Enable minimal metadata requirements for processing
Summary
To generalise aliby to multiple setups we need to remove the assumptions we have made while developing exclusively for the microfluidics setup.
Current behaviour/setbacks
Tiling, segmentation and extraction require explicit definition of channels.
Desired behaviour/advantages
The pipeline should be able to run with a minimum amount of metadata.
Implementation sketch
Expect indication of channel id (and, if cannot be inffered from filenames, dimension). Segment the remaining channels as fluorescence. Name the segmentation channel "general" or segmentation for extraction processes, and the rest of the extraction groups "fluorescence1, fluorescence2, ...", unless names are specified in PipelineParameters.