The CellProfiler application is designed to help biologist process large collections of images in order to measure phenotypes. The CellProfiler Analyst companion app allows them to analyze the derived data and learn more about subtle, or complex phenotypes.

Right off the bat, CellProfiler Analyst prompts you to specify the location of the properties file that contains all the details about the image and object tables you want to analyze.

This information is usually stored in MySQL or SQLite databases, or in a set of CSV files, and the properties text file is telling the app how to connect to the database.

Within the CellProfiler application you can quickly generate a properties file that is almost ready to use by employing the “Export to Database” function, but you can also create one manually, by following the example template.

To help you get started, CellProfiler Analyst comes with example images and pipelines which you must download separately. The documentation included in the software archive helps you understand how everything works.

CellProfiler Analyst automatically tracks your activity, and you get to see the logs in the app’s main window. All included analysis tools can be easily accessed via self explanatory buttons included in a toolbar placed in the top area of the window.

CellProfiler Analyst will launch a new window each time you activate any of the 8 built-in analysis tools (Classifier, PlateViewer, TableViewer, ImageViewer, ScatterPlot, Histogram, DensityPlot, and BoxPlot), so you will have the option to evaluate the same data from different angles.

To conclude, if you are using the CellProfiler application to measure phenotypes from thousands of images, the CellProfiler Analyst companion application allows you to further analyze the derived data in a user friendly GUI.