My group are planning to conduct a 15k compound high content biology screen and I'm looking into options for analysing the image data. We'd probably just be doing a simple cell count and maybe cell size to start with. Although we have commerical software to do this (Definiens), I'm not sure how well our set-up will scale given the hardware it's on. Another option is to use our institute's NGS compute cluster, and analyse the data using the Bioconductor package EBImage which I think would scale much better.
In terms of learning resources there's the package vignette and the following tutorial from CSAMA2015, but are there any additional workflow papers or other resources that might be helpful to me in setting this up?