ome_types.model

AffineTransform

Bases: OMEType

A matrix used to transform the shape.

⎡ A00, A01, A02 ⎤ ⎢ A10, A11, A12 ⎥ ⎣ 0, 0, 1 ⎦

Annotation

Bases: KindMixin, OMEType

An annotation from which all others are ultimately derived.

Attributes:

Name	Type	Description
description	None | str	A description for the annotation. [plain-text multi-line string]
annotation_refs	list[AnnotationRef]	(The Annotation AnnotationRefs).
id	str	(The Annotation ID).
namespace	None | str	We recommend the inclusion of a namespace for annotations you define. If it is absent then we assume the annotation is to use our (OME's) default interpretation for this type.
annotator	None | str	The Annotator is the person who attached this annotation. e.g. If UserA annotates something with TagB, owned by UserB, UserA is still the Annotator.

AnnotationRef

Bases: Reference

The AnnotationRef element is a reference to an element derived from the CommonAnnotation element.

Arc

Bases: LightSource

The Arc element is used to describe various kinds of Arc lamps - Hg, Xe, HgXe. The Power of the Arc is now stored in the LightSource.

Attributes:

Name	Type	Description
type	None | Arc_Type	The type of Arc lamp.

BasicAnnotation

Bases: Annotation

An abstract Basic Annotation from which some others are derived.

BinData

Bases: OMEType

The contents of this element are base64-encoded.

These are not CDATA sections, just a base64 stream.

Attributes:

Name	Type	Description
value	bytes	(The BinData value).
compression	BinData_Compression	Specifies the compression scheme used to encode the data.
big_endian	bool	This is true if the binary data was written in BigEndian order. This is dependent on the system architecture of the machine that wrote the pixels. True for essentially all modern CPUs other than Intel and Alpha. All Binary data must be written in the same endian order.
length	int	Character count attribute for the BinData field. This is the length of the base-64 encoded block. It allows easy skipping of the block when parsing the file. [unit:bytes]

BinaryFile

Bases: OMEType

Describes a binary file.

Attributes:

Name	Type	Description
external	None | External	(The BinaryFile External).
bin_data	None | BinData	(The BinaryFile BinData).
file_name	str	(The BinaryFile FileName).
size	int	Size of the uncompressed file. [unit:bytes]
mime_type	None | str	(The BinaryFile MIMEType).

Binning

Bases: Enum

Represents the number of pixels that are combined to form larger pixels.

{used:CCD,EMCCD}

Attributes:

Name	Type	Description
ONEBYONE	str	No binning.
TWOBYTWO	str	2×2 binning.
FOURBYFOUR	str	4×4 binning.
EIGHTBYEIGHT	str	8×8 binning.
OTHER	str	Other binning value.

BooleanAnnotation

Bases: BasicAnnotation

A simple boolean annotation of type xsd:boolean.

Channel

Bases: OMEType

There must be one per channel in the Image, even for a single-plane image. And information about how each of them was acquired is stored in the various optional *Ref elements. Each Logical Channel is composed of one or more ChannelComponents. For example, an entire spectrum in an FTIR experiment may be stored in a single Logical Channel with each discrete wavenumber of the spectrum.

constituting a ChannelComponent of the FTIR Logical Channel. An RGB image where the Red, Green and Blue components do not reflect discrete probes but are instead the output of a color camera would be treated similarly - one Logical channel with three ChannelComponents in this case. The total number of ChannelComponents for a set of pixels must equal SizeC. The IlluminationType attribute is a string enumeration which may be set to 'Transmitted', 'Epifluorescence', 'Oblique', or 'NonLinear'. The user interface logic for labeling a given channel for the user should use the first existing attribute in the following sequence: Name -> Fluor -> EmissionWavelength -> ChannelComponent/Index.

Attributes:

Name	Type	Description
light_source_settings	None | LightSourceSettings	(The Channel LightSourceSettings).
detector_settings	None | DetectorSettings	(The Channel DetectorSettings).
filter_set_ref	None | FilterSetRef	(The Channel FilterSetRef).
annotation_refs	list[AnnotationRef]	(The Channel AnnotationRefs).
light_path	None | LightPath	(The Channel LightPath).
id	str	(The Channel ID).
name	None | str	A name for the channel that is suitable for presentation to the user.
samples_per_pixel	None | int	The number of samples the detector takes to form each pixel value. [units:none] Note: This is not the same as "Frame Averaging" - see Integration in DetectorSettings
illumination_type	None | Channel_IlluminationType	The method of illumination used to capture the channel.
pinhole_size	None | float	The optional PinholeSize attribute allows specifying adjustable pin hole diameters for confocal microscopes. Units are set by PinholeSizeUnit.
pinhole_size_unit	UnitsLength	The units of the pin hole diameter for confocal microscopes - default:microns[µm].
acquisition_mode	None | Channel_AcquisitionMode	AcquisitionMode describes the type of microscopy performed for each channel
contrast_method	None | Channel_ContrastMethod	ContrastMethod describes the technique used to achieve contrast for each channel
excitation_wavelength	None | float	Wavelength of excitation for a particular channel. Units are set by ExcitationWavelengthUnit.
excitation_wavelength_unit	UnitsLength	The units of the wavelength of excitation - default:nanometres[nm].
emission_wavelength	None | float	Wavelength of emission for a particular channel. Units are set by EmissionWavelengthUnit.
emission_wavelength_unit	UnitsLength	The units of the wavelength of emission - default:nanometres[nm].
fluor	None | str	The Fluor attribute is used for fluorescence images. This is the name of the fluorophore used to produce this channel [plain text string]
nd_filter	None | float	The NDfilter attribute is used to specify the combined effect of any neutral density filters used. The amount of light the filter transmits at a maximum [units:none] A fraction, as a value from 0.0 to 1.0. NOTE: This was formerly described as "units optical density expressed as a PercentFraction". This was how the field had been described in the schema from the beginning but all the use of it has been in the opposite direction, i.e. as a amount transmitted, not the amount blocked. This change has been made to make the model reflect this usage.
pockel_cell_setting	None | int	The PockelCellSetting used for this channel. This is the amount the polarization of the beam is rotated by. [units:none]
color	Color	A color used to render this channel - 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.

CommentAnnotation

Bases: TextAnnotation

A simple comment annotation.

Dataset

Bases: OMEType

An element specifying a collection of images that are always processed together.

Images can belong to more than one Dataset, and a Dataset may contain more than one Image. Images contain one or more DatasetRef elements to specify what datasets they belong to. Once a Dataset has been processed in any way, its collection of images cannot be altered. The ExperimenterRef and ExperimenterGroupRef elements specify the person and group this Dataset belongs to. Projects may contain one or more Datasets, and Datasets may belong to one or more Projects. This relationship is specified by listing DatasetRef elements within the Project element.

Attributes:

Name	Type	Description
description	None | str	A description for the dataset. [plain-text multi-line string]
experimenter_ref	None | ExperimenterRef	(The Dataset ExperimenterRef).
experimenter_group_ref	None | ExperimenterGroupRef	(The Dataset ExperimenterGroupRef).
image_refs	list[ImageRef]	(The Dataset ImageRefs).
annotation_refs	list[AnnotationRef]	(The Dataset AnnotationRefs).
name	None | str	A name for the dataset that is suitable for presentation to the user.
id	str	(The Dataset ID).

DatasetRef

Bases: Reference

The DatasetRef element refers to a Dataset by specifying the Dataset ID attribute.

One or more DatasetRef elements may be listed within the Image element to specify what Datasets the Image belongs to.

Detector

Bases: ManufacturerSpec

The type of detector used to capture the image.

The Detector ID can be used as a reference within the Channel element in the Image element. The values stored in Detector represent the fixed values, variable values modified during the acquisition go in DetectorSettings Each attribute now has an indication of what type of detector it applies to. This is preparatory work for cleaning up and possibly splitting this object into sub-types.

Attributes:

Name	Type	Description
annotation_refs	list[AnnotationRef]	(The Detector AnnotationRefs).
gain	None | float	The Detector Gain for this detector, as a float. [units:none] {used:CCD,EMCCD,PMT}
voltage	None | float	The Voltage of the detector (e.g. PMT voltage) as a float. {used:PMT} Units are set by VoltageUnit.
voltage_unit	UnitsElectricPotential	The units of the Voltage - default:volts[V].
offset	None | float	The Detector Offset. [units:none] {used:CCD,EMCCD}
zoom	None | float	The fixed Zoom for a detector. [units:none] {used:PMT}
amplification_gain	None | float	Gain applied to the detector signal. This is the electronic gain (as apposed to the inherent gain) that is set for the detector. [units:none] {used:EMCCD#EMGain}
id	str	(The Detector ID).
type	None | Detector_Type	The Type of detector. E.g. CCD, PMT, EMCCD etc.

DetectorSettings

Bases: Settings

This holds the setting applied to a detector as well as a reference to the detector.

The ID is the detector used in this case. The values stored in DetectorSettings represent the variable values, fixed values not modified during the acquisition go in Detector. Each attribute now has an indication of what type of detector it applies to. This is preparatory work for cleaning up and possibly splitting this object into sub-types.

Attributes:

Name	Type	Description
id	str	(The DetectorSettings ID).
offset	None | float	The Offset of the detector. [units none] {used:CCD,EMCCD}
gain	None | float	The Gain of the detector. [units:none] {used:CCD,EMCCD,PMT}
voltage	None | float	The Voltage of the detector. {used:PMT} Units are set by VoltageUnit.
voltage_unit	UnitsElectricPotential	The units of the Voltage of the detector - default:volts[V]
zoom	None | float	The Zoom or "Confocal Zoom" or "Scan Zoom" for a detector. [units:none] {used:PMT}
read_out_rate	None | float	The speed at which the detector can count pixels. {used:CCD,EMCCD} This is the bytes per second that can be read from the detector (like a baud rate). Units are set by ReadOutRateUnit.
read_out_rate_unit	UnitsFrequency	The units of the ReadOutRate - default:megahertz[Hz].
binning	None | Binning	Represents the number of pixels that are combined to form larger pixels. {used:CCD,EMCCD}
integration	None | int	This is the number of sequential frames that get averaged, to improve the signal-to-noise ratio. [units:none] {used:CCD,EMCCD}

Dichroic

Bases: ManufacturerSpec

The dichromatic beamsplitter or dichroic mirror used for this filter combination.

DoubleAnnotation

Bases: NumericAnnotation

A simple numerical annotation of type xsd:double.

Ellipse

Bases: Shape

A simple ellipse object.

If rotation is required apply a transformation at the Shape level.

Attributes:

Name	Type	Description
x	float	The X coordinate of the center of the ellipse. [units pixels]
y	float	The Y coordinate of the center of the ellipse. [units pixels]
radius_x	float	The horizontal radius of the ellipse. [units pixels]
radius_y	float	The vertical radius of the ellipse. [units pixels]

Experiment

Bases: OMEType

This element describes the type of experiment.

The required Type attribute must contain one or more entries from the following list: FP FRET Time-lapse 4-D+ Screen Immunocytochemistry FISH Electrophysiology Ion-Imaging Colocalization PGI/Documentation FRAP Photoablation Optical-Trapping Photoactivation Fluorescence-Lifetime Spectral-Imaging Other FP refers to fluorescent proteins, PGI/Documentation is not a 'data' image. The optional Description element may contain free text to further describe the experiment.

Attributes:

Name	Type	Description
description	None | str	A description for the experiment. [plain-text multi-line string]
experimenter_ref	None | ExperimenterRef	This is a link to the Experimenter who conducted the experiment
microbeam_manipulations	list[MicrobeamManipulation]	(The Experiment MicrobeamManipulations).
type	list[Experiment_value]	A term to describe the type of experiment.
id	str	(The Experiment ID).

Experimenter

Bases: OMEType

This element describes a person who performed an imaging experiment.

This person may also be a user of the OME system, in which case the UserName element contains their login name. Experimenters may belong to one or more groups which are specified using one or more ExperimenterGroupRef elements.

Attributes:

Name	Type	Description
annotation_refs	list[AnnotationRef]	(The Experimenter AnnotationRefs).
id	str	(The Experimenter ID).
first_name	None | str	First name, sometime called christian name or given name or forename. [plain text string]
middle_name	None | str	Any other names. [plain text string]
last_name	None | str	A person's last name sometimes called surname or family name. [plain text string]
email	None | str	A person's email address. [valid email address as string]
institution	None | str	A person's Institution The organizing structure that people belong to other than groups. A university, or company, etc. We do not specify a department element, and do not mean for Institution to be used in this way. We simply wish to say XXX at YYY. Where YYY has a better chance of being tied to a geographically fixed location and of being more recognizable than a group of experimenters. [plain text string]
user_name	None | str	This is the username of the experimenter (in a 'unix' or 'database' sense). [plain text string]

ExperimenterGroup

Bases: OMEType

The ExperimenterGroupID is required.

Information should ideally be specified for at least one Leader as a contact for the group. The Leaders are themselves Experimenters.

Attributes:

Name	Type	Description
description	None | str	A description for the group. [plain-text multi-line string]
experimenter_refs	list[ExperimenterRef]	(The ExperimenterGroup ExperimenterRefs).
leaders	list[Leader]	(The ExperimenterGroup Leaders).
annotation_refs	list[AnnotationRef]	(The ExperimenterGroup AnnotationRefs).
name	None | str	(The ExperimenterGroup Name).
id	str	(The ExperimenterGroup ID).

ExperimenterGroupRef

Bases: Reference

This empty element has a reference (the ExperimenterGroup ID attribute) to a ExperimenterGroup defined within OME.

ExperimenterRef

Bases: Reference

This empty element has a required Experimenter ID and an optional DocumentID attribute which refers to one of the Experimenters defined within OME.

External

Bases: OMEType

Describes a file location.

Can optionally specify a portion of a file using Offset and a ReadLength. If Offset and ReadLength are specified in conjuction with Compression, then they point into the uncompressed file.

Attributes:

Name	Type	Description
href	str	file location
sha1	bytes	The digest of the file specified in href.
compression	External_Compression	Specifies the compression scheme used to encode the data.

Filament

Bases: LightSource

The Filament element is used to describe various kinds of filament bulbs such as Incadescent or Halogen.

The Power of the Filament is now stored in the LightSource.

Attributes:

Name	Type	Description
type	None | Filament_Type	The type of filament.

FileAnnotation

Bases: TypeAnnotation

A file object annotation.

Filter

Bases: ManufacturerSpec

A filter is either an excitation or emission filters. There should be one filter element specified per wavelength in the image. The channel number associated with a filter set is specified in Channel. It is based on the FilterSpec type, so has the required attributes Manufacturer, Model, and LotNumber. It may also contain a Type attribute which may be set to 'LongPass', 'ShortPass', 'BandPass', 'MultiPass',.

'Dichroic', 'NeutralDensity', 'Tuneable' or 'Other'. It can be associated with an optional FilterWheel - Note: this is not the same as a FilterSet

Attributes:

Name	Type	Description
transmittance_range	None | TransmittanceRange	(The Filter TransmittanceRange).
annotation_refs	list[AnnotationRef]	(The Filter AnnotationRefs).
type	None | Filter_Type	(The Filter Type).
filter_wheel	None | str	A filter 'wheel' in OME can refer to any arrangement of filters in a filter holder of any shape. It could, for example, be a filter slider. [plain text string]
id	str	(The Filter ID).

FilterSet

Bases: ManufacturerSpec

Filter set manufacturer specification.

Attributes:

Name	Type	Description
excitation_filters	list[FilterRef]	The Filters placed in the Excitation light path.
dichroic_ref	None | DichroicRef	(The FilterSet DichroicRef).
emission_filters	list[FilterRef]	The Filters placed in the Emission light path.
id	str	(The FilterSet ID).

Folder

Bases: OMEType

An element specifying a possibly heterogeneous collection of data.

Folders may contain Folders so that data may be organized within a tree of Folders. Data may be in multiple Folders but a Folder may not be in more than one other Folder.

Attributes:

Name	Type	Description
description	None | str	A description for the folder. [plain-text multi-line string]
folder_refs	list[FolderRef]	(The Folder FolderRefs).
image_refs	list[ImageRef]	(The Folder ImageRefs).
roi_refs	list[ROIRef]	(The Folder ROIRefs).
annotation_refs	list[AnnotationRef]	(The Folder AnnotationRefs).
id	str	(The Folder ID).
name	None | str	A name for the folder that is suitable for presentation to the user.

FolderRef

Bases: Reference

The FolderRef element refers to a Folder by specifying the Folder ID attribute.

One or more FolderRef elements may be listed within the Folder element to specify what Folders the Folder contains. This tree hierarchy must be acyclic.

GenericExcitationSource

Bases: LightSource

The GenericExcitationSource element is used to represent a source as a collection of key/value pairs, stored in a Map.

The other lightsource objects should always be used in preference to this if possible.

Image

Bases: OMEType

This element describes the actual image and its meta-data.

The elements that are references (ending in Ref or Settings) refer to elements defined outside of the Image element. Ref elements are simple links, while Settings elements are links with additional values. If any of the required Image attributes or elements are missing, its guaranteed to be an invalid document. The required attributes and elements are ID and Pixels. ExperimenterRef is required for all Images with well formed LSIDs. ImageType is a vendor-specific designation of the type of image this is. Examples of ImageType include 'STK', 'SoftWorx', etc. The Name attributes are in all cases the name of the element instance. In this case, the name of the image, not necessarily the filename. Physical size of pixels are microns[µm].

Attributes:

Name	Type	Description
acquisition_date	None | datetime	The acquisition date of the Image. The element contains an xsd:dateTime string based on the ISO 8601 format (i.e. 1988-04-07T18:39:09.359) YYYY-MM- DDTHHSS.sssZ Y - Year M - Month D - Day H - Hour m - minutes S - Seconds s - sub-seconds (optional) Z - Zone (optional) +HH:mm or -HH:mm or Z for UTC Note: xsd:dataTime supports a very wide date range with unlimited precision. The full date range and precision are not typically supported by platform- and language-specific libraries. Where the supported time precision is less than the precision used by the xsd:dateTime timestamp there will be loss of precision; this will typically occur via direct truncation or (less commonly) rounding. The year value can be large and/or negative. Any value covering the current or last century should be correctly processed, but some systems cannot process earlier dates. The sub-second value is defined as an unlimited number of digits after the decimal point. In Java a minimum of millisecond precision is guaranteed. In C++ microsecond precision is guaranteed, with nanosecond precision being available on some platforms. Time zones are supported, eg '2013-10-24T11:52:33+01:00' for Paris, but in most cases it will be converted to UTC when the timestamp is written.
experimenter_ref	None | ExperimenterRef	(The Image ExperimenterRef).
description	None | str	A description for the image. [plain-text multi-line string]
experiment_ref	None | ExperimentRef	(The Image ExperimentRef).
experimenter_group_ref	None | ExperimenterGroupRef	(The Image ExperimenterGroupRef).
instrument_ref	None | InstrumentRef	(The Image InstrumentRef).
objective_settings	None | ObjectiveSettings	(The Image ObjectiveSettings).
imaging_environment	None | ImagingEnvironment	(The Image ImagingEnvironment).
stage_label	None | StageLabel	(The Image StageLabel).
pixels	Pixels	(The Image Pixels).
roi_refs	list[ROIRef]	(The Image ROIRefs).
microbeam_manipulation_refs	list[MicrobeamManipulationRef]	(The Image MicrobeamManipulationRefs).
annotation_refs	list[AnnotationRef]	(The Image AnnotationRefs).
id	str	(The Image ID).
name	None | str	(The Image Name).

ImageRef

Bases: Reference

The ImageRef element is a reference to an Image element.

ImagingEnvironment

Bases: OMEType

This describes the environment that the biological sample was in during the experiment.

Attributes:

Name	Type	Description
map	None | Map	(The ImagingEnvironment Map).
temperature	None | float	The Temperature is the define units.
temperature_unit	UnitsTemperature	The units the Temperature is in - default:Celsius[°C].
air_pressure	None | float	AirPressure is the define units.
air_pressure_unit	UnitsPressure	The units the AirPressure is in - default:millibars[mbar].
humidity	None | float	Humidity around the sample [units:none] A fraction, as a value from 0.0 to 1.0.
co2_percent	None | float	Carbon Dioxide concentration around the sample [units:none] A fraction, as a value from 0.0 to 1.0.

Instrument

Bases: OMEType, InstrumentMixin

This element describes the instrument used to capture the Image.

It is primarily a container for manufacturer's model and catalog numbers for the Microscope, LightSource, Detector, Objective and Filters components. The Objective element contains the additional elements LensNA and Magnification. The Filters element can be composed either of separate excitation, emission filters and a dichroic mirror or a single filter set. Within the Image itself, a reference is made to this one Filter element. There may be multiple light sources, detectors, objectives and filters on a microscope. Each of these has their own ID attribute, which can be referred to from Channel. It is understood that the light path configuration can be different for each channel, but cannot be different for each timepoint or each plane of an XYZ stack.

InstrumentRef

Bases: Reference

This empty element can be used (via the required Instrument ID attribute) to refer to an Instrument defined within OME.

Label

Bases: Shape

The text label.

Any transformation should be applied at the shape level.

Attributes:

Name	Type	Description
x	float	This defines the X coordinate of the current text position of the first character in the string. [units pixels]
y	float	This defines the Y coordinate of the current text position of the first character in the string. [units pixels]

Laser

Bases: LightSource

Laser types are specified using two attributes - the Type and the LaserMedium.

Attributes:

Name	Type	Description
pump	None | Pump	The Laser element may contain a Pump sub-element which refers to a LightSource used as a laser pump.
type	None | Laser_Type	Type is the general category of laser.
laser_medium	None | Laser_LaserMedium	The Medium attribute specifies the actual lasing medium for a given laser type.
wavelength	None | float	The Wavelength of the laser. Units are set by WavelengthUnit.
wavelength_unit	UnitsLength	The units of the Wavelength - default:nanometres[nm].
frequency_multiplication	None | int	FrequencyMultiplication that may be specified. [units:none]
tuneable	None | bool	Whether or not the laser is Tuneable [flag]
pulse	None | Laser_Pulse	The Pulse mode of the laser.
pockel_cell	None | bool	If true the laser has a PockelCell to rotate the polarization of the beam. [flag]
repetition_rate	None | float	The is the rate in Hz at which the laser pulses if the Pulse type is 'Repetitive'. hertz[Hz] Units are set by RepetitionRateUnit.
repetition_rate_unit	UnitsFrequency	The units of the RepetitionRate - default:hertz[Hz].

Leader

Bases: Reference

Contact information for a ExperimenterGroup leader specified using a reference to an Experimenter element defined elsewhere in the document.

LightEmittingDiode

Bases: LightSource

The LightEmittingDiode element is used to describe various kinds of LED lamps. As the LightEmittingDiode is inside a LightSource it already has available the values from ManufacturerSpec (Manufacturer, Model, SerialNumber, LotNumber) And the values from LightSource which includes Power in milliwatts We have looked at extending this element but have had a problem producing a generic solution.

Possible attributes talked about adding include: Power in lumens - but this is complicated by multi-channel devices like CoolLED where each channel's power is different Wavelength Range - not a simple value so would require multiple attributes or a child element Angle of Projection - this would be further affected by the optics used for filtering the naked LED or that combine power from multiple devices These values are further affected if you over-drive the LED resulting in a more complex system Another issue is that LED's may not be used directly for illumination but as drivers for secondary emissions from doped fiber optics. This would require the fiber optics to be modeled. Thanks to Paul Goodwin of Applied Precision of information about this topic.

LightPath

Bases: OMEType

A description of the light path.

Attributes:

Name	Type	Description
excitation_filters	list[FilterRef]	The Filters placed in the Excitation light path.
dichroic_ref	None | DichroicRef	(The LightPath DichroicRef).
emission_filters	list[FilterRef]	The Filters placed in the Emission light path.
annotation_refs	list[AnnotationRef]	(The LightPath AnnotationRefs).

LightSource

Bases: ManufacturerSpec

The lightsource for the instrument.

An instrument may have several light sources. The type of lightsource is specified by one of the child-elements which are 'Laser', 'Filament', 'Arc' or 'LightEmittingDiode'. Each of the light source types has its own Type attribute to further differentiate the light source (eg, Nd-YAG for Laser or Hg for Arc).

Attributes:

Name	Type	Description
annotation_refs	list[AnnotationRef]	(The LightSource AnnotationRefs).
id	str	A LightSource ID must be specified for each light source, and the individual light sources can be referred to by their LightSource IDs (eg from Channel).
power	None | float	The light-source power. Units are set by PowerUnit.
power_unit	UnitsPower	The units of the Power - default:milliwatts[mW].

LightSourceSettings

Bases: Settings

Attributes:

Name	Type	Description
id	str	(The LightSourceSettings ID).
attenuation	None | float	The Attenuation of the light source [units:none] A fraction, as a value from 0.0 to 1.0.
wavelength	None | float	The Wavelength of the light source. Units are set by WavelengthUnit.
wavelength_unit	UnitsLength	The units of the Wavelength of the light source - default:nanometres[nm]

Line

Bases: Shape

A straight line defined by it's end points.

Attributes:

Name	Type	Description
x1	float	The X coordinate of the start of the line. [units pixels]
y1	float	The Y coordinate of the start of the line. [units pixels]
x2	float	The X coordinate of the end of the line. [units pixels]
y2	float	The Y coordinate of the end of the line. [units pixels]
marker_start	None | Marker	(The Line MarkerStart).
marker_end	None | Marker	(The Line MarkerEnd).

ListAnnotation

Bases: Annotation

This annotation is a grouping object.

It uses the sequence of annotation refs from the base Annotation to form the list.

LongAnnotation

Bases: NumericAnnotation

A simple numerical annotation of type xsd:long.

ManufacturerSpec

Bases: KindMixin, OMEType

This is the base from which many microscope components are extended.

E.g Objective, Filter etc. Provides attributes for recording common properties of these components such as Manufacturer name, Model etc, all of which are optional.

Attributes:

Name	Type	Description
manufacturer	None | str	The manufacturer of the component. [plain text string]
model	None | str	The Model of the component. [plain text string]
serial_number	None | str	The serial number of the component. [plain text string]
lot_number	None | str	The lot number of the component. [plain text string]

Map

Bases: OMEType, MapMixin

This is a Mapping of key/value pairs.

Attributes:

Name	Type	Description
ms	list[M]	This is a key/value pair used to build up a Mapping. The Element and Attribute name are kept to single letters to minimize the length at the expense of readability as they are likely to occur many times.

MapAnnotation

Bases: Annotation

An map annotation.

The contents of this is a list of key/value pairs.

Marker

Bases: Enum

Shape of marker on the end of a line.

[enumeration]

Mask

Bases: Shape

The Mask ROI shape is a link to a BinData object that is a BIT mask drawn on top of the image as an ROI.

It is applied at the same scale, pixel to pixel, as the Image the ROI is applied to, unless a transform is applied at the shape level.

Attributes:

Name	Type	Description
bin_data	BinData	(The Mask BinData).
x	float	The X coordinate of the left side of the image. [units pixels]
y	float	The Y coordinate of the top side of the image. [units pixels]
width	float	The width of the mask. [units pixels]
height	float	The height of the mask. [units pixels]

MetadataOnly

Bases: OMEType

This place holder means there is on pixel data in this file.

MicrobeamManipulation

Bases: OMEType

Defines a microbeam operation type and the region of the image it was applied to.

The LightSourceRef element is a reference to a LightSource specified in the Instrument element which was used for a technique other than illumination for the purpose of imaging. For example, a laser used for photobleaching.

Attributes:

Name	Type	Description
description	None | str	A description for the Microbeam Manipulation. [plain-text multi-line string]
roi_refs	list[ROIRef]	(The MicrobeamManipulation ROIRefs).
experimenter_ref	ExperimenterRef	(The MicrobeamManipulation ExperimenterRef).
light_source_settings_combinations	list[LightSourceSettings]	(The MicrobeamManipulation LightSourceSettingsCombinations).
id	str	(The MicrobeamManipulation ID).
type	list[MicrobeamManipulation_value]	The type of manipulation performed.

Microscope

Bases: ManufacturerSpec

The microscope's manufacturer specification.

NamingConvention

Bases: Enum

Predefined list of values for the well labels.

Attributes:

Name	Type	Description
LETTER	str	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.
NUMBER	str	1, 2, 3, ...

NumericAnnotation

Bases: BasicAnnotation

An abstract Numeric Annotation from which some others are derived.

OME

Bases: OMEMixin, OMEType

The OME element is a container for all information objects accessible by OME.

These information objects include descriptions of the imaging experiments and the people who perform them, descriptions of the microscope, the resulting images and how they were acquired, the analyses performed on those images, and the analysis results themselves. An OME file may contain any or all of this information. With the creation of the Metadata Only Companion OME-XML and Binary Only OME-TIFF files the top level OME node has changed slightly. It can EITHER: Contain all the previously expected elements OR: Contain a single BinaryOnly element that points at its Metadata Only Companion OME-XML file.

Attributes:

Name	Type	Description
rights	None | Rights	(The OME Rights).
projects	list[Project]	(The OME Projects).
datasets	list[Dataset]	(The OME Datasets).
folders	list[Folder]	(The OME Folders).
experiments	list[Experiment]	(The OME Experiments).
plates	list[Plate]	(The OME Plates).
screens	list[Screen]	(The OME Screens).
experimenters	list[Experimenter]	(The OME Experimenters).
experimenter_groups	list[ExperimenterGroup]	(The OME ExperimenterGroups).
instruments	list[Instrument]	(The OME Instruments).
images	list[Image]	(The OME Images).
structured_annotations	None | StructuredAnnotations	(The OME StructuredAnnotations).
rois	list[ROI]	(The OME ROIs).
binary_only	None | BinaryOnly	Pointer to an external metadata file. If this element is present, then no other metadata may be present in this file, i.e. this file is a place- holder.
uuid	None | str	This unique identifier is used to keep track of multi part files. It allows the links between files to survive renaming. While OPTIONAL in the general case this is REQUIRED in a MetadataOnly Companion to a collection of BinaryOnly files.
creator	None | str	This is the name of the creating application of the OME-XML and preferably its full version. e.g "CompanyName, SoftwareName, V2.6.3456" This is optional but we hope it will be set by applications writing out OME-XML from scratch.

BinaryOnly

Bases: OMEType

Attributes:

Name	Type	Description
metadata_file	str	Filename of the OME-XML metadata file for this binary data. If the file cannot be found, a search can be performed based on the UUID.
uuid	str	The unique identifier of another OME-XML block whose metadata describes the binary data in this file. This UUID is considered authoritative regardless of mismatches in the filename.

Objective

Bases: ManufacturerSpec

A description of the microscope's objective lens.

Required elements include the lens numerical aperture, and the magnification, both of which a floating point (real) numbers. The values are those that are fixed for a particular objective: either because it has been manufactured to this specification or the value has been measured on this particular objective. Correction: This is the type of correction coating applied to this lens. Immersion: This is the types of immersion medium the lens is designed to work with. It is not the same as 'Medium' in ObjectiveRef (a single type) as here Immersion can have compound values like 'Multi'. LensNA: The numerical aperture of the lens (as a float) NominalMagnification: The specified magnification e.g. x10 CalibratedMagnification: The measured magnification e.g. x10.3 WorkingDistance: WorkingDistance of the lens.

Attributes:

Name	Type	Description
annotation_refs	list[AnnotationRef]	(The Objective AnnotationRefs).
id	str	(The Objective ID).
correction	None | Objective_Correction	The correction applied to the lens
immersion	None | Objective_Immersion	The immersion medium the lens is designed for
lens_na	None | float	The numerical aperture of the lens expressed as a floating point (real) number. Expected range 0.02 - 1.5 [units:none]
nominal_magnification	None | float	The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. [units:none] Note: The type of this has been changed from int to float to allow the specification of additional lenses e.g. 0.5X lens
calibrated_magnification	None | float	The magnification of the lens as measured by a calibration process- i.e. '59.987' for a 60X lens. [units:none]
working_distance	None | float	The working distance of the lens expressed as a floating point (real) number. Units are set by WorkingDistanceUnit.
working_distance_unit	UnitsLength	The units of the working distance - default:microns[µm].
iris	None | bool	Records whether or not the objective was fitted with an Iris. [flag]

ObjectiveSettings

Bases: Settings

This holds the setting applied to an objective as well as a reference to the objective.

The ID is the objective used in this case.

Attributes:

Name	Type	Description
id	str	(The ObjectiveSettings ID).
correction_collar	None | float	The CorrectionCollar is normally an adjustable ring on the objective. Each has an arbitrary scale on it so the values is unit-less. [units:none]
medium	None | ObjectiveSettings_Medium	A description of a Medium used for the lens. The Medium is the actual immersion medium used in this case.
refractive_index	None | float	The RefractiveIndex is that of the immersion medium. This is a ratio so it also unit-less. [units:none]

ObjectiveSettings_Medium

Bases: Enum

A description of a Medium used for the lens.

The Medium is the actual immersion medium used in this case.

PixelType

Bases: Enum

The number size/kind used to represent a pixel.

Attributes:

Name	Type	Description
INT8	str	8 bit signed integer.
INT16	str	16 bit signed integer.
INT32	str	32 bit signed integer.
UINT8	str	8 bit unsigned integer.
UINT16	str	16 bit unsigned integer.
UINT32	str	32 bit unsigned integer.
FLOAT	str	single-precision floating point.
DOUBLE	str	double-precision floating point.
COMPLEXFLOAT	str	complex single-precision floating point.
COMPLEXDOUBLE	str	complex double-precision floating point.
BIT	str	bit mask.

Pixels

Bases: OMEType

Pixels is going to be removed in the future, but it is still required.

This is just notice that the contents of Pixels will be moved up to Image in a future release. This is because there has only been 1 Pixels object in each Image for some time. The concept of multiple Pixels sets for one Image failed to take off. It is therefore redundant. The Image will be unreadable if any of the required Pixel attributes are missing. The Pixels themselves can be stored within the OME-XML compressed by plane, and encoded in Base64. Or the Pixels may be stored in TIFF format. The Pixels element should contain a list of BinData or TiffData, each containing a single plane of pixels. These Pixels elements, when read in document order, must produce a 5-D pixel array of the size specified in this element, and in the dimension order specified by 'DimensionOrder'. All of the values in the Pixels object when present should match the same value stored in any associated TIFF format (e.g. SizeX should be the same). Where there is a mismatch our readers will take the value from the TIFF structure as overriding the value in the OME- XML. This is simply a pragmatic decision as it increases the likelihood of reading data from a slightly incorrect file.

Attributes:

Name	Type	Description
channels	list[Channel]	(The Pixels Channels).
bin_data_blocks	list[BinData]	(The Pixels BinDataBlocks).
tiff_data_blocks	list[TiffData]	(The Pixels TiffDataBlocks).
metadata_only	None | MetadataOnly	(The Pixels MetadataOnly).
planes	list[Plane]	(The Pixels Planes).
id	str	(The Pixels ID).
dimension_order	Pixels_DimensionOrder	The order in which the individual planes of data are interleaved.
type	PixelType	The variable type used to represent each pixel in the image.
significant_bits	None | int	The number of bits within the type storing each pixel that are significant. e.g. you can store 12 bit data within a 16 bit type. This does not reduce the storage requirements but can be a useful indicator when processing or viewing the image data.
interleaved	None | bool	How the channels are arranged within the data block: true if channels are stored RGBRGBRGB...; false if channels are stored RRR...GGG...BBB...
big_endian	None | bool	This is true if the pixels data was written in BigEndian order. If this value is present it should match the value used in BinData or TiffData. If it does not a reader should honour the value used in the BinData or TiffData. This values is useful for MetadataOnly files and is to allow for future storage solutions.
size_x	int	Dimensional size of pixel data array [units:none]
size_y	int	Dimensional size of pixel data array [units:none]
size_z	int	Dimensional size of pixel data array [units:none]
size_c	int	Dimensional size of pixel data array [units:none]
size_t	int	Dimensional size of pixel data array [units:none]
physical_size_x	None | float	Physical size of a pixel. Units are set by PhysicalSizeXUnit.
physical_size_x_unit	UnitsLength	The units of the physical size of a pixel - default:microns[µm].
physical_size_y	None | float	Physical size of a pixel. Units are set by PhysicalSizeYUnit.
physical_size_y_unit	UnitsLength	The units of the physical size of a pixel - default:microns[µm].
physical_size_z	None | float	Physical size of a pixel. Units are set by PhysicalSizeZUnit.
physical_size_z_unit	UnitsLength	The units of the physical size of a pixel - default:microns[µm].
time_increment	None | float	TimeIncrement is used for time series that have a global timing specification instead of per-timepoint timing info. For example in a video stream. Units are set by TimeIncrementUnit.
time_increment_unit	UnitsTime	The units of the TimeIncrement - default:seconds[s].

Plane

Bases: OMEType

The Plane object holds microscope stage and image timing data for a given channel/z-section/timepoint.

Attributes:

Name	Type	Description
hash_sha1	None | bytes	(The Plane HashSHA1).
annotation_refs	list[AnnotationRef]	(The Plane AnnotationRefs).
the_z	int	The Z-section this plane is for. [units:none] This is numbered from 0.
the_t	int	The timepoint this plane is for. [units:none] This is numbered from 0.
the_c	int	The channel this plane is for. [units:none] This is numbered from 0.
delta_t	None | float	Time since the beginning of the experiment. Units are set by DeltaTUnit.
delta_t_unit	UnitsTime	The units of the DeltaT - default:seconds[s].
exposure_time	None | float	The length of the exposure. Units are set by ExposureTimeUnit.
exposure_time_unit	UnitsTime	The units of the ExposureTime - default:seconds[s].
position_x	None | float	The X position of the stage. Units are set by PositionXUnit.
position_x_unit	UnitsLength	The units of the X stage position - default:[reference frame].
position_y	None | float	The Y position of the stage. Units are set by PositionYUnit.
position_y_unit	UnitsLength	The units of the Y stage position - default:[reference frame].
position_z	None | float	The Z position of the stage. Units are set by PositionZUnit.
position_z_unit	UnitsLength	The units of the Z stage position - default:[reference frame].

Plate

Bases: OMEType

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)

Attributes:

Name	Type	Description
description	None | str	A description for the plate.
wells	list[Well]	(The Plate Wells).
annotation_refs	list[AnnotationRef]	(The Plate AnnotationRefs).
plate_acquisitions	list[PlateAcquisition]	(The Plate PlateAcquisitions).
id	str	(The Plate ID).
name	None | str	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.
status	None | str	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.
external_identifier	None | str	The ExternalIdentifier attribute may contain a reference to an external database.
column_naming_convention	None | NamingConvention	The ColumnNamingConvention
row_naming_convention	None | NamingConvention	The RowNamingConvention
well_origin_x	None | float	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 are set by WellOriginXUnit. In the OMERO clients by convention we display the WellOrigin in the center of the view.
well_origin_x_unit	UnitsLength	The units of the well origin in X - default:reference frame.
well_origin_y	None | float	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 are set by WellOriginYUnit. In the OMERO clients by convention we display the WellOrigin in the center of the view.
well_origin_y_unit	UnitsLength	The units of the well origin in Y - default:reference frame.
rows	None | int	The number of rows in the plate
columns	None | int	The number of columns in the plate
field_index	None | int	The index of the WellSample to display as the default Field

PlateAcquisition

Bases: OMEType

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.

Attributes:

Name	Type	Description
description	None | str	A description for the PlateAcquisition.
well_sample_refs	list[WellSampleRef]	(The PlateAcquisition WellSampleRefs).
annotation_refs	list[AnnotationRef]	(The PlateAcquisition AnnotationRefs).
id	str	(The PlateAcquisition ID).
name	None | str	(The PlateAcquisition Name).
end_time	None | datetime	Time when the last image of this acquisition was collected
start_time	None | datetime	Time when the first image of this acquisition was collected
maximum_field_count	None | int	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.

Point

Bases: Shape

Attributes:

Name	Type	Description
x	float	The X coordinate of the point. [units pixels]
y	float	The Y coordinate of the point. [units pixels]

Polygon

Bases: Shape

The Polygon defines closed shapes formed of straight lines.

Note: Polygon uses counterclockwise winding (this is the default OpenGL behavior)

Attributes:

Name	Type	Description
points	str	The points of the Polygon are defined as a list of comma separated x,y coordinates seperated by spaces like "x1,y1 x2,y2 x3,y3" e.g. "0,0 1,2 3,5"

Polyline

Bases: Shape

The Polyline defines open shapes formed of straight lines.

Note: Polyline uses counterclockwise winding (this is the default OpenGL behavior)

Attributes:

Name	Type	Description
points	str	The points of the polyline are defined as a list of comma separated x,y coordinates seperated by spaces like "x1,y1 x2,y2 x3,y3" e.g. "0,0 1,2 3,5"
marker_start	None | Marker	(The Polyline MarkerStart).
marker_end	None | Marker	(The Polyline MarkerEnd).

Project

Bases: OMEType

The Project ID is required. Datasets can be grouped into projects using a many-to-many relationship.

A Dataset may belong to one or more Projects by including one or more ProjectRef elements which refer to Project IDs. Projects do not directly contain images - only by virtue of containing datasets, which themselves contain images.

Attributes:

Name	Type	Description
description	None | str	A description for the project. [plain-text multi-line string]
experimenter_ref	None | ExperimenterRef	(The Project ExperimenterRef).
experimenter_group_ref	None | ExperimenterGroupRef	(The Project ExperimenterGroupRef).
dataset_refs	list[DatasetRef]	(The Project DatasetRefs).
annotation_refs	list[AnnotationRef]	(The Project AnnotationRefs).
name	None | str	(The Project Name).
id	str	(The Project ID).

ProjectRef

Bases: Reference

There may be one or more of these in a Dataset.

This empty element has a required Project ID attribute that refers to Projects defined within the OME element.

Pump

Bases: Reference

The Pump element is a reference to a LightSource.

It is used within the Laser element to specify the light source for the laser's pump (if any).

ROI

Bases: OMEType

A four dimensional 'Region of Interest'.

If they are not used, and the Image has more than one plane, the entire set of planes is assumed to be included in the ROI. Multiple ROIs may be specified.

Attributes:

Name	Type	Description
union	Union	(The ROI Union).
annotation_refs	list[AnnotationRef]	(The ROI AnnotationRefs).
description	None | str	A description for the ROI. [plain-text multi-line string]
id	str	(The ROI ID).
name	None | str	The Name identifies the ROI to the user. [plain-text string]

Reagent

Bases: OMEType

Reagent is used to describe a chemical or some other physical experimental parameter.

Attributes:

Name	Type	Description
description	None | str	A long description for the reagent.
annotation_refs	list[AnnotationRef]	(The Reagent AnnotationRefs).
id	str	(The Reagent ID).
name	None | str	A short name for the reagent
reagent_identifier	None | str	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 referred to as ExternalIdentifier.

Rectangle

Bases: Shape

A simple rectangle object.

If rotation is required apply a transformation at the Shape level.

Attributes:

Name	Type	Description
x	float	The X value of the left edge or the rectangle. [units pixels]
y	float	The y value of the top edge or the rectangle. [units pixels]
width	float	The width of the rectangle. [units pixels]
height	float	The height of the rectangle. [units pixels]

Reference

Bases: ReferenceMixin, OMEType

Reference is an empty complex type that is contained and extended by all the Ref elements and also the Settings Complex Type Each Ref element defines an attribute named ID of simple type ID and no other information Each simple type ID is restricted to the base type LSID with an appropriate pattern.

Rights

Bases: OMEType

The rights holder of this data and the rights held.

Attributes:

Name	Type	Description
rights_holder	None | str	The rights holder for this data. [plain-text multi-line string] e.g. "Copyright (C) 2002 - 2016 Open Microscopy Environment"
rights_held	None | str	The rights held by the rights holder. [plain-text multi-line string] e.g. "All rights reserved" or "Creative Commons Attribution 3.0 Unported License"

Screen

Bases: OMEType

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.

Attributes:

Name	Type	Description
description	None | str	A description for the screen.
reagents	list[Reagent]	(The Screen Reagents).
plate_refs	list[PlateRef]	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.
annotation_refs	list[AnnotationRef]	(The Screen AnnotationRefs).
id	str	(The Screen ID).
name	None | str	(The Screen Name).
protocol_identifier	None | str	A pointer to an externally defined protocol, usually in a screening database.
protocol_description	None | str	A description of the screen protocol; may contain very detailed information to reproduce some of that found in a screening database.
reagent_set_description	None | str	A description of the set of reagents; may contain very detailed information to reproduce some of that information found in a screening database.
reagent_set_identifier	None | str	A pointer to an externally defined set of reagents, usually in a screening database/automation database.
type	None | str	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.

Settings

Bases: Reference

Settings is an empty complex type that is contained and extended by all the Settings elements Each Settings element defines an attribute named ID of simple type *ID and the other information that is needed.

Each simple type *ID is restricted to the base type LSID with an appropriate pattern

Shape

Bases: KindMixin, OMEType

The shape element contains a single specific ROI shape and links that to any channels, and a timepoint and a z-section.

It also records any transform applied to the ROI shape.

Attributes:

Name	Type	Description
transform	None | AffineTransform	This is a matrix used to transform the shape. The element has 6 xsd:float attributes. If the element is present then all 6 values must be included.
annotation_refs	list[AnnotationRef]	(The Shape AnnotationRefs).
fill_color	None | Color	The color of the fill - encoded as RGBA The 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.
fill_rule	None | Shape_FillRule	The rule used to decide which parts of the shape to fill. [enumeration]
stroke_color	None | Color	The color of the stroke - encoded as RGBA The 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.
stroke_width	None | float	The width of the stroke. Units are set by StrokeWidthUnit.
stroke_width_unit	UnitsLength	The units used for the stroke width.
stroke_dash_array	None | str	e.g. "none", "10 20 30 10"
text	None | str	(The Shape Text).
font_family	None | Shape_FontFamily	The font family used to draw the text. [enumeration] Note: these values are all lower case so they match the standard HTML/CSS values. "fantasy" has been included for completeness; we do not recommend its regular use. This attribute is under consideration for removal from the OME-XML schema.
font_size	None | int	Size of the font. Units are set by FontSizeUnit.
font_size_unit	UnitsLength	The units used for the font size.
font_style	None | Shape_FontStyle	The style and weight applied to the text. [enumeration] This is a simplified combination of the HTML/CSS attributes font-style AND font- weight.
locked	None | bool	Controls whether the shape is locked and read only, true is locked, false is editable.
id	str	(The Shape ID).
the_z	None | int	The z-section the ROI applies to. If not specified then the ROI applies to all the z-sections of the image. [units:none] This is numbered from 0.
the_t	None | int	The timepoint the ROI applies to. If not specified then the ROI applies to all the timepoints of the image. [units:none] This is numbered from 0.
the_c	None | int	The channel the ROI applies to. If not specified then the ROI applies to all the channels of the image. [units:none] This is numbered from 0.

Shape_FillRule

Bases: Enum

The rule used to decide which parts of the shape to fill.

[enumeration]

Shape_FontFamily

Bases: Enum

The font family used to draw the text.

[enumeration] Note: these values are all lower case so they match the standard HTML/CSS values. "fantasy" has been included for completeness; we do not recommend its regular use. This attribute is under consideration for removal from the OME-XML schema.

Shape_FontStyle

Bases: Enum

The style and weight applied to the text.

[enumeration] This is a simplified combination of the HTML/CSS attributes font-style AND font-weight.

StageLabel

Bases: OMEType

The StageLabel is used to specify a name and position for a stage position in the microscope's reference frame.

Attributes:

Name	Type	Description
name	str	(The StageLabel Name).
x	None | float	The X position of the stage label. Units are set by XUnit.
x_unit	UnitsLength	The units of the X stage position - default:[reference frame].
y	None | float	The Y position of the stage label. Units are set by YUnit.
y_unit	UnitsLength	The units of the Y stage position - default:[reference frame].
z	None | float	The Z position of the stage label. Units are set by ZUnit.
z_unit	UnitsLength	The units of the Z stage position - default:[reference frame].

StructuredAnnotations

Bases: StructuredAnnotationsMixin, OMEType

An unordered collection of annotation attached to objects in the OME data model.

TagAnnotation

Bases: TextAnnotation

A tag annotation (represents a tag or a tagset).

TermAnnotation

Bases: BasicAnnotation

A ontology term annotation.

TextAnnotation

Bases: Annotation

An abstract Text Annotation from which some others are derived.

TiffData

Bases: OMEType

This described the location of the pixel data in a tiff file.

Attributes:

Name	Type	Description
uuid	None | UUID	This must be used when the IFDs are located in another file. Note: It is permissible for this to be self referential.
ifd	int	Gives the IFD(s) for which this element is applicable. Indexed from 0. Default is 0 (the first IFD). [units:none]
first_z	int	Gives the Z position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first Z position). [units:none]
first_t	int	Gives the T position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first T position). [units:none]
first_c	int	Gives the C position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first C position). [units:none]
plane_count	None | int	Gives the number of IFDs affected. Dimension order of IFDs is given by the enclosing Pixels element's DimensionOrder attribute. Default is the number of IFDs in the TIFF file, unless an IFD is specified, in which case the default is 1. [units:none]

UUID

Bases: OMEType

Attributes:

Name	Type	Description
value	str	(The UUID value).
file_name	None | str	This can be used when the IFDs are located in another file. The / (forward slash) is used as the path separator. A relative path is recommended. However an absolute path can be specified. Default is to use the file the ome-xml data has been pulled from. Note: It is permissible for this to be self referential. The file image1.tiff may contain ome-xml data that has FilePath="image1.tiff" or "./image1.tiff"

TimestampAnnotation

Bases: BasicAnnotation

A date/time annotation of type xsd:dateTime.

TransmittanceRange

Bases: OMEType

This records the range of wavelengths that are transmitted by the filter.

It also records the maximum amount of light transmitted.

Attributes:

Name	Type	Description
cut_in	None | float	CutIn is the wavelength below which there is less than 50% transmittance for a filter. Units are set by CutInUnit.
cut_in_unit	UnitsLength	The units of the CutIn - default:nanometres[nm].
cut_out	None | float	CutOut is the wavelength above which there is less than 50% transmittance for a filter. Units are set by CutOutUnit.
cut_out_unit	UnitsLength	The units of the CutOut - default:nanometres[nm].
cut_in_tolerance	None | float	CutInTolerance. Units are set by CutInToleranceUnit.
cut_in_tolerance_unit	UnitsLength	The units of the CutInTolerance - default:nanometres[nm].
cut_out_tolerance	None | float	CutOutTolerance. Units are set by CutOutToleranceUnit.
cut_out_tolerance_unit	UnitsLength	The units of the CutOutTolerance - default:nanometres[nm].
transmittance	None | float	The amount of light the filter transmits at a maximum [units:none] A fraction, as a value from 0.0 to 1.0.

TypeAnnotation

Bases: Annotation

An abstract Type Annotation from which some others are derived.

UnitsElectricPotential

Bases: Enum

The units used to represent an electric potential.

Attributes:

Name	Type	Description
YOTTAVOLT	str	yottavolt unit.
ZETTAVOLT	str	zettavolt unit.
EXAVOLT	str	exavolt unit.
PETAVOLT	str	petavolt unit.
TERAVOLT	str	teravolt unit.
GIGAVOLT	str	gigavolt unit.
MEGAVOLT	str	megavolt unit.
KILOVOLT	str	kilovolt unit.
HECTOVOLT	str	hectovolt unit.
DECAVOLT	str	decavolt unit.
VOLT	str	volt unit.
DECIVOLT	str	decivolt unit.
CENTIVOLT	str	centivolt unit.
MILLIVOLT	str	millivolt unit.
MICROVOLT	str	microvolt unit.
NANOVOLT	str	nanovolt unit.
PICOVOLT	str	picovolt unit.
FEMTOVOLT	str	femtovolt unit.
ATTOVOLT	str	attovolt unit.
ZEPTOVOLT	str	zeptovolt unit.
YOCTOVOLT	str	yoctovolt unit.

UnitsFrequency

Bases: Enum

The units used to represent frequency.

Attributes:

Name	Type	Description
YOTTAHERTZ	str	yottahertz unit.
ZETTAHERTZ	str	zettahertz unit.
EXAHERTZ	str	exahertz unit.
PETAHERTZ	str	petahertz unit.
TERAHERTZ	str	terahertz unit.
GIGAHERTZ	str	gigahertz unit.
MEGAHERTZ	str	megahertz unit.
KILOHERTZ	str	kilohertz unit.
HECTOHERTZ	str	hectohertz unit.
DECAHERTZ	str	decahertz unit.
HERTZ	str	hertz unit.
DECIHERTZ	str	decihertz unit.
CENTIHERTZ	str	centihertz unit.
MILLIHERTZ	str	millihertz unit.
MICROHERTZ	str	microhertz unit.
NANOHERTZ	str	nanohertz unit.
PICOHERTZ	str	picohertz unit.
FEMTOHERTZ	str	femtohertz unit.
ATTOHERTZ	str	attohertz unit.
ZEPTOHERTZ	str	zeptohertz unit.
YOCTOHERTZ	str	yoctohertz unit.

UnitsLength

Bases: Enum

The units used to represent a length.

Attributes:

Name	Type	Description
YOTTAMETER	str	yottameter SI unit.
ZETTAMETER	str	zettameter SI unit.
EXAMETER	str	exameter SI unit.
PETAMETER	str	petameter SI unit.
TERAMETER	str	terameter SI unit.
GIGAMETER	str	gigameter SI unit.
MEGAMETER	str	megameter SI unit.
KILOMETER	str	kilometer SI unit.
HECTOMETER	str	hectometer SI unit.
DECAMETER	str	decameter SI unit.
METER	str	meter SI unit.
DECIMETER	str	decimeter SI unit.
CENTIMETER	str	centimeter SI unit.
MILLIMETER	str	millimeter SI unit.
MICROMETER	str	micrometer SI unit.
NANOMETER	str	nanometer SI unit.
PICOMETER	str	picometer SI unit.
FEMTOMETER	str	femtometer SI unit.
ATTOMETER	str	attometer SI unit.
ZEPTOMETER	str	zeptometer SI unit.
YOCTOMETER	str	yoctometer SI unit.
ANGSTROM	str	ångström SI-derived unit.
THOU	str	thou Imperial unit (or mil, 1/1000 inch).
LINE	str	line Imperial unit (1/12 inch).
INCH	str	inch Imperial unit.
FOOT	str	foot Imperial unit.
YARD	str	yard Imperial unit.
MILE	str	terrestrial mile Imperial unit.
ASTRONOMICALUNIT	str	astronomical unit SI-derived unit. The official term is ua as the SI standard assigned AU to absorbance unit.
LIGHTYEAR	str	light year.
PARSEC	str	parsec.
POINT	str	typography point Imperial-derived unit (1/72 inch). Use of this unit should be limited to font sizes.
PIXEL	str	pixel abstract unit. This is not convertible to any other length unit without a calibrated scaling factor. Its use should should be limited to ROI objects, and converted to an appropriate length units using the PhysicalSize units of the Image the ROI is attached to.
REFERENCEFRAME	str	reference frame abstract unit. This is not convertible to any other length unit without a scaling factor. Its use should be limited to uncalibrated stage positions, and converted to an appropriate length unit using a calibrated scaling factor.

UnitsPower

Bases: Enum

The units used to represent power.

Attributes:

Name	Type	Description
YOTTAWATT	str	yottawatt unit.
ZETTAWATT	str	zettawatt unit.
EXAWATT	str	exawatt unit.
PETAWATT	str	petawatt unit.
TERAWATT	str	terawatt unit.
GIGAWATT	str	gigawatt unit.
MEGAWATT	str	megawatt unit.
KILOWATT	str	kilowatt unit.
HECTOWATT	str	hectowatt unit.
DECAWATT	str	decawatt unit.
WATT	str	watt unit.
DECIWATT	str	deciwatt unit.
CENTIWATT	str	centiwatt unit.
MILLIWATT	str	milliwatt unit.
MICROWATT	str	microwatt unit.
NANOWATT	str	nanowatt unit.
PICOWATT	str	picowatt unit.
FEMTOWATT	str	femtowatt unit.
ATTOWATT	str	attowatt unit.
ZEPTOWATT	str	zeptowatt unit.
YOCTOWATT	str	yoctowatt unit.

UnitsPressure

Bases: Enum

The units used to represent a pressure.

Attributes:

Name	Type	Description
YOTTAPASCAL	str	yottapascal SI unit.
ZETTAPASCAL	str	zettapascal SI unit.
EXAPASCAL	str	exapascal SI unit.
PETAPASCAL	str	petapascal SI unit.
TERAPASCAL	str	terapascal SI unit.
GIGAPASCAL	str	gigapascal SI unit.
MEGAPASCAL	str	megapascal SI unit.
KILOPASCAL	str	kilopascal SI unit.
HECTOPASCAL	str	hectopascal SI unit.
DECAPASCAL	str	decapascal SI unit.
PASCAL	str	pascal SI unit. Note the C++ enum is mixed case due to PASCAL being a macro used by the Microsoft C and C++ compiler.
DECIPASCAL	str	decipascal SI unit.
CENTIPASCAL	str	centipascal SI unit.
MILLIPASCAL	str	millipascal SI unit.
MICROPASCAL	str	micropascal SI unit.
NANOPASCAL	str	nanopascal SI unit.
PICOPASCAL	str	picopascal SI unit.
FEMTOPASCAL	str	femtopascal SI unit.
ATTOPASCAL	str	attopascal SI unit.
ZEPTOPASCAL	str	zeptopascal SI unit.
YOCTOPASCAL	str	yoctopascal SI unit.
BAR	str	bar SI-derived unit.
MEGABAR	str	megabar SI-derived unit.
KILOBAR	str	kilobar SI-derived unit.
DECIBAR	str	decibar SI-derived unit.
CENTIBAR	str	centibar SI-derived unit.
MILLIBAR	str	millibar SI-derived unit.
ATMOSPHERE	str	standard atmosphere SI-derived unit.
PSI	str	pound-force per square inch Imperial unit.
TORR	str	torr SI-derived unit.
MILLITORR	str	millitorr SI-derived unit.
MMHG	str	millimetre of mercury SI-derived unit

UnitsTemperature

Bases: Enum

The units used to represent a temperature.

Attributes:

Name	Type	Description
CELSIUS	str	degree Celsius unit.
FAHRENHEIT	str	degree Fahrenheit unit.
KELVIN	str	Kelvin unit.
RANKINE	str	degree Rankine unit.

UnitsTime

Bases: Enum

The units used to represent a time interval.

Attributes:

Name	Type	Description
YOTTASECOND	str	yottasecond SI unit.
ZETTASECOND	str	zettasecond SI unit.
EXASECOND	str	exasecond SI unit.
PETASECOND	str	petasecond SI unit.
TERASECOND	str	terasecond SI unit.
GIGASECOND	str	gigasecond SI unit.
MEGASECOND	str	megasecond SI unit.
KILOSECOND	str	kilosecond SI unit.
HECTOSECOND	str	hectosecond SI unit.
DECASECOND	str	decasecond SI unit.
SECOND	str	second SI unit.
DECISECOND	str	decisecond SI unit.
CENTISECOND	str	centisecond SI unit.
MILLISECOND	str	millisecond SI unit.
MICROSECOND	str	microsecond SI unit.
NANOSECOND	str	nanosecond SI unit.
PICOSECOND	str	picosecond SI unit.
FEMTOSECOND	str	femtosecond SI unit.
ATTOSECOND	str	attosecond SI unit.
ZEPTOSECOND	str	zeptosecond SI unit.
YOCTOSECOND	str	yoctosecond SI unit.
MINUTE	str	minute SI-derived unit.
HOUR	str	hour SI-derived unit.
DAY	str	day SI-derived unit.

Well

Bases: OMEType

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)

Attributes:

Name	Type	Description
well_samples	list[WellSample]	(The Well WellSamples).
reagent_ref	None | ReagentRef	(The Well ReagentRef).
annotation_refs	list[AnnotationRef]	(The Well AnnotationRefs).
id	str	(The Well ID).
column	int	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.
row	int	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.
external_description	None | str	A description of the externally defined identifier for this plate.
external_identifier	None | str	The ExternalIdentifier attribute may contain a reference to an external database.
type	None | str	A human readable identifier for the screening status. e.g. empty, positive control, negative control, control, experimental, etc.
color	Color	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.

WellSample

Bases: OMEType

WellSample is an individual image that has been captured within a Well.

Attributes:

Name	Type	Description
image_ref	None | ImageRef	This is the main link to the core Image element
id	str	(The WellSample ID).
position_x	None | float	The X position of the field (image) within the well relative to the well origin defined on the Plate. Units are set by PositionXUnit.
position_x_unit	UnitsLength	The units of the position in X - default:reference frame.
position_y	None | float	The Y position of the field (image) within the well relative to the well origin defined on the Plate. Units are set by PositionYUnit.
position_y_unit	UnitsLength	The units of the position in Y - default:reference frame.
timepoint	None | datetime	The time-point at which the image started to be collected
index	int	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.

WellSampleRef

Bases: Reference

The WellSampleRef element is a reference to a WellSample element.

XMLAnnotation

Bases: TextAnnotation

An general xml annotation.

The contents of this is not processed as OME XML but should still be well-formed XML.

---

Extra types

Color

Bases: Color

A Pydantic Color subclass that converts to and from OME int32 types.

as_int32() -> int

Convert to an int32, with alpha in the least significant byte.