Colour options

Two settings are grouped in the tab colours of the options dialogue box. They are set via the Options menu, or by clicking on the Colours button:

colour components to analyse
red, green, blue	It is possible to include all three colour channels red, green and blue (RGB) into the analysis. This means that the brightness of each pixel is calculated as the mean of its three components red, green and blue, the same as when colours are converted to grey tones. It is also possible to choose weights to be applied to each component. Usually, analysing only the blue channel (i.e. 0% R + 0% G + 100% B) is a good choice because it increases the brightness of the (blue) sky, while reducing the brightness of the (green) canopy, thus enhancing the contrast between both. If all your pictures are with a grey sky, it is well possible to use all 3 channels (RGB). Essentially any linear combination of colours is possible, even for example giving a negative weight to the green channel to counteract bright green leaves. This may work very well on some pictures, but is less reproducible over different pictures taken under different conditions. Using a custom linear combination, it is best to keep the sum of all 3 weights (R+G+B) at 100%. This avoids to loose information from the high and low ends of the scale. The frequencies of brightness values can be displayed as a graph via the view menu. This graph can help choosing the best colour channels for the analysis.
fixed setting	This option allows to keep the setting chosen here, overriding the settings of the parameter files (which will thus be ignored when a new file is loaded).

colour components to analyse

red, green, blue

It is possible to include all three colour channels red, green and blue (RGB) into the analysis. This means that the brightness of each pixel is calculated as the mean of its three components red, green and blue, the same as when colours are converted to grey tones. It is also possible to choose weights to be applied to each component. Usually, analysing only the blue channel (i.e. 0% R + 0% G + 100% B) is a good choice because it increases the brightness of the (blue) sky, while reducing the brightness of the (green) canopy, thus enhancing the contrast between both. If all your pictures are with a grey sky, it is well possible to use all 3 channels (RGB). Essentially any linear combination of colours is possible, even for example giving a negative weight to the green channel to counteract bright green leaves. This may work very well on some pictures, but is less reproducible over different pictures taken under different conditions. Using a custom linear combination, it is best to keep the sum of all 3 weights (R+G+B) at 100%. This avoids to loose information from the high and low ends of the scale. The frequencies of brightness values can be displayed as a graph via the view menu. This graph can help choosing the best colour channels for the analysis.

fixed setting

This option allows to keep the setting chosen here, overriding the settings of the parameter files (which will thus be ignored when a new file is loaded).

colour to be ignored
colour box	Clicking on the coloured box allows to choose a colour to be ignored. You can paint portions of the pictures with this colour to exclude them from the analysis. This can be useful for example to use only part of a picture taken at the edge of a plot, to set aside a big tree trunk or a tall mountain in the background etc. In most cases, red can be chosen as colour to be ignored because it is easily distinguished from both the sky and the canopy.
tolerance	In JPEG files, the colours are not saved exactly because of the compression process used to make these files smaller. As a consequence, the colour chosen to be ignored will not be rendered exactly on JPEG image. In this case, use a tolerance to recognise also these imprecisions. With high-quality JPEG, a tolerance of 40 should be sufficient. Make a few tests before analysing large batches of pictures. The number of ignored pixels can be taken from the results file (in full results mode).
fixed setting	This options works as described above for the colour components to be analysed.
ignore colour	This option controls if there is a colour to be ignored. In this case, it will be displayed in the small control box at the bottom. If no colour is to be ignored, an X will be displayed in this control box.