Using Spreadsheets and DatabasesΒΆ

CellProfiler can save measurements as a spreadsheet or as a database. Which format you use will depend on some of the considerations below:

  • Learning curve: Applications that handle spreadsheets (e.g., Excel, Calc or Google Docs) are easy for beginners to use. Databases are more sophisticated and require knowledge of specialized languages (e.g., MySQL, Oracle, etc); a popular freeware access tool is SQLyog.
  • Capacity and speed: Databases are designed to hold larger amounts of data than spreadsheets. Spreadsheets may contain a few thousand rows of data, whereas databases can hold many millions of rows of data. Accessing a particular portion of data in a database is optimized for speed.
  • Downstream application: If you wish to use Excel or another simple tool to analyze your data, a spreadsheet is likely the best choice. If you intend to use CellProfiler Analyst, you must create a database. If you plan to use a scripting language, most languages have ways to import data from either format.