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The OME Data Model specification
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Open Microscopy Environment
Screen, Plate, and Well XML Schema
Author: Andrew J Patterson
Plates
This element identifies microtiter plates within a screen.
A plate can belong to more than one screen.
The Screen(s) that a plate belongs to are specified by the ScreenRef element.
The Plate ID and Name attributes are required.
The Wells in a plate are numbers from the top-left corner in a grid starting at zero.
i.e. The top-left well of a plate is index (0,0)
A description for the plate.
The Name identifies the plate to the user.
It is used much like the ID, and so must be
unique within the document.
If a plate name is not available when one is needed
it will be constructed in the following order:
1. If name is available use it.
2. If not use "Start time - End time"
(NOTE: Not a subtraction! A string representation
of the two times separated by a dash.)
3. If these times are not available use the Plate ID.
A textual annotation of the current state of the plate with respect to the
experiment work-flow; e.g.
1. Seed cell: done; 2. Transfection: done; 3. Gel doc: todo.
The ExternalIdentifier attribute may contain a reference to an external database.
The ColumnNamingConvention
The RowNamingConvention
This defines the X position to use for the origin of the
fields (individual images) taken in a well. It is used
with the X in the WellSample to display the fields
in the correct position relative to each other. Each Well
in the plate has the same well origin. [units:none]
In the OMERO clients by convention we display the WellOrigin
in the center of the view.
This defines the Y position to use for the origin of the
fields (individual images) taken in a well. It is used
with the Y in the WellSample to display the fields
in the correct position relative to each other. Each Well
in the plate has the same well origin. [units:none]
In the OMERO clients by convention we display the WellOrigin
in the center of the view.
The number of rows in the plate
The number of columns in the plate
The index of the WellSample to display as the default Field
Predefined list of values for the well labels
While the label type 'number' has a clear meaning the 'letter'
type is more complex.
If you have less than 26 values use letters A to Z.
Once you get more than 26 values there are several different
approaches in use.
One we have see include:
Single letter, then double letter each running A to Z, right first
e.g. A, B, C, ... X, Y, Z, AA, AB, AC, ... AY, AZ, BA, BB, ...
This is the format used by Microsoft Excel so users may be familiar with it.
This is the approach we use in the OMERO client applications.
CAPITALsmall, each running A to Z, small first
e.g. Aa, Ab, Ac, ... Ax, Ay, Az, Ba, Bb, Bc, ... By, Bz, Ca, Cb, ...
This is in use by some plate manufactures.
Single letter, then double letter, then triple letter, and so on
e.g. A, B, C, ... X, Y, Z, AA, BB, CC, ... YY, ZZ, AAA, BBB, ...
This has the advantage that the first 26 are the same as the standard
but has a problem an the labels get wider and wider leading to user
interface problems.
1, 2, 3, ...
Reagents
Reagent is used to describe a chemical or some other physical experimental parameter.
A long description for the reagent.
A short name for the reagent
This is a reference to an external (to OME) representation of the Reagent.
It serves as a foreign key into an external database. - It is sometimes refereed to as ExternalIdentifier.
Screens
The Screen element is a grouping for Plates.
The required attribute is the Screen's Name and ID - both must be unique within the document.
The Screen element may contain an ExternalRef attribute that refers to an external database.
A description of the screen may be specified in the Description element.
Screens may contain overlapping sets of Plates i.e. Screens and Plates have a many-to-many relationship.
Plates contain one or more ScreenRef elements to specify what screens they belong to.
A description for the screen.
The PlateRef element is a reference to a Plate element.
Screen elements may have one or more PlateRef elements to define the plates that are part of the screen.
Plates may belong to more than one screen.
A pointer to an externally defined protocol, usually in a screening database.
A description of the screen protocol; may contain very detailed information to
reproduce some of that found in a screening database.
A description of the set of reagents; may contain very detailed information to
reproduce some of that information found in a screening database.
A pointer to an externally defined set of reagents, usually in a screening
database/automation database.
A human readable identifier for the screen type; e.g. RNAi, cDNA, SiRNA, etc.
This string is likely to become an enumeration in future releases.
PlateAcquisitions
PlateAcquisition is used to describe a single acquisition run for a plate.
This object is used to record the set of images acquired in a single
acquisition run. The Images for this run are linked to PlateAcquisition
through WellSample.
A description for the PlateAcquisition.
Time when the last image of this acquisition was collected
Time when the first image of this acquisition was collected
The maximum number of fields (well samples) in any well
in this PlateAcquisition.
This is only used to speed up user interaction by stopping
the reading of every well sample.
Wells
A Well is a component of the Well/Plate/Screen construct to describe screening applications.
A Well has a number of WellSample elements that link to the Images collected in this well.
The ReagentRef links any Reagents that were used in this Well. A well is part of only one Plate.
The origin for the row and column identifiers is the top left corner of the plate starting at zero.
i.e The top left well of a plate is index (0,0)
This is the column index of the well, the origin is the top left corner of the plate
with the first column of cells being column zero. i.e top left is (0,0)
The combination of Row, Column has to be unique for each well in a plate.
This is the row index of the well, the origin is the top left corner of the plate
with the first row of wells being row zero. i.e top left is (0,0)
The combination of Row, Column has to be unique for each well in a plate.
A description of the externally defined identifier for this plate.
The ExternalIdentifier attribute may contain a reference to an external database.
A human readable identifier for the screening status.
e.g. empty, positive control, negative control, control, experimental, etc.
A marker color used to highlight the well - encoded as RGBA
The default value "-1" is #FFFFFFFF so solid white (it is a signed 32 bit value)
NOTE: Prior to the 2012-06 schema the default value was incorrect and produced a transparent red not solid white.
WellSamples
WellSample is an individual image that has been captured within a Well.
This is the main link to the core Image element
The X position of the field (image) within the well relative to
the well origin defined on the Plate.
The Y position of the field (image) within the well relative to
the well origin defined on the Plate.
The time-point at which the image started to be collected
This records the order of the well samples. Each
index should be unique for a given plate but they do not
have to be sequential, there may be gaps if part of the
dataset is missing. In the user interface the displayed
value of the index will be calculated modulo the number
of PlateAcquisitions for the plate.
The WellSampleRef element is a reference to a WellSample element.