From Cell Profiler to Cell Classifier

Hi everybody, I am new user of Cell Classifier and Cell Profiler 2.0 programs, I understand the basic configuration of the Cell Profler, but, my problem is in the creation of the .mat file, this file is the input to the Cell Classifier (Cell Classifier doesn’t recognize like a valid input). I appreciate some collaboration or guidance to solve my problem.

Kind Regards,


Hi Luis,

The output .mat file actually is not the file used for CellProfiler Analyst (CPA, which includes the classifer). The measurements generated by CellProfiler can also be exported to a comma-delimited file (.csv) or a database-ready format using the ExportToDatabase module. The main settings to note in that module are:

  • Select the database type: Use MySQL
    if your database is on a remote server, use MySQL/CSV or SQLite if you want to create a database on your own computer.
  • Select that you want to create a CellProfiler Analyst properties file.

Read the help for the module to see how the other setting work. You can get CPA from here; also on that page is the manual plus example data to get you started.

Remember you can post in the CPA forum if you run into CPA-specific problems. Good luck!

Thanks Mark for your reply.

But, I’m sorry for do not give you a better explanation of the question in my first post …
I have no problem with the basic use of “Cell Profiler and Cell Profiler Analysis” (I have been read the manual and I ran the examples given on the Cell’s Profiler website), my problem is in the use of Cell Profiler *.mat file , that file will be used like input to “Enhanced Cell Classifier” ( ), to perform complex image analysis tasks.

Currently , I’m don’t able to do, that “Enhanced Cell Classifier” recognize the *.mat file , like a valid input.



Thanks for clarifying. I think you may be better served by posing your question to the people at ETH who designed Enhanced Cell Classifier. They can tell you how the output file is interpreted and might be able to help you if the output file is somehow different that what they normally use.

Good luck!