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Fluorescence Microscopy Annotation SchemaVersion 1, February 15, 2002 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 255 characters. Laboratory 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_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_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.
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_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. Double 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).
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.
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.
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_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.
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. Text field. Ligand_class Class of ligand used. Text field.
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. Long integer. Emission_max Maximum dye emission wavelength. Long integer.
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. Double number field. Y_coor Y coordinate of the field of view. Double number field.
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.
Microscopy_id ID referencing linked record from Microscopy which contains details about the microscopy 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. Text
field.
Name Description Num_dimensions Num_channels
Stack_id ID referencing linked record from Stack. Feature_id ID referencing linked record from Feature Value Calculated value of a single stack feature. Double number
field.
Stack_id1 ID referencing linked record from Stack. Contains the record for one stack of two that is used for this double stack feature calculation. Stack_id2 ID referencing linked record from Stack. Contains the record for the second of two stacks 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.
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. Long integer. X_dim X dimension of the image. This should be automatically obtained from the image file information. Long integer. Required. Y_dim Y dimension of the image. This should be automatically obtained from the image file information. Long integer. Required. Z_coor Z coordinate of image. Double number field.
Image_id ID referencing linked record from Image. Feature_id ID referencing linked record from Feature Value Calculated value of a single image feature. Double number
field.
Image_id1 ID referencing linked record from Image. Contains record of one of the two images to be used for the double image feature calculation. Image_id2 ID referencing a different linked record from Image. Contains record of the second of two images 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
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. Double number field. Exposure_time Exposure time for taking the image. Short time format.
Entered as mm:ss.
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. Double number field. Voltage Voltage setting used for the PMT. Units of volts. Double number field. Offset Offset setting used to make the baseline intensity reading zero. Double number field. X_res X resolution setting. Long integer field. Y_res Y resolution setting. Long integer field. Bit_depth Bit depth setting. Long integer field. Detector_processing List of image processing operations performed "inside"
the detector (e.g., flat field divide). Comma delimited, restricted text
list field.
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.
Name Name of filter used. Text field. Pass_type Pass type used to acquire images. Text field. Upper Upper wavelength passed by filter. Long integer field. Lower Lower wavelength passed by filter. Long integer field. Thickness Thickness of filter in millimeters. Double number field. Spectrum URL of text file containing spectrum of filter as wavelength,
transmittance pairs one per line. Text field.
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. Double 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. Double number field.
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. Long integer field.
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.
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. |