Most BOM detection and measurement engines require grayscale input, one number per pixel. A single-channel input lets an engine work on intensity without untangling correlations between channels.
So a typical fluorescence pipeline starts from the DAPI or FITC channel image itself, which StrataQuest offers directly as an engine input, and feeds that grayscale image to Pre-Processing filters and Detection engines. A typical brightfield pipeline starts with color-space conversionLoading... to grayscale, or with stain separation that produces one grayscale image per chromogen.
The exceptions are engines built for color, such as the color conversionsLoading... or the ClassifierLoading... when trained on RGB features. Those take multi-channel input. Most engines don't.