Screen Plate Well
=================
The Screen Plate Well (SPW) model is designed to support High Content
Screening (HCS). It is aimed at providing a flexible framework to organize the
images that result from such a screen and link to external systems that
contain full information about the components and products used.
Throughout the model, there are several **External Identifier** strings
that can be attached to support this.
The top level of the SPW model has two objects that exist side by side -
**Screen** and **Plate**. It is important to stress that **Plate** is
not a child of **Screen**, they are equals. This is necessary to cater
for the fact that while a **Screen** can contain many **Plate**\ s, a
**Plate** can also be used in more than one **Screen**. This allows less
common scenarios where, for example, there are two screens against two
different reagent sets but only one set of control plates that are used
in common.
**Reagent**\ s are children of a **Screen** and as such are designed to be
referenced from each **Screen** they are part of. It is worth covering
the exact meaning of a **Reagent** within SPW. The storing of detailed
information about biological reagents is beyond the scope of the OME
model. There are several other systems that are designed to handle this
type of information. What the **Reagent** element in SPW provides is
useful descriptions and an external reagent identifier, that can be used
to find detailed information about the reagent in another system. A side
effect of this is that any change to an external reagent requires a new
SPW reagent. This could be a change of dilution, supplier, or
lot-number.
.. note:: Refer to :omexml_downloads:`OME-XML downloads <>` to find
sample files for different combinations of Screens, Plates and Wells.
Example
-------
Two chemical reagents, Monastrol and VX680, applied to samples in various
concentrations; Monastrol at 100, 300, and 900 nM concentrations, and VX680 at
300, 900, 2700 nM concentrations. This requires a total of 6 reagents to be
defined in the OME file:
::
<spw:Screen …>
…
<spw:Reagent ID="Reagent:001" Description="Monastrol at a 100nM concentration from XYZ Supplier" Name="Monastrol-100nM" ReagentIdentifier="R-XYZ-Mon-100-nm-00345"/>
<spw:Reagent ID="Reagent:002" Description="Monastrol at a 300nM concentration from XYZ Supplier" Name="Monastrol-300nM" ReagentIdentifier="R-XYZ-Mon-300-nm-01245"/>
<spw:Reagent ID="Reagent:003" Description="Monastrol at a 900nM concentration from XYZ Supplier" Name="Monastrol-900nM" ReagentIdentifier="R-XYZ-Mon-900-nm-00875"/>
<spw:Reagent ID="Reagent:004" Description="VX680 at a 300nM concentration from XYZ Supplier" Name="VX680-300nM" ReagentIdentifier="R-XYZ-VX680-300-nm-00256"/>
<spw:Reagent ID="Reagent:005" Description="VX680 at a 900nM concentration from XYZ Supplier" Name="VX680-900nM" ReagentIdentifier="R-XYZ-VX680-900-nm-00257"/>
<spw:Reagent ID="Reagent:006" Description="VX680 at a 2700nM concentration from XYZ Supplier" Name="VX680-2700nM" ReagentIdentifier="R-XYZ-VX680-2700-nm-00258"/>
…
</spw:Screen>
Elements and Attributes
-----------------------
Plate
^^^^^
**ID** - used by the system to identify the plate.
**Name** - chosen by the user to identify the plate.
**Description** - a free text description.
**ColumnNamingConvention** - the column naming convention.
**Columns** - the number of columns in the plate.
**ExternalIdentifier** - an identifier for the plate used by an
external system. This may be a barcode printed on the plate by the
manufacturer.
**RowNamingConvention** - the row naming convention.
**Rows** - the number of rows in the plate.
**Status** - the current state of the plate in the experiment work-flow.
**WellOriginX** - the X position to use for the origin of the fields
(individual images) taken in a well.
**WellOriginY** - the Y position to use for the origin of the fields
(individual images) taken in a well.
Reagent
^^^^^^^
**ID** - used by the system to identify the reagent.
**Name** - a short name for the reagent.
**Description** - a long description for the reagent.
**ReagentIdentifier** - a reference to an external (to OME)
representation of the Reagent. It serves as a foreign key into an external
database.
Screen
^^^^^^
**ID** - used by the system to identify the screen.
**Name** - chosen by the user to identify the screen.
**Description** - a long description for the screen.
**ProtocolDescription** - a description of the screen protocol; may contain
very detailed information to reproduce some of that found in a screening
database.
**ProtocolIdentifier** - a pointer to an externally defined protocol, usually
in a screening database.
**ReagentSetDescription** - a description of the reagent set; may contain very
detailed information to reproduce some of that found in a screening database.
**ReagentSetIdentifier** - a pointer to an externally defined reagent set,
usually in a screening database/automation database.
**Type** - a human-readable identifier for the screen type e.g. RNAi, cDNA,
SiRNA.
PlateAcquisition
^^^^^^^^^^^^^^^^
PlateAcquisition is used to describe a single acquisition run for a
plate. Since Plates are abstract, 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.
**ID** - used by the system to identify the plate acquisition.
**Name** - chosen by the user to identify the plate acquisition.
**EndTime** - time when the last image of this acquisition was collected.
**MaximumFieldCount** - the maximum number of fields (well samples) in any
well in this PlateAcquisition.
**StartTime** - time when the first image of this acquisition was collected
Well
^^^^
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 one or more
Plates. The origin for the row and column identifiers is the top left
corner of the plate, starting at zero.
**ID** - used by the system to identify the well.
**Color** - a marker color used to highlight the well.
**Column** - 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).
**ExternalDescription** - a description of the externally defined identifier
for this plate.
**ExternalIdentifier** - a pointer to an externally defined identifier for
this plate.
**Row** - 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).
**Status** - a human-readable identifier for the screening status e.g. empty,
positive control, negative control, control, experimental. This string is
likely to become an enumeration in future releases.
WellSample
^^^^^^^^^^
WellSample is an individual image that has been captured within a Well.
**ID** - used by the system to identify the well sample.
**Index** - records the order of the well samples. Each index should be
unique for a given plate but they do not have to be sequential.
**PositionX** - the X position of the field (image) within the well relative
to the well origin defined on the Plate.
**PositionY** - the Y position of the field (image) within the well relative
to the well origin defined on the Plate.
**Timepoint** - the time-point at which the image started to be collected.
ScreenAcquisition rename
^^^^^^^^^^^^^^^^^^^^^^^^
In the previous version of the SPW Model, the acquisition information was
recorded below **Screen**. During use, it was discovered that this did
not best reflect the way data was collected. This difference between the
structure and the collected data produced a performance bottleneck when
dealing with the large structures necessary for HCS data. The decision
was taken to rework the model to store the acquisition information on
**Plate** instead. The structure was moved in the model to below
**Plate** and renamed **PlateAcquisition**.
Index was also added to **WellSample** at this time. This
records the order of the well samples and should be unique within a
given **Plate**. It does not however, have to be sequential so supports
the collection of sparse datasets.
SPW Schema structure
--------------------
Within the OME data model **Screen**, **Plate** and **Image** are top
level structures. A file can contain multiple instances of these
elements.
Each **Plate** can contain multiple **Well**\ s, **PlateAcquisition**\ s,
and **ScreenRef**\ s i.e. a plate can belong to multiple screens. Each
**Well** in turn can have one (or zero) **ReagentRef**, and zero or more
**WellSample**\ s. Each of the well samples defines the location of an
image within the well, and the time at which the sample started to be
collected. It also references the **Image** itself.
Each **Screen** contains multiple **Reagent**\ s, and **PlateRef**\ s i.e.
a screen can use many plates. A **PlateAcquisition** is best viewed as a
pass over some or all of the **Well**\ s in a **Plate**, usually
associated with some time-point or step in a protocol. It is a
collection of individual **WellSample**\ s across the **Plate**\ s collected
between two time points.
.. figure:: /images/hcs_structures.png
:align: center
:width: 80%
:alt: SPW Schema structure
SPW Schema structure
The dashed arrows on the structure diagram show the
inter-dependencies between the ''Screen'' branch and the ''Plate''
branch of the schema, as well as the ultimate link to ''Image''.
.. figure:: /images/screen_well_plate.png
:align: center
:alt: Screen Well Plate visualization
Inter-dependencies of objects in the sample file structure