I’ve been really impressed with CellProfiler and it’s doing a great job with my analysis tasks… but analysis is one thing, and pretty graphs are another.
Right now, my post-CP “pipeline” looks something like:
- use CP to generate .tab output
- run .tab files through a brief Python script to make them more database-friendly (delete dubiously useful header at top of file, copy the set name down to each individual row)
- import modified .tab files into Access and apply filters and get counts using SQL queries
- export count data into Excel and manually compute statistics and generate graphs
This has been fine for development but I’m not looking forward to trying to automate and scale this. What kind of solutions do you all have in place? I’ve been trying to avoid installing MySQL so I haven’t taken a look at CP Analyst yet… will it ease some of my pain?