its name, ligand class, and what it binds to.

Position

Stores the position (order) of label relative to other labels in this combination for this slide. Integer number.

Target This table contains information on the macromolecule that is the target of the labeling.

Target_id

Name

Name of the target of the labeling . Text field.

MESH_Heading

The MeSH term for the labeling target. Text field.

MESH_Tree_Number

The location in the MeSH hiearchy for the labeling target. Text field.

Label This table contains information about labels themselves.
Label_id

Dye_id

ID referencing linked record from Dye containing information about the dye itself such as its name and pertinent wavelength information.

Name

A descriptive name for the label. "Mouse anti-human immunoglobulin" is an example entry for this field. This will be the field by which the user references a particular label. Text field.

Target_id

The target that the label binds to. Integer field.

Ligand_class

Class of ligand used. Text field.

Dye

This table contains detailed information about the dyes attached to the labels.
Dye_id

Name

Name of the dye. Text field.

MESH_Heading

The MeSH term for the dye (e.g., "Fluorescein-5-isothiocyanate" for FITC). Text field.

Excitation_max

Maximum dye excitation wavelength. Integer field.

Emission_max

Maximum dye emission wavelength. Integer field.

Field_of_View This table contains information about a specific "field of view" on the slide.
Field_of_view_id

Slide_id

ID referencing linked record from Slide which will like to other relevant records dealing with this particular slide.

X_coor

X coordinate of the field of view. Float number field.

Y_coor

Y coordinate of the field of view. Float number field.

Time

This table contains information about images taken at the same time.
Time_id

Field_of_view_id

ID referencing linked record from Field_of_View which contains information about the slide being examined and the coordinates of the field of view.

Time

Absolute time at which the current image was taken. Date field.

Stack This table contains information about an entire stack of images.
Stack_id

Microscopy_Filter_id

ID referencing linked record from Microscopy_Filter which contains details about the microscopy and filter set up.

Time_id

ID referencing linked record from Time which references images taken at the same time.

Description

A written description of the stack. This is just intended as a reference for the user and is Text field.

Target_id

ID referencing linked record label_id from Label. Integer field.

Feature This table contains information about the features of an image.
Feature_id

Name

                          Unique SLF (Subcellular Location Feature) designation (e.g., SLF1.1 for __). Text field.
Description                            Brief description of the feature.
Num_dimensions                           The number of dimensions that are required to be present in an image to calculate this feature (e.g., "2" for a feature that can be calculated from a single 2D plane).
                         Integer field.
Num_channels                           The number of channels (colors) that are required to calculate this feature. Integer field. FeatureSet                           This table contains information about the predefined feature subsets.
FeatureSet_name

Predefined feature subset names, such as SLF1 and SLF2. Text field.

Features

Ordered features in a specific feature subset, such as SLF3.1, SLF3.2, ..., SLF3.78. Text field.

Convention_name

Unique name of features in a specific feature set that linked to the Name field in Feature. Text field.

Sets This table contains information about a query result that has been saved as a set before doing sets comparison.
Set_id

Set_name

Name of the set specified by user. Text field.

Stack_id

ID referencing linked record from Stack containing the details about a stack. Integer field.

Removable

Sign showing whether a set is removable or not. Integer field.

Mask This table contains information about a mask that can be applied to a slice image to get a single-cell image.
Mask_id

Mask_url

URL or path describing where the mask is stored. Text field.

Mask_x_dim

X dimension of the mask. Integer field.

Mask_y_dim

Y dimension of the mask. Integer field.

Region This table contains the cropping information of a slice image using a specific mask.
Region_id

Image_id

ID referencing linked record from Image. Integer field.

Mask_id

ID referencing linked record from Mask. Integer field.

3DRegion

This table contains the cropping information of a stack using a specific mask.
3DRegion_id

Stack_id

ID referencing linked record from Stack. Integer field.

Mask_id

ID referencing linked record from Mask. Integer field.

Single_Stack_Feature_Values

The features calculated from an individual 3D image.
Single_stack_feture_values_id

3DRegion_id

ID referencing linked record from 3DRegion.

Feature_id

ID referencing linked record from Feature

Value

Calculated value of a single stack feature. Double number field.

Double_Stack_Feature_Values The features calculated from two 3D images.
Double_stack_feture_values_id

3DRegion_id1

ID referencing linked record from 3DRegion. Contains the record for one stack region of two that is used for this double stack feature calculation.

3DRegion_id2

ID referencing linked record from 3DRegion. Contains the record for the second of two stack regions that is used for this double stack feature calculation.

Feature_id

ID referencing linked record from Feature

Value

Calculated value of the double stack feature. Double number field.

Image This table contains information about individual images.
Image_id

Stack_id

ID referencing linked record from Stack.

URL

URL or path describing where the image is stored. Text field.

Stack_pos

Position of the image relative to others in the same stack. Integer field.

X_dim

X dimension of the image. This should be automatically obtained from the image file information. Integer field.

Y_dim

Y dimension of the image. This should be automatically obtained from the image file information. Integer field.

Z_coor

Z coordinate of image. Float number field.

Single_Image_Feature_Values The features calculated from an individual 2D image.
Single_image_feture_values_id

Region_id

ID referencing linked record from Region.

Feature_id

ID referencing linked record from Feature

Value

Calculated value of a single image feature. Float number field.

Double_Image_Feature_Values The features calculated from two 2D images.
Double_image_feture_values_id

Region_id1

ID referencing linked record from Region. Contains record of one of the two image regions to be used for the double image feature calculation.

Region_id2

ID referencing a different linked record from Region. Contains record of the second of two image regions to be used for the double image feature calculation.

Feature_id

ID referencing linked record from Feature. Contains details about which feature was calculated.

Value

Calculated value of the double image feature. Float number field.

Microscopy

Contains information about microscopy set up.
Microscopy_id

Name

Name of microscopy setup. Used for common reference. Text field.

Objective_id

ID referencing linked record from Objective.

Detector_id

ID referencing linked record from Detector.

Condenser_id

ID referencing linked record from Condenser.

Illumination_id

ID referencing linked record from Illumination.

Microscope_id

ID referencing linked record from Microscope.

Emission_magnification

Magnification (if any) between the image plane and the detector. Float number field.

Exposure_time

Exposure time for taking the image. Text format. Entered as mm:ss.

Detector Contains information about detector set up.
Detector_id

Name

Name of detector set up. Text field.

Type

Type of detector used (e.g., CCD, Scanned PMT) Restricted text field.

Manufacturer

Manufacturer of detector used. Text field.

Model

Model of detector used. Text field.

Serial_number

Serial number of detector used. Text field.

Gain

Gain setting used to acquire image. Float number field.

Voltage

Voltage setting used for the PMT. Units of volts. Float number field.

Offset

Offset setting used to make the baseline intensity reading zero. Float number field.

X_res

X resolution setting. Integer field.

Y_res

Y resolution setting. Integer field.

Bit_depth

Bit depth setting. Integer field.

Detector_processing

List of image processing operations performed "inside" the detector (e.g., flat field divide). Comma delimited, restricted text list field.

Microscope Contains information about microscope used.
Microscope_id

Name

Name of microscope. Text field.

Manufacturer

Manufacturer of microscope used. Text field.

Model

Model of microscope used. Text field.

Serial_number

Serial number of microscope used. Text field.

Filter Contains information about filter used.
Filter_id

Name

Name of filter used. Text field.

Pass_type

Pass type used to acquire images. Text field.

Upper

Upper wavelength passed by filter. Integer field.

Lower

Lower wavelength passed by filter. Integer field.

Thickness

Thickness of filter in millimeters. Float number field.

Spectrum

URL of text file containing spectrum of filter as wavelength, transmittance pairs one per line. Text field.

Microscopy_Filter Contains links between excitation and emission filters and specific microscopy setups.
Microscopy_filter_id

Microscopy_id

ID referencing linked record from Microscopy.

Ex_filter_id

ID referencing a filter from Filter that was used in the excitation path.

Excitation_filter_angle

Angle at which excitation filter was placed relative to direction of exciting light. Float number field.

Em_filter_id

ID referencing a filter from Filter that was used in the emission path.

Emission_filter_angle

Angle at which emission filter was placed relative to direction of exciting light. Float number field.

Objective Contains information about objective used.
Objective_id

Name

Name of objective. Text field.

Manufacturer

Manufacturer of objective used. Text field.

Model

Model of objective used. Text field.

Serial_number

Serial number of objective used. Text field.

Magnification

Amount of magnification used to acquire image. Integer field.

Num_app

Numerical aperture setting used. Integer field.

Condenser Contains information about condenser used.
Condenser_id

Name

Name of condenser. Text field.

Manufacturer

Manufacturer of condenser used. Text field.

Model

Model of condenser used. Text field.

Serial_number

Serial number of condenser used. Text field.

Illumination Contains information about type of illumination used.
Illumination_id

Name

Name of illuminator. Text field.

Type

Type of illumination used. Text field.

Manufacturer

Manufacturer of illuminator used. Text field.

Model

Model of illuminator used. Text field.

Serial_number

Serial number of illuminator used. Text field.

Spectrum

URL of text file containing spectrum of illuminator as wavelength, transmittance pairs one per line. Text field.

Last Updated: 01 Dec 2004