Image colors and channels#
Minimal
Annotation of channels (staining, marker etc.) visible
Add the staining or marker within or beside the relevant image (panel).
Adjust brightness/contrast, report adjustments, use uniform color-scales
Intensity range adjustments should be monitored with the image histogram and done with care: a too wide intensity range results in ‘faded’ images that lack details, while a too narrow intensity range removes data. Use a range indicator LUT (e.g. HiLo in Fiji) to highlight pixels where data was removed due to a too narrow intensity range
Image comparison: use same adjustments
Any adjustments to the image, such as brightness/contrast must be consistent across all images within an experiment, that might be directly compared.
Channel colors high visibility on background. Best visibility: grayscale
Ensure the use of highly contrastive colors when choosing for your individual microscopy channels. Darker colors, like blue, are less visible on a black background while lighter colors, like yellow, are highly visible on a black background but less so on a brightfield image with a white background.
Multi-color: provide grayscale for each color channel
Grayscale images are often easier to visually distinguish fine detail within than color channels; providing them ensures the reader can see your phenotype to best effect.
Multi-color: if channels are merged, make accessible to color blind
If creating merged images, ensure the LUTs chosen are separable for color-blind readers; online simulations can help you check this.
Recommended
Provide intensity scales (calibration bar) for grayscale, color, pseudocolor
Ideal