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Interfacing with other software

David Stirling edited this page Feb 26, 2021 · 8 revisions
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This page contains instructions on how to interface other software with CellProfiler and CellProfiler Analyst. Many other interfaces are described on CellProfiler's main website.


See our RunImageJMacro page or the CellProfiler 2 ImageJ page.


See our OMERO page.


See our ilastik page.


Knime (from University of Konstanz) is a modular data exploration platform that enables the user to visually create data flows, selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models.

To use CellProfiler output (MySQL database) in Knime

Note: This has only been tested with Mac OS X

  1. Download and install Knime Desktop
  2. Download the MySQL driver and unzip it somewhere on your local machine. Note: it's easiest if you choose the 'Platform-independent zip file download, even if on Windows
  3. Launch Knime
    1. In Knime -> Preferences, open the settings for Knime->Database Driver

      1. Add a new driver file and point it to the MySQL driver .jar file you just unzipped. Click OK and exit Preferences
    2. Add the Database Reader Node to your Project workspace

      1. Right-click and Configure Database Reader Node
      2. Choose Database Driver from dropdown as "com.mysql.jdbc.Driver" (others not tested)
      3. EnterDatabase URL, e.g., "jdbc:mysql://YourHost:YourPort/YourDatabase"
      4. Fill in MySQL username and password
      5. Need to fill in "SQL statement" to get the columns of data you want to work with, e.g. "SELECT COL FROM TABLE"
      6. The Database Browser->Fetch Metadata button may help guide you to the database entries. Double-click entries to enter them into the SQL Statement field
    3. You can now connect this node to other analysis nodes and access the database columns SELECTed above