General experience and feedback for CellProfiler Analyst


Dear CellProfiler Analyst team,

I have used C.A. for 2 weeks now and would like to thank you very much for making it publicly available. It is amazing and it’s great how well the Classify algorithm and interface are working. It is a great help for me.
I am using it on Windows and would like to tell you about the problems I encountered until I got it working, even with the ExampleDB from your website:

  1. Setting up mysql was not straightforward but doable, and you mention in the manual that it is not trivial.
  2. To start CPAnalyst with the .bat file, you need to add the java command to your Windows system path, otherwise it is not recognized as a command on the command line.
  3. When you try to load the example database into mysql, an error message appears that the table (.csv) files were not found. This is because the path to the files is missing in the sql setup file. The same applies to files generated by CellProfiler with my own data.

After solving these problems, I got CPAnalyst working with the ExampleDB.

There were some additional problems with files generated with CellProfiler with my own data:

  1. If the output .csv files generated by CellProfiler contain any file paths (like the path to the images for example), they use backslash as a separator in the path. My default sql installation on Windows requires however normal slashes. This means that images cannot be loaded by CPA because the path is not interpreted correctly. I had to change this by hand.
  2. I also had to add the path for the .csv data files to the .sql setup file, as mentioned before.
  3. Finally, at the beginning of the .sql file, in files generated by CP, this line is missing: DROP DATABASE IF EXISTS allstats; If I don’t include it in the file, I get an error message from MySql.

Except for these details, everything works great so thanks a lot again,



Thanks for your feedback, Stefan! It’s great to hear that folks like yourself are starting to use CPAnalyst. Admittedly, most of our development and testing has been done on Mac, and so the detailed feedback on your Windows experience is great. We’ll address these issues in our next release.



Yes, thank you Stefan for the feedback. Development on CPA has only in the past few months turned over to windows, but we still run it for the most part on Macs. Anyway, as one of the developers of the software, I appreciate the constructive criticism as much as the kudos. I’ll personally add your comments to my to-do list.