Rendering of Channel Colours

[wmoore]

Need to consider emission filters when choosing channel colours, when emission wavelength is not given.

Look for wavelength metadata in this order of preference for colouring the channel.

EmWavelength
FilterSet->EmFilter
SecondaryEmFilter
Laser->Wavelength
ExWave
FilterSet->ExFitler
SecondaryExFitler

Then check if each Channel has Emission data. If a single channel lacks emission data, this is likely to be a "Trans" channel and should be Greyscale.

Also, need to adjust the wavelength cut-off between GREEN and RED to 560 nm (currently it is 600nm). E.g. Longpass 560 filter should be rendered RED.

To get the 'emission wavelength' from a filter, use the average of CutIn and CutOut for Band-Pass filters, and for LongPass, maybe take 10nm above the CutIn.

Confocal formats often have no emission wavelength OR emission filter for the 'Transmitted Light' channel, which should be rendered GREY.
Also possible to use the channel name to identify the transmitted light channel?

LSM 510: ChD

Olympus FV1000: TD1

Leica: PMT Trans? (not done in BioFormats yet)

[jburel]

r5077.
I did not use the name strategy to set the color of the transmitted light

[jburel]

implementation for transmitted light:

If the image has several channels, if some of them have emission information (i.e. emission wavelength or filter+transmittance+cutIn), the channel without any emission information will be set to grey.
jmarie

[wmoore]

See r5123 and r5125

[jburel]

implemented r5136