Class: Channel

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

light_source_settings : None | LightSourceSettings (The Channel LightSourceSettings). detector_settings : None | DetectorSettings (The Channel DetectorSettings). filter_set_ref : None | FilterSetRef (The Channel FilterSetRef). annotation_ref : 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.

URI: core:Channel

Attributes

Own

• ➞light_source_settings _0..1

  • Range: LightSourceSettings

• ➞detector_settings _0..1

  • Range: DetectorSettings

• ➞filter_set _0..1

  • Range: FilterSet

• ➞light_path _0..1

  • Range: LightPath

• ➞samples_per_pixel _0..1

  • Range: Integer

• ➞illumination_type _0..1

  • Range: Channel_IlluminationType

• ➞pinhole_size _0..1

  • Range: Integer

• ➞acquisition_mode _0..1

  • Range: Channel_AcquisitionMode

• ➞contrast_method _0..1

  • Range: Channel_ContrastMethod

• ➞excitation_wavelength _0..1

  • Range: Integer

• ➞emission_wavelength _0..1

  • Range: Integer

• ➞fluor _0..1

  • Range: String

• ➞nd_filter _0..1

  • Range: Integer

• ➞pockel_cell_setting _0..1

  • Range: Integer