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diagram
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| description |
There must be one per channel in the Image, even for a single-plane image. In OME, Channels (e.g. 'FITC', 'Texas Red', etc) are specified as Logical Channels,
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 AuxLightSourceRef 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.
The SamplesPerPixel attribute is the number of channel components in the logical channel.
The IlluminationType attribute is a string enumeration which may be set to 'Transmitted', 'Epifluorescence', or 'Oblique'.
The optional PinholeAize attribute allows specifying adjustable pin hole diameters for confocal microscopes.
The PhotometricInterpretation attribute is used to describe how to display a multi-component channel. This attribute may be set to:
'monochrome', 'RGB', 'ARGB', 'CMYK', 'HSV'. The default for single-component channels is 'monochrome'.
The Model attribute describes the type of microscopy performed for each channel. This may be set to:
'Wide-field','Wide-field','Laser Scanning Microscopy','Laser Scanning Confocal','Spinning Disk Confocal','Slit Scan Confocal','Multi-Photon Microscopy',
'Structured Illumination','Single Molecule Imaging','Total Internal Reflection','Fluorescence-Lifetime','Spectral Imaging',
'Fluorescence Correlation Spectroscopy','Near Field Scanning Optical Microscopy','Second Harmonic Generation Imaging'.
The ContrastMethod attribute may be set to 'Brightfield','Phase','DIC','Hoffman Modulation','Oblique Illumination','Polarized Light','Darkfield','Fluorescence'.
The ExWave, EmWave and Fluor attributes allow specifying the nominal excitation and emission wavelengths and the type of fluor being imaged in a particular channel.
The Fluor attribute is used for fluorescence images, while the Name attribute is used to name channels that are not imaged using fluorescence techniques.
The user interface logic for labeling a given channel for the user should use the first existing attribute in the following sequence:
Name -> Fluor -> EmWave -> ChannelComponent/Index.
The NDfilter attribute is used to specify (in O.D. units) the combined effect of any neutral density filters used.
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| uses elements |
AuxLightSourceRef, ChannelComponent, DetectorRef, FilterRef, LightSourceRef, OTFRef
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| uses attributes |
ChannelInfo/ContrastMethod, ChannelInfo/EmWave, ChannelInfo/ExWave, ChannelInfo/Fluor, ChannelInfo/ID, ChannelInfo/IlluminationType, ChannelInfo/Mode, ChannelInfo/Name, ChannelInfo/NDfilter, ChannelInfo/PhotometricInterpretation, ChannelInfo/PinholeSize, ChannelInfo/SamplesPerPixel
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