The Carpenter paper1 is a review of the overall methods and individual steps for conducting a high content screening(HCS). First the author briefly introduced the key concepts of visual assays and its development to HCS. In visual assays, cells are labeled flurescently and can be observed using a microscope of their phenotype changes. The recent development of automated microscopes and cell image analysis software have made visual assays to a large scale that is compatible with HTS. The author then discussed the following HCS components in detail:
1. Assay development: One goal of the assay development is to label protein with fluoreescent protein to probe the phenotype of interests.
2. Image acquisition and storage: The microscopy instruments have become increasingly automated, but attention needed for critical issues such as experiment environment control, image format. Image storage is another critical issue as a large image set could require TB spaces. The author listed a few image storage repository softwares and services in image screening centers as solutions to this issue.
3. Image analysis: this is required to extract quantitative measurements from images. The current available commercial software can process cell counting, protein expression, translocation and neurite outgrowth but the results can be less reliable in certain circumstances. Open-source software are also being developed to address these issues generically but it requires long term development. Finally the author pointed out that data quality, speed and flexibility, cost and ease of use are parameters to consider when choosing a image analysis software.
4. Data analysis ad exploration: The quantitative measurements can be used for statistical analysis. The study still need to address two major areas, how to correct biases in data caused by experiment variations, and how to select hits from the screen. Another issue needs to address is how to explore the data and discover the full spectrum of information, as currently many potentially useful data are discarded or not included in analysis. Better analysis and exploration tools are needed, and methods also need to be developed and improved to make the most of the useful information from HCS.

1. Carpenter, A.E. Image-based chemical screening. Nat Chem Biol 3, 461-465(2007).