  As microscopy diversifies and becomes ever-more complex, the problem of
quantification of microscopy images has emerged as a major roadblock for many
researchers. All researchers must face certain challenges in turning microscopy
images into answers, independent of their scientific question and the images
they've generated. Challenges may arise at many stages throughout the analysis
process, including handling of the image files, image pre-processing, object
finding, or measurement, and statistical analysis. While the exact solution
required for each obstacle will be problem-specific, by understanding tools and
tradeoffs, optimizing data quality, breaking workflows and data sets into
chunks, talking to experts, and thoroughly documenting what has been done,
analysts at any experience level can learn to overcome these challenges and
create better and easier image analyses.
