I have been using cell profiler for about 1 year now and I am very happy with it. I want to start using cell profiler analyst now. I do have some problems . I can start the software and use the example data set. However when I want to create a data set from my own images I have some problems getting it from cell profiler. As I understand I have to first segment and measure the images in cell profiler. Then export to a database which can be used by cell profiler analyst. Is this correct? Or is there another way to get data into cell profiler analyst? I am asking because I am not used to work with data bases and I am finding it a bit difficult.
You are correct in that CellProfiler Analyst needs a database from which to read measurement values. The most common (by far) way to do this is, just as you say, using ExportToDatabase at the end of your pipeline in in CellProfiler. You can export to either MySql or Sqlite databases. Sqlite is likely the easiest to deal with because you don’t need to set up a server, per se. In a perfect world, you wouldn’t need to know anything about databases other than the location of the database tables in order to run CellProfiler Analyst, however there is a large likelihood that you will need to spend some time learning the basics of database at some time. The example database is an Sqlite database, for example.
The best place to start is the CPAnalyst manual here: cellprofiler.org/linked_files/Do … manual.pdf
The Preliminary Data Requirements section is illustrative (I hope).