A description for the annotation. [plain-text multi-line string]

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.

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

The method of illumination used to capture the channel. NOTE: OME-XML uses enum

The optional PinholeSize attribute allows specifying adjustable pin hole diameters for confocal microscopes. Units are set by PinholeSizeUnit.

The units of the pin hole diameter for confocal microscopes - default:microns[µm].

AcquisitionMode describes the type of microscopy performed for each NOTE: OME-XML uses enum

ContrastMethod describes the technique used to achieve contrast for each channel NOTE: OME-XML uses enum

Wavelength of excitation for a particular channel. Units are set by ExcitationWavelengthUnit.

The units of the wavelength of excitation - default:nanometres[nm].

Wavelength of emission for a particular channel. Units are set by EmissionWavelengthUnit.

The units of the wavelength of emission - default:nanometres[nm].

The Fluor attribute is used for fluorescence images. This is the name of the fluorophore used to produce this channel [plain text string]

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.

The PockelCellSetting used for this channel. This is the amount the polarization of the beam is rotated by. [units:none]

A color (RGBA) used to render this channel If unset, the color should be solid white

A name for the dataset that is suitable for presentation to the user.

A description for the dataset. [plain-text multi-line string]

references to other metadata

The Detector Gain for this detector, as a float. [units:none] {used:CCD,EMCCD,PMT}

The Voltage of the detector (e.g. PMT voltage) as a float. {used:PMT} Units are set by VoltageUnit.

The Detector Offset. [units:none] {used:CCD,EMCCD}

The fixed Zoom for a detector. [units:none] {used:PMT}

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}

references

The Offset of the detector. [units none] {used:CCD,EMCCD}

The Gain of the detector. [units:none] {used:CCD,EMCCD,PMT}

The Voltage of the detector. {used:PMT} Units are set by VoltageUnit.

The units of the Voltage of the detector - default:volts[V]

The Zoom or "Confocal Zoom" or "Scan Zoom" for a detector. [units:none] {used:PMT}

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.

The units of the ReadOutRate - default:megahertz

Represents the number of pixels that are combined to form larger pixels. {used:CCD,EMCCD} Note: was an enum in OME-XML

This is the number of sequential frames that get averaged, to improve the signal-to-noise ratio. [units:none] {used:CCD,EMCCD}

The X coordinate of the center of the ellipse. [units pixels]

The Y coordinate of the center of the ellipse. [units pixels]

The horizontal radius of the ellipse. [units pixels]

The vertical radius of the ellipse. [units pixels]

A description for the dataset. [plain-text multi-line string]

This is a link to the Experimenter who conducted the experiment

First name, sometime called christian name or given name or forename. [plain text string]

Any other names. [plain text string]

A person's last name sometimes called surname or family name. [plain text string]

A person's email address. [valid email address as string]

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]

This is the username of the experimenter (in a 'unix' or 'database' sense). [plain text string]

references

A description for the group. [plain-text multi-line string]

Group members

Group leader(s)

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]

The Filters placed in the Excitation light path.

The Filters placed in the Emission light path.

A name for the folder that is suitable for presentation to the user.

A description for the folder. [plain-text multi-line string]

Subfolders. This is different from OME-XML implementation, which uses references. Here we use the sematically more nataul recusive composition instead. Composition avoids circular references and is well-supported in protobuf.

References to other metadata

A description for the image. [plain-text multi-line string]

Even only the date information is relavent here, we use the datatime structure to be consistent with the OME-XML

References

Settings

pixle

The Temperature is the define units.

The units the Temperature is in - default:Celsius[°C].

AirPressure is the define units.

The units the AirPressure is in - default:millibars[mbar].

Humidity around the sample [units:none] A fraction, as a value from 0.0 to 1.0.

Carbon Dioxide concentration around the sample [units:none] A fraction, as a value from 0.0 to 1.0.

This defines the X coordinate of the current text position of the first character in the string. [units pixels]

required

This defines the Y coordinate of the current text position of the first character in the string. [units pixels]

required

The Medium attribute specifies the actual lasing medium for a given laser type. NOTE: OME-XML uses Enum here

The Wavelength of the laser. Units are set by WavelengthUnit.

default is "nm"

FrequencyMultiplication that may be specified. [units:none]

Whether or not the laser is Tuneable [flag]

The Pulse mode of the laser, e.g. "CW", "QSwitch" NOTE: OME-XML uses an Enum here

If true the laser has a PockelCell to rotate the polarization of the beam. [flag]

The is the rate in Hz at which the laser pulses if the Pulse type is 'Repetitive'. hertz[Hz] Units are set by RepetitionRateUnit.

The Filters placed in the Excitation light path.

The Filters placed in the Emission light path.

The light-source power. Units are set by PowerUnit.

The units of the Power - default:milliwatts[mW]

References

required

The Attenuation of the light source [units:none] A fraction, as a value from 0.0 to 1.0.

The Wavelength of the light source. Units are set by WavelengthUnit.

The units of the Wavelength of the light source - default:nanometres[nm]

The X coordinate of the start of the line. [units pixels]

The Y coordinate of the start of the line. [units pixels]

The X coordinate of the end of the line. [units pixels]

The Y coordinate of the end of the line. [units pixels]

The manufacturer of the component. [plain text string]

The Model of the component. [plain text string]

The serial number of the component. [plain text string]

The lot number of the component. [plain text string]

The X coordinate of the left side of the image. [units pixels]

The Y coordinate of the top side of the image. [units pixels]

required

required

required

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}

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.

A description for the Microbeam Manipulation. [plain-text multi-line string]

The microscope's manufacturer specification

copy rights information

The reason for the OME specification. This should be considered a required field. A unset (null) filed means using default value. The exact value for "default" is context-dependent. For example, in a streaming GRPC session, the "default" is likely the value transimitted in a previous message.

OME allows "binary-only" data, for which the metadata are supplied from a reference. This is needed in order to support multi-part data storage, where most of the files are binary-only and share metadata with a metadata-only file.

We replicate this field for consistency, but discourage its use. For protobuf it has no real usecase.

This unique identifier is used in conjuction with `MetadataRef`` to keep track of multi part files. Should be unset in most cases.

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.

The immersion medium the lens is designed for Note: OME-XML uses Enum here

The numerical aperture of the lens expressed as a floating point (real) number. Expected range 0.02 - 1.5 [units:none]

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

The magnification of the lens as measured by a calibration process- i.e. '59.987' for a 60X lens. [units:none]

The working distance of the lens expressed as a floating point (real) number. Units are set by WorkingDistanceUnit.

The units of the working distance - default:microns[µm].

Records whether or not the objective was fitted with an Iris. [flag]

Reference

required

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]

A description of a Medium used for the lens. The Medium is the actual immersion medium used in this case. NOTE: OME-XML use enum here

The RefractiveIndex is that of the immersion medium. This is a ratio so it also unit-less. [units:none]

If specified, the length should match size_z

If specified, the length should match bindata.

Pixel values Note: We only support BinData, not TiffData as in OME-XML Note: use an empty list to indicate metadata-only

A string describing the dimension order of the pixel data, e.g. "XYZCT" The string must be a permutaion of these 5 letters even if some of the dimension doesn't exist in the data. NOTE: OME-XML uses enum

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.

Default (0) is all bits

How the channels are arranged within the data block: true if channels are stored RGBRGBRGB...; false if channels are stored RRR...GGG...BBB...

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.

Dimensional size of pixel data array [units:none]

Physical size of a pixel.

physical size unit, default "µm" Note: OME-XML allows different units for X-Y-Z

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 unit, default "s"

This optional element is a hash of the plane's image data.

The Z-section this plane is for. [units:none] This is numbered from 0.

The T-section this plane is for. [units:none] This is numbered from 0.

The C-section this plane is for. [units:none] This is numbered from 0.

Time since the beginning of the experiment. Units are set by DeltaTUnit.

The units of the DeltaT - default:seconds[s]

The length of the exposure. Units are set by ExposureTimeUnit.

The units of the ExposureTime - default:seconds[s]

The X position of the stage. Units are set by PositionXUnit.

The Y position of the stage. Units are set by PositionYUnit.

The Z position of the stage. Units are set by PositionZUnit.

The units of the stage position - default:[reference frame] Note: OME-XML allows different units for X-Y-Z

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 description for the plate.

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 are set by WellOriginXUnit.

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 are set by WellOriginYUnit.

In the OMERO clients by convention we display the WellOrigin in the center of the view.

NOTE: OME-XML uses enum for length unit. Here we just use string. RATIONALE: strong-typing length unit might be too restrictive.

NOTE: OME-XML uses enum for length unit. Here we just use string.

Number of rows in the plate The default value (0) should be intepreted as "unspecfied"

Number of columns in the plate The default value (0) should be intepreted as "unspecfied"

Collection of wells in the plate, indexed by well IDs.

Information regarding the acquistions, indexed by PlateAcquisition IDs.

The index of the WellSample to display as the default Field. This is marked specifically as optional, so 0 is distinguishable from missing value

References

human readable name

A description for the plate acquistion.

Time when the first image of this acquisition was collected

Time when the last 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.

links to the well_samples (and thus images) collected

links to the annotations

The points of the polyline NOTE:OME-XML uses a string representation here

The points of the polygon NOTE:OME-XML uses a string representation here

Name of the project

A description for the project. [plain-text multi-line string]

References to other metadata fields

The Name identifies the ROI to the user. [plain-text string]

A description for the ROI. [plain-text multi-line string]

A short name for the reagent

A long description 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 referred to as ExternalIdentifier.

References to other metadata

The X value of the left edge or the rectangle. [units pixels]

required

The Y value of the left edge or the rectangle. [units pixels]

required

required

required

The rights holder for this data. [plain-text multi-line string] e.g. "Copyright (C) 2002 - 2016 Open Microscopy Environment"

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 name

Reagent information, indexed by Reagent IDs. These will be referenced in Wells.

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.

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.

The color of the fill. Default is solid white

The color of the stroke. Default is solid white.

The width of the stroke. Units are set by StrokeWidthUnit.

The units used for the stroke width. default is "pixel"

e.g. "none", "10 20 30 10"

Text lable

The font family used to draw the text. 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.

Size of the font. Units are set by FontSizeUnit.

The units used for the font size.

The style and weight applied to the text. This is a simplified combination of the HTML/CSS attributes font-style AND font-weight.

Controls whether the shape is locked and read only, true is locked, false is editable.

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 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 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.

The X position of the stage label. Units are set by XUnit.

The units of the X stage position - default:[reference frame]

The Y position of the stage label. Units are set by YUnit.

The units of the Y stage position - default:[reference frame]

The Z position of the stage label. Units are set by ZUnit.

The units of the Z stage position - default:[reference frame]

CutIn is the wavelength below which there is less than 50% transmittance for a filter. Units are set by CutInUnit.

default is "nm"

CutOut is the wavelength above which there is less than 50% transmittance for a filter. Units are set by CutOutUnit.

default is "nm"

CutInTolerance. Units are set by CutInToleranceUnit.

The units of the CutInTolerance - default:nanometres[nm].

CutOutTolerance. Units are set by CutInToleranceUnit.

The units of the CutOutTolerance - default:nanometres[nm].

The amount of light the filter transmits at a maximum [units:none] A fraction, as a value from 0.0 to 1.0.

Well samples in this well. We use a dictionary so that the keys (IDs) can be referenced in other data structures, e.g. PlateAcquisition

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.

Required.

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.

Required.

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. The default value is solid white.

references

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. Units are set by PositionXUnit.

The Y position of the field (image) within the well relative to the well origin defined on the Plate. Units are set by PositionYUnit.

NOTE: OME-XML uses enum for length unit. Here we just use string.

NOTE: OME-XML uses enum for length unit. Here we just use string.

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.

required

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, ...

PT_ prefix to avoid c++ enum name collision