Exporting CellProfiler Analyist data


I am doing analysis of images using cellprofiler (CP) and cellprofiler analyst (CPA). I have several experiments stained with basic histologic stains. It is important to me to train CPA classifier on all experiments at once, however, due to variation between experiments I couldn’t create a CP pipeline that could be applied to all images, so I created a pipeline for each experiment separately and I have merged output files from each experiment. I have used ‘export to database’ to create a database and properties file for CPA.

Everything worked great. I can use CPA and classifier gives me great results. However, I would like to move all my files to another computer now.

When I just move database and properties file on another pc, I can’t open them in CPA. After starting CPA and selecting properties file, nothing happens. No error message.
So I tried to open the properties file on my mac, just to be sure the problem is not on my pc. After starting CPA and selecting properties file I got an error message “CellProfiler Analyst error.”.

I have attached screenshots of settings used for creating properties and database file.

I appreciate any help,
Thank you very much

Hi Ivan,

The Analyst .properties file needs to point to the database file in order for Analyst to launch successfully. You’ll need to open the properties file in a text editor and update the line “db_sqlite_file = ____” to point to the new location of the database.

The database itself also stores file locations for each image. If the images are on a network drive which has the same path on both systems this should be ok, but if you’re copying them to a local drive or switching OS you’ll probably need to run some commands to update the SQL database itself. That’s a bit more complicated to do but we could help you with that if needed.


Thank you very much,
I have change the db_sqlite_file parameter and then managed to change the paths to each of the image. Now everything works!

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